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Dexheimer S, Shrestha N, Chapagain BS, Bujarski JJ, Yin Y. Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing. Pathogens 2024; 13:96. [PMID: 38276169 PMCID: PMC10819421 DOI: 10.3390/pathogens13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and CCMV. Intra-segmental crosses were more frequent than the inter-segmental ones. Most intra-segmental junctions carried short insertions/deletions (indels) and caused frameshift mutations. The mutation hotspots clustered mainly within the open reading frames. Substitutions of various lengths were also identified, whereas a small fraction of crosses occurred between viral and their host RNAs. Our data reveal that the virions can package detectable amounts of multivariate recombinant RNAs, contributing to the flexible nature of the viral genomes.
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Affiliation(s)
- Sarah Dexheimer
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Nipin Shrestha
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Bandana Sharma Chapagain
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Jozef J. Bujarski
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln, NE 68588, USA
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2
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Dominguez F, Palchevska O, Frolova EI, Frolov I. Alphavirus-based replicons demonstrate different interactions with host cells and can be optimized to increase protein expression. J Virol 2023; 97:e0122523. [PMID: 37877718 PMCID: PMC10688356 DOI: 10.1128/jvi.01225-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023] Open
Abstract
IMPORTANCE Alphavirus replicons are being developed as self-amplifying RNAs aimed at improving the efficacy of mRNA vaccines. These replicons are convenient for genetic manipulations and can express heterologous genetic information more efficiently and for a longer time than standard mRNAs. However, replicons mimic many aspects of viral replication in terms of induction of innate immune response, modification of cellular transcription and translation, and expression of nonstructural viral genes. Moreover, all replicons used in this study demonstrated expression of heterologous genes in cell- and replicon's origin-specific modes. Thus, many aspects of the interactions between replicons and the host remain insufficiently investigated, and further studies are needed to understand the biology of the replicons and their applicability for designing a new generation of mRNA vaccines. On the other hand, our data show that replicons are very flexible expression systems, and additional modifications may have strong positive impacts on protein expression.
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Affiliation(s)
- Francisco Dominguez
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Oksana Palchevska
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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3
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Filomatori CV, Merwaiss F, Bardossy ES, Alvarez DE. Impact of alphavirus 3'UTR plasticity on mosquito transmission. Semin Cell Dev Biol 2020; 111:148-155. [PMID: 32665176 DOI: 10.1016/j.semcdb.2020.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 07/04/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
Abstract
Alphaviruses such as chikungunya and western equine encephalitis viruses are important human pathogens transmitted by mosquitoes that have recently caused large epidemic and epizootic outbreaks. The epidemic potential of alphaviruses is often related to enhanced mosquito transmission. Tissue barriers and antiviral responses impose bottlenecks to viral populations in mosquitoes. Substitutions in the envelope proteins and the presence of repeated sequence elements (RSEs) in the 3'UTR of epidemic viruses were proposed to be specifically associated to efficient replication in mosquito vectors. Here, we discuss the molecular mechanisms that originated RSEs, the evolutionary forces that shape the 3'UTR of alphaviruses, and the significance of RSEs for mosquito transmission. Finally, the presence of RSEs in the 3'UTR of viral genomes appears as evolutionary trait associated to mosquito adaptation and emerges as a common feature among viruses from the alphavirus and flavivirus genera.
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Affiliation(s)
- Claudia V Filomatori
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Fernando Merwaiss
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Eugenia S Bardossy
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, Argentina.
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4
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Filomatori CV, Bardossy ES, Merwaiss F, Suzuki Y, Henrion A, Saleh MC, Alvarez DE. RNA recombination at Chikungunya virus 3'UTR as an evolutionary mechanism that provides adaptability. PLoS Pathog 2019; 15:e1007706. [PMID: 30986247 PMCID: PMC6502353 DOI: 10.1371/journal.ppat.1007706] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 05/06/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022] Open
Abstract
The potential of RNA viruses to adapt to new environments relies on their ability to introduce changes in their genomes, which has resulted in the recent expansion of re-emergent viruses. Chikungunya virus is an important human pathogen transmitted by mosquitoes that, after 60 years of exclusive circulation in Asia and Africa, has rapidly spread in Europe and the Americas. Here, we examined the evolution of CHIKV in different hosts and uncovered host-specific requirements of the CHIKV 3'UTR. Sequence repeats are conserved at the CHIKV 3'UTR but vary in copy number among viral lineages. We found that these blocks of repeated sequences favor RNA recombination processes through copy-choice mechanism that acts concertedly with viral selection, determining the emergence of new viral variants. Functional analyses using a panel of mutant viruses indicated that opposite selective pressures in mosquito and mammalian cells impose a fitness cost during transmission that is alleviated by recombination guided by sequence repeats. Indeed, drastic changes in the frequency of viral variants with different numbers of repeats were detected during host switch. We propose that RNA recombination accelerates CHIKV adaptability, allowing the virus to overcome genetic bottlenecks within the mosquito host. These studies highlight the role of 3'UTR plasticity on CHIKV evolution, providing a new paradigm to explain the significance of sequence repetitions.
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Affiliation(s)
- Claudia V. Filomatori
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Eugenia S. Bardossy
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Fernando Merwaiss
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Yasutsugu Suzuki
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Annabelle Henrion
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - María Carla Saleh
- Institut Pasteur, Viruses and RNA Interference Unit, Centre National de la Recherche Scientifique UMR 3569, Paris, France
| | - Diego E. Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
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5
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Bentley K, Evans DJ. Mechanisms and consequences of positive-strand RNA virus recombination. J Gen Virol 2018; 99:1345-1356. [PMID: 30156526 DOI: 10.1099/jgv.0.001142] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genetic recombination in positive-strand RNA viruses is a significant evolutionary mechanism that drives the creation of viral diversity by the formation of novel chimaeric genomes. The process and its consequences, for example the generation of viruses with novel phenotypes, has historically been studied by analysis of the end products. More recently, with an appreciation that there are both replicative and non-replicative mechanisms at work, and with new approaches and techniques to analyse intermediate products, the viral and cellular factors that influence the process are becoming understood. The major influence on replicative recombination is the fidelity of viral polymerase, although RNA structures and sequences may also have an impact. In replicative recombination the viral polymerase is necessary and sufficient, although roles for other viral or cellular proteins may exist. In contrast, non-replicative recombination appears to be mediated solely by cellular components. Despite these insights, the relative importance of replicative and non-replicative mechanisms is not clear. Using single-stranded positive-sense RNA viruses as exemplars, we review the current state of understanding of the processes and consequences of recombination.
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Affiliation(s)
- Kirsten Bentley
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, UK
| | - David J Evans
- Biomedical Sciences Research Complex and School of Biology, University of St Andrews, St Andrews, UK
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6
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Pietilä MK, Hellström K, Ahola T. Alphavirus polymerase and RNA replication. Virus Res 2017; 234:44-57. [DOI: 10.1016/j.virusres.2017.01.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022]
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7
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Morley VJ, Turner PE. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 2017; 71:872-883. [PMID: 28121018 PMCID: PMC5382103 DOI: 10.1111/evo.13193] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
Abstract
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520
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Petterson E, Guo TC, Evensen Ø, Mikalsen AB. Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA. Sci Rep 2016; 6:36317. [PMID: 27805034 PMCID: PMC5090867 DOI: 10.1038/srep36317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/07/2016] [Indexed: 11/22/2022] Open
Abstract
RNA recombination in non-segmented RNA viruses is important for viral evolution and documented for several virus species through in vitro studies. Here we confirm viral RNA recombination in vivo using an alphavirus, the SAV3 subtype of Salmon pancreas disease virus. The virus causes pancreas disease in Atlantic salmon and heavy losses in European salmonid aquaculture. Atlantic salmon were injected with a SAV3 6K-gene deleted cDNA plasmid, encoding a non-viable variant of SAV3, together with a helper cDNA plasmid encoding structural proteins and 6K only. Later, SAV3-specific RNA was detected and recombination of viral RNA was confirmed. Virus was grown from plasmid-injected fish and shown to infect and cause pathology in salmon. Subsequent cloning of PCR products confirming recombination, documented imprecise homologous recombination creating RNA deletion variants in fish injected with cDNA plasmid, corresponding with deletion variants previously found in SAV3 from the field. This is the first experimental documentation of alphavirus RNA recombination in an animal model and provides new insight into the production of defective virus RNA.
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Affiliation(s)
- Elin Petterson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine and Biosciences, P.O. Box 8146 Dep., N-0033 Oslo, Norway
| | - Tz-Chun Guo
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine and Biosciences, P.O. Box 8146 Dep., N-0033 Oslo, Norway
| | - Øystein Evensen
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine and Biosciences, P.O. Box 8146 Dep., N-0033 Oslo, Norway
| | - Aase B Mikalsen
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine and Biosciences, P.O. Box 8146 Dep., N-0033 Oslo, Norway
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9
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Kim DY, Reynaud JM, Rasalouskaya A, Akhrymuk I, Mobley JA, Frolov I, Frolova EI. New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes. PLoS Pathog 2016; 12:e1005810. [PMID: 27509095 PMCID: PMC4980055 DOI: 10.1371/journal.ppat.1005810] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 11/18/2022] Open
Abstract
The positive-strand RNA viruses initiate their amplification in the cell from a single genome delivered by virion. This single RNA molecule needs to become involved in replication process before it is recognized and degraded by cellular machinery. In this study, we show that distantly related New World and Old World alphaviruses have independently evolved to utilize different cellular stress granule-related proteins for assembly of complexes, which recruit viral genomic RNA and facilitate formation of viral replication complexes (vRCs). Venezuelan equine encephalitis virus (VEEV) utilizes all members of the Fragile X syndrome (FXR) family, while chikungunya and Sindbis viruses exploit both members of the G3BP family. Despite being in different families, these proteins share common characteristics, which determine their role in alphavirus replication, namely, the abilities for RNA-binding and for self-assembly into large structures. Both FXR and G3BP proteins interact with virus-specific, repeating amino acid sequences located in the C-termini of hypervariable, intrinsically disordered domains (HVDs) of viral nonstructural protein nsP3. We demonstrate that these host factors orchestrate assembly of vRCs and play key roles in RNA and virus replication. Only knockout of all of the homologs results in either pronounced or complete inhibition of replication of different alphaviruses. The use of multiple homologous proteins with redundant functions mediates highly efficient recruitment of viral RNA into the replication process. This independently evolved acquisition of different families of cellular proteins by the disordered protein fragment to support alphavirus replication suggests that other RNA viruses may utilize a similar mechanism of host factor recruitment for vRC assembly. The use of different host factors by alphavirus species may be one of the important determinants of their pathogenesis. Many viruses encode proteins containing intrinsically disordered domains, whose functions are as yet unknown. Here we show that such a domain (HVD) in the alphavirus nsP3 protein orchestrates assembly of viral replication complexes through interaction with RNA-binding cellular factors. Surprisingly, geographically isolated viruses have evolved to utilize different cellular proteins: the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV) binds all members of the FXR family, while nsP3 HVDs of Sindbis and chikungunya viruses interact with G3BP proteins. Despite being in different families, G3BPs and FXRs have similar domain organization, and assemble into higher order complexes, such as stress granules. Alphaviruses exploit their abilities for complex self-assembly and RNA binding to build RNA-containing pre-replication complexes. Using CRISPR/Cas9 mediated knockouts, we show that deletion of all homologs strongly affects virus replication, while knockout of a single FXR or G3BP homolog has no or mild effect. Our data suggest that an alphavirus HVD serves as a hub to recruit host factors for replication complex assembly and may determine virus adaptation to distinct cellular environments. Notably, the improved understanding of HVD interactions allows alphavirus replication to be switched from an FXR- to G3BP-dependent mode and opens new possibilities for development of antiviral therapeutics.
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Affiliation(s)
- Dal Young Kim
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Josephine M. Reynaud
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Aliaksandra Rasalouskaya
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Ivan Akhrymuk
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - James A. Mobley
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ilya Frolov
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
| | - Elena I. Frolova
- Department of Microbiology, University of Alabama at Birmingham, Alabama, United States of America
- * E-mail:
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10
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Kolondam B, Rao P, Sztuba-Solinska J, Weber PH, Dzianott A, Johns MA, Bujarski JJ. Co-infection with two strains of Brome mosaic bromovirus reveals common RNA recombination sites in different hosts. Virus Evol 2015; 1:vev021. [PMID: 27774290 PMCID: PMC5014487 DOI: 10.1093/ve/vev021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have previously reported intra-segmental crossovers in Brome mosaic virus (BMV) RNAs. In this work, we studied the homologous recombination of BMV RNA in three different hosts: barley (Hordeum vulgare), Chenopodium quinoa, and Nicotiana benthamiana that were co-infected with two strains of BMV: Russian (R) and Fescue (F). Our work aimed at (1) establishing the frequency of recombination, (2) mapping the recombination hot spots, and (3) addressing host effects. The F and R nucleotide sequences differ from each other at many translationally silent nucleotide substitutions. We exploited this natural variability to track the crossover sites. Sequencing of a large number of cDNA clones revealed multiple homologous crossovers in each BMV RNA segment, in both the whole plants and protoplasts. Some recombination hot spots mapped at similar locations in different hosts, suggesting a role for viral factors, but other sites depended on the host. Our results demonstrate the chimeric ('mosaic') nature of the BMV RNA genome.
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Affiliation(s)
- Beivy Kolondam
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Parth Rao
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Philipp H Weber
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Aleksandra Dzianott
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Mitrick A Johns
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and
| | - Jozef J Bujarski
- Department of Biological Sciences and Plant Molecular Biology Center, Northern Illinois University, DeKalb, IL 60115, USA and; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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11
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Rapid selection against arbovirus-induced apoptosis during infection of a mosquito vector. Proc Natl Acad Sci U S A 2015; 112:E1152-61. [PMID: 25713358 DOI: 10.1073/pnas.1424469112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Millions of people are infected each year by arboviruses (arthropod-borne viruses) such as chikungunya, dengue, and West Nile viruses, yet for reasons that are largely unknown, only a relatively small number of mosquito species are able to transmit arboviruses. Understanding the complex factors that determine vector competence could facilitate strategies for controlling arbovirus infections. Apoptosis is a potential antiviral defense response that has been shown to be important in other virus-host systems. However, apoptosis is rarely seen in arbovirus-infected mosquito cells, raising questions about its importance as an antiviral defense in mosquitoes. We tested the effect of stimulating apoptosis during arbovirus infection by infecting Aedes aegypti mosquitoes with a Sindbis virus (SINV) clone called MRE/Rpr, in which the MRE-16 strain of SINV was engineered to express the proapoptotic gene reaper from Drosophila. MRE/Rpr exhibited an impaired infection phenotype that included delayed midgut infection, delayed virus replication, and reduced virus accumulation in saliva. Nucleotide sequencing of the reaper insert in virus populations isolated from individual mosquitoes revealed evidence of rapid and strong selection against maintenance of Reaper expression in MRE/Rpr-infected mosquitoes. The impaired phenotype of MRE/Rpr, coupled with the observed negative selection against Reaper expression, indicates that apoptosis is a powerful defense against arbovirus infection in mosquitoes and suggests that arboviruses have evolved mechanisms to avoid stimulating apoptosis in mosquitoes that serve as vectors.
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Guo TC, Johansson DX, Haugland Ø, Liljeström P, Evensen Ø. A 6K-deletion variant of salmonid alphavirus is non-viable but can be rescued through RNA recombination. PLoS One 2014; 9:e100184. [PMID: 25009976 PMCID: PMC4091863 DOI: 10.1371/journal.pone.0100184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 05/23/2014] [Indexed: 01/13/2023] Open
Abstract
Pancreas disease (PD) of Atlantic salmon is an emerging disease caused by Salmonid alphavirus (SAV) which mainly affects salmonid aquaculture in Western Europe. Although genome structure of SAV has been characterized and each individual viral protein has been identified, the role of 6K protein in viral replication and infectivity remains undefined. The 6K protein of alphaviruses is a small and hydrophobic protein which is involved in membrane permeabilization, protein processing and virus budding. Because these common features are shared across many viral species, they have been named viroporins. In the present study, we applied reverse genetics to generate SAV3 6K-deleted (Δ6K) variant and investigate the role of 6K protein. Our findings show that the 6K-deletion variant of salmonid alphavirus is non-viable. Despite viral proteins of Δ6K variant are detected in the cytoplasm by immunostaining, they are not found on the cell surface. Further, analysis of viral proteins produced in Δ6K cDNA clone transfected cells using radioimmunoprecipitation (RIPA) and western blot showed a protein band of larger size than E2 of wild-type SAV3. When Δ6K cDNA was co-transfected with SAV3 helper cDNA encoding the whole structural genes including 6K, the infectivity was rescued. The development of CPE after co-transfection and resolved genome sequence of rescued virus confirmed full-length viral genome being generated through RNA recombination. The discovery of the important role of the 6K protein in virus production provides a new possibility for the development of antiviral intervention which is highly needed to control SAV infection in salmonids.
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Affiliation(s)
- Tz-Chun Guo
- Norwegian University of Life Sciences, Department of Basic Sciences and Aquatic Medicine, Oslo, Norway
| | - Daniel X. Johansson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Øyvind Haugland
- Norwegian University of Life Sciences, Department of Basic Sciences and Aquatic Medicine, Oslo, Norway
| | - Peter Liljeström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Øystein Evensen
- Norwegian University of Life Sciences, Department of Basic Sciences and Aquatic Medicine, Oslo, Norway
- * E-mail:
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Hyvärinen A, Yongabi F, Mäkinen K, Wahlfors J, Pellinen R. Recombination of replicon and helper RNAs and the emergence of propagation-competent vectors upon Sindbis virus vector production. Int J Mol Med 2013; 32:410-22. [PMID: 23716190 DOI: 10.3892/ijmm.2013.1395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 03/21/2013] [Indexed: 11/05/2022] Open
Abstract
Sindbis vectors have shown remarkable antitumor efficacy and tumor-targeting capacity in animal models and hold promise for cancer therapy. Different packaging systems are used to produce propagation-incompetent Sindbis vectors. However, the vectors produced using either DH-BB single helper RNA or split helper RNA can spread in permissive cell cultures. We investigated the mechanisms of vector spreading and show, here, that recombination occurs between the replicon and DH-BB helper RNA, leading to formation of the full-length virus genome. Split helper RNA may not completely prevent wild-type reversion, although the frequency is greatly reduced. Contrary to propagation of Sindbis DH-BB vectors, Sindbis split helper vectors were frequently able to spread without cytopathic effect (CPE), a feature that was linked to wild-type reversion. Our results support the hypothesis that the non-cytopathic local spreading constantly observed with Sindbis split helper vector results from unspecific packaging of helper RNAs into vector particles and co-infection with particles containing replicon and helper RNAs. Several malignant cell lines with defective interferon responses were found to be permissive for non-cytopathic spreading of the Sindbis split helper vector. Interferon-α suppressed the spreading providing a possible option to control the vector.
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Affiliation(s)
- Anna Hyvärinen
- Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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14
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Pseudoinfectious Venezuelan equine encephalitis virus: a new means of alphavirus attenuation. J Virol 2012; 87:2023-35. [PMID: 23221545 DOI: 10.1128/jvi.02881-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is a reemerging virus that causes a severe and often fatal disease in equids and humans. In spite of a continuous public health threat, to date, no vaccines or antiviral drugs have been developed for human use. Experimental vaccines demonstrate either poor efficiency or severe adverse effects. In this study, we developed a new strategy of alphavirus modification aimed at making these viruses capable of replication and efficient induction of the immune response without causing a progressive infection, which might lead to disease development. To achieve this, we developed a pseudoinfectious virus (PIV) version of VEEV. VEE PIV mimics natural viral infection in that it efficiently replicates its genome, expresses all of the viral structural proteins, and releases viral particles at levels similar to those found in wild-type VEEV-infected cells. However, the mutations introduced into the capsid protein make this protein almost incapable of packaging the PIV genome, and most of the released virions lack genetic material and do not produce a spreading infection. Thus, VEE PIV mimics viral infection in terms of antigen production but is safer due to its inability to incorporate the viral genome into released virions. These genome-free virions are referred to as virus-like particles (VLPs). Importantly, the capsid-specific mutations introduced make the PIV a very strong inducer of the innate immune response and add self-adjuvant characteristics to the designed virus. This unique strategy of virus modification can be applied for vaccine development against other alphaviruses.
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Abstract
The alphavirus replicon technology has been utilized for many years to develop vaccines for both veterinary and human applications. Many developments have been made to the replicon platform recently, resulting in improved safety and efficacy of replicon particle (RP) vaccines. This review provides a broad overview of the replicon technology and safety features of the system and discusses the current literature on RP and replicon-based vaccines.
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16
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McGee CE, Tsetsarkin KA, Guy B, Lang J, Plante K, Vanlandingham DL, Higgs S. Stability of yellow fever virus under recombinatory pressure as compared with chikungunya virus. PLoS One 2011; 6:e23247. [PMID: 21826243 PMCID: PMC3149644 DOI: 10.1371/journal.pone.0023247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/11/2011] [Indexed: 02/08/2023] Open
Abstract
Recombination is a mechanism whereby positive sense single stranded RNA viruses exchange segments of genetic information. Recent phylogenetic analyses of naturally occurring recombinant flaviviruses have raised concerns regarding the potential for the emergence of virulent recombinants either post-vaccination or following co-infection with two distinct wild-type viruses. To characterize the conditions and sequences that favor RNA arthropod-borne virus recombination we constructed yellow fever virus (YFV) 17D recombinant crosses containing complementary deletions in the envelope protein coding sequence. These constructs were designed to strongly favor recombination, and the detection conditions were optimized to achieve high sensitivity recovery of putative recombinants. Full length recombinant YFV 17D virus was never detected under any of the experimental conditions examined, despite achieving estimated YFV replicon co-infection levels of ∼2.4×106 in BHK-21 (vertebrate) cells and ∼1.05×105 in C710 (arthropod) cells. Additionally YFV 17D superinfection resistance was observed in vertebrate and arthropod cells harboring a primary infection with wild-type YFV Asibi strain. Furthermore recombination potential was also evaluated using similarly designed chikungunya virus (CHIKV) replicons towards validation of this strategy for recombination detection. Non-homologus recombination was observed for CHIKV within the structural gene coding sequence resulting in an in-frame duplication of capsid and E3 gene. Based on these data, it is concluded that even in the unlikely event of a high level acute co-infection of two distinct YFV genomes in an arthropod or vertebrate host, the generation of viable flavivirus recombinants is extremely unlikely.
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Affiliation(s)
- Charles E McGee
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America.
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17
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Abstract
Formation of virus-specific replicative complexes (RCs) in infected cells is one of the most intriguing and important processes that determine virus replication and ultimately their pathogenesis on the molecular and cellular levels. Alphavirus replication was known to lead to formation of so-called type 1 cytopathic vacuoles (CPV1s), whose distinguishing feature is the presence of numerous membrane invaginations (spherules) and accumulation of viral nonstructural proteins (nsPs) at the cytoplasmic necks of these spherules. These CPV1s, modified endosomes and lysosomes, were proposed as the sites of viral RNA synthesis. However, our recent studies have demonstrated that Sindbis virus (SINV)-specific, double-stranded RNA (dsRNA)- and nonstructural protein (nsP)-containing RCs are initially formed at the plasma membrane. In this new study, we present extensive evidence that (i) in cells of vertebrate origin, at early times postinfection, viral nsPs colocalize with spherules at the plasma membrane; (ii) viral dsRNA intermediates are packed into membrane spherules and are located in their cavities on the external surface of the plasma membrane; (iii) formation of the membrane spherules is induced by the partially processed nonstructural polyprotein P123 and nsP4, but synthesis of dsRNA is an essential prerequisite of their formation; (iv) plasma membrane-associated dsRNA and protein structures are the active sites of single-stranded RNA (ssRNA) synthesis; (v) at late times postinfection, only a small fraction of SINV nsP-containing complexes are relocalized into the cytoplasm on the endosome membrane. (vi) pharmacological drugs inhibiting different endocytotic pathways have either only minor or no negative effects on SINV RNA replication; and (vii) in mosquito cells, at any times postinfection, dsRNA/nsP complexes and spherules are associated with both endosomal/lysosomal and plasma membranes, suggesting that mechanisms of RC formation may differ in cells of insect and vertebrate origins.
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18
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In vitro and in vivo characterization of microRNA-targeted alphavirus replicon and helper RNAs. J Virol 2010; 84:7713-25. [PMID: 20504925 DOI: 10.1128/jvi.00310-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alphavirus-based replicon vector systems (family Togaviridae) have been developed as expression vectors with demonstrated potential in vaccine development against both infectious diseases and cancer. The single-cycle nature of virus-like replicon particles (VRP), generated by supplying the structural proteins from separate replicable helper RNAs, is an attractive safety component of these systems. MicroRNAs (miRNAs) have emerged as important cellular RNA regulation elements. Recently, miRNAs have been employed as a mechanism to attenuate or restrict cellular tropism of replication-competent viruses, such as oncolytic adenoviruses, vesicular stomatitis virus, and picornaviruses as well as nonreplicating lentiviral and adenoviral vectors. Here, we describe the incorporation of miRNA-specific target sequences into replicable alphavirus helper RNAs that are used in trans to provide the structural proteins required for VRP production. VRP were found to be efficiently produced using miRNA-targeted helper RNAs if miRNA-specific inhibitors were introduced into cells during VRP production. In the absence of such inhibitors, cellular miRNAs were capable of downregulating helper RNA replication in vitro. When miRNA targets were incorporated into a replicon RNA, cellular miRNAs were capable of downregulating replicon RNA replication upon delivery of VRP into animals, demonstrating activity in vivo. These data provide the first example of miRNA-specific repression of alphavirus replicon and helper RNA replication and demonstrate the feasibility of miRNA targeting of expression vector helper functions that are provided in trans.
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19
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Kamrud KI, Alterson K, Custer M, Dudek J, Goodman C, Owens G, Smith JF. Development and characterization of promoterless helper RNAs for the production of alphavirus replicon particle. J Gen Virol 2010; 91:1723-7. [PMID: 20181749 PMCID: PMC2888770 DOI: 10.1099/vir.0.020081-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Alphavirus-based replicon systems are frequently used as preclinical vectors and as antigen discovery tools, and they have recently been assessed in clinical vaccine trials. Typically, alphavirus replicon RNAs are delivered within virus-like replicon particles (VRP) that are produced following transfection of replicon RNA and two helper RNAs into permissive cells in vitro. The non-structural proteins expressed from the replicon RNA amplify the replicon RNA in cis and the helper RNAs in trans, the latter providing the viral structural proteins necessary to package the replicon RNA into VRP. Current helper RNA designs incorporate the alphavirus 26S promoter to direct the transcription of high levels of structural gene mRNAs. We demonstrate here that the 26S promoter is not required on helper RNAs to produce VRP and propose that such promoterless helper RNAs, by design, reduce the probability of generating replication-competent virus that may otherwise result from RNA recombination.
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Affiliation(s)
- K I Kamrud
- AlphaVax, Inc., 2 Triangle Drive, Research Triangle Park, NC 27709, USA.
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20
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A trans-complementing recombination trap demonstrates a low propensity of flaviviruses for intermolecular recombination. J Virol 2010; 84:599-611. [PMID: 19864381 DOI: 10.1128/jvi.01063-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Intermolecular recombination between the genomes of closely related RNA viruses can result in the emergence of novel strains with altered pathogenic potential and antigenicity. Although recombination between flavivirus genomes has never been demonstrated experimentally, the potential risk of generating undesirable recombinants has nevertheless been a matter of concern and controversy with respect to the development of live flavivirus vaccines. As an experimental system for investigating the ability of flavivirus genomes to recombine, we developed a "recombination trap," which was designed to allow the products of rare recombination events to be selected and amplified. To do this, we established reciprocal packaging systems consisting of pairs of self-replicating subgenomic RNAs (replicons) derived from tick-borne encephalitis virus (TBEV), West Nile virus (WNV), and Japanese encephalitis virus (JEV) that could complement each other in trans and thus be propagated together in cell culture over multiple passages. Any infectious viruses with intact, full-length genomes that were generated by recombination of the two replicons would be selected and enriched by end point dilution passage, as was demonstrated in a spiking experiment in which a small amount of wild-type virus was mixed with the packaged replicons. Using the recombination trap and the JEV system, we detected two aberrant recombination events, both of which yielded unnatural genomes containing duplications. Infectious clones of both of these genomes yielded viruses with impaired growth properties. Despite the fact that the replicon pairs shared approximately 600 nucleotides of identical sequence where a precise homologous crossover event would have yielded a wild-type genome, this was not observed in any of these systems, and the TBEV and WNV systems did not yield any viable recombinant genomes at all. Our results show that intergenomic recombination can occur in the structural region of flaviviruses but that its frequency appears to be very low and that therefore it probably does not represent a major risk in the use of live, attenuated flavivirus vaccines.
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Structural and functional elements of the promoter encoded by the 5' untranslated region of the Venezuelan equine encephalitis virus genome. J Virol 2009; 83:8327-39. [PMID: 19515761 DOI: 10.1128/jvi.00586-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is one of the most pathogenic members of the Alphavirus genus in the Togaviridae family. The pathogenesis of this virus depends strongly on the sequences of the structural proteins and on the mutations in the RNA promoter encoded by the 5' untranslated region (5'UTR) of the viral genome. In this study, we performed a detailed investigation of the structural and functional elements of the 5'-terminal promoter and analyzed the effect of multiple mutations introduced into the VEEV 5'UTR on virus and RNA replication. The results of this study demonstrate that RNA replication is determined by two synergistically functioning RNA elements. One of them is a very 5'-terminal AU dinucleotide, which is not involved in the stable RNA secondary structure, and the second is a short, G-C-rich RNA stem. An increase or decrease in the stem's stability has deleterious effects on virus and RNA replication. In response to mutations in these RNA elements, VEEV replicative machinery was capable of developing new, compensatory sequences in the 5'UTR either containing 5'-terminal AUG or AU repeats or leading to the formation of new, heterologous stem-loops. Analysis of the numerous compensatory mutations suggested that at least two different mechanisms are involved in their generation. Some of the modifications introduced into the 5' terminus of the viral genome led to an accumulation of the mutations in the VEEV nsPs, which suggested to us that there is a direct involvement of these proteins in promoter recognition. Furthermore, our data provide new evidence that the 3' terminus of the negative-strand viral genome in the double-stranded RNA replicative intermediate is represented by a single-stranded RNA. Both the overall folding and the sequence determine its efficient function as a promoter for VEEV positive-strand RNA genome synthesis.
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22
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Tan LV, Ha DQ, Hien VM, van der Hoek L, Farrar J, de Jong MD. Me Tri virus: a Semliki Forest virus strain from Vietnam? J Gen Virol 2008; 89:2132-2135. [PMID: 18753222 DOI: 10.1099/vir.0.2008/002121-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Me Tri virus (MTV) is a member of the Semliki Forest virus (SFV) complex in the genus Alphavirus, first isolated from Culex tritaeniorhynchus mosquitoes in Vietnam in 1971 and described as a newly recognized alphavirus, based on antigenic characterization. However, based on a partial nucleotide sequence of the E1 envelope glycoprotein gene, it has recently been argued that MTV may represent a variant of SFV rather than a separate species. To enable definitive classification, we determined the complete genome sequence of MTV from original virus stock. Nucleotide homology, as well as phylogenetic analyses based on whole and partial genome sequences confirmed that MTV is an isolate of SFV. Notable differences to other reported SFV sequences included a 122 nt insertion at the 5' non-translated region (NTR), likely resulting from homologous recombination of part of the nsP2 gene, and differences in the sequence length of the 3' NTR. To our knowledge, this is the first and only documentation of SFV isolation outside Africa. Further research is needed to clarify whether SFV continues to circulate in Vietnam.
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Affiliation(s)
- Le Van Tan
- Oxford University Clinical Research Unit, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam
| | - Do Quang Ha
- Oxford University Clinical Research Unit, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam
| | - Vo Minh Hien
- Hospital for Tropical Diseases, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam
| | - Lia van der Hoek
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Jeremy Farrar
- Centre for Tropical Medicine, Oxford University, UK.,Oxford University Clinical Research Unit, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam
| | - Menno D de Jong
- Centre for Tropical Medicine, Oxford University, UK.,Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.,Oxford University Clinical Research Unit, 190 Ben Ham Tu, Ho Chi Minh City, Vietnam
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23
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Tseng JC, Daniels G, Meruelo D. Controlled propagation of replication-competent Sindbis viral vector using suicide gene strategy. Gene Ther 2008; 16:291-6. [PMID: 18818670 DOI: 10.1038/gt.2008.153] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A major concern of using viral gene therapy is the potential for uncontrolled vector propagation and infection that might result in serious deleterious effects. To enhance the safety, several viral vectors, including vectors based on Sindbis virus, were engineered to lose their capability to replicate and spread after transduction of target cells. Such designs, however, could dramatically reduce the therapeutic potency of the viral vectors, resulting in the need for multiple dosages to achieve treatment goals. Earlier, we showed that a replication-defective (RD) Sindbis vector achieved specific tumor targeting without any adverse effects in vivo. Here, we present a replication-competent Sindbis viral vector that has an hsvtk suicide gene incorporated into ns3, an indispensable non-structural gene for viral survival. The capability of viral propagation significantly increases tumor-specific infection and enhances growth suppression of tumor compared with the conventional RD vectors. Furthermore, in the presence of the prodrug ganciclovir, the hsvtk suicide gene serves as a safety mechanism to prevent uncontrolled vector propagation. In addition to suppressing vector propagation, toxic metabolites, generated by prodrug activation, could spread to neighboring uninfected tumor cells to further enhance tumor killing.
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Affiliation(s)
- J-C Tseng
- NYU Cancer Institute and the NYU Gene Therapy Center, Department of Pathology, NYU School of Medicine, New York University, New York, NY 10016, USA
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24
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Liljeström P, Garoff H. Expression of proteins using Semliki Forest virus vectors. ACTA ACUST UNITED AC 2008; Chapter 16:Unit16.20. [PMID: 18265128 DOI: 10.1002/0471142727.mb1620s29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Semliki Forest virus (SFV) vectors have been developed to provide a convenient system to express protein-encoding sequences in virtually any animal cell. This unit presents two strategies for protein expression using SFV vectors. In both cases the protein-coding sequence of interest is cloned into a plasmid vector, which is subsequently used to produce recombinant RNA in vitro. This RNA, which is of positive polarity, is transfected into cells and there is amplified by virtue of its self-encoded RNA replicase. The same replicase also produces a shorter RNA species that encodes the protein of interest. In the first protocol, cells are transfected (either by electroporation or liposome-mediated transfection) and directly analyzed for expression of the heterologous protein. Accompanying support protocols provide methods for checking expression and transfection through galactosidase assays of transfected cells and cell lysates. The other strategy employs in vivo packaging of the RNA into SFV particles; recombinant RNA is cotransfected with a special helper RNA that codes for the structural proteins needed for virus assembly. SFV particles carrying only recombinant RNA are formed and are used to infect cells for analysis of protein expression. Accompanying support protocols describe methods for titrating and purifying recombinant virus stocks. Although the protocols presented here are designed for use with BHK (baby hamster kidney) cells, the virus has a very broad host range and can be used with many different cell types.
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Affiliation(s)
- P Liljeström
- Karolinska Institute, Novum Research Center, Huddinge, Sweden
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25
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26
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Reimann I, Semmler I, Beer M. Packaged replicons of bovine viral diarrhea virus are capable of inducing a protective immune response. Virology 2007; 366:377-86. [PMID: 17544049 DOI: 10.1016/j.virol.2007.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 04/12/2007] [Accepted: 05/04/2007] [Indexed: 12/17/2022]
Abstract
Bovine viral diarrhea virus (BVDV) replicons with deletions within the capsid, E(RNS) or E1 encoding region were constructed and efficiently packaged with a helper cell line. High titres of packaged replicons were observed as early as 24 h after transfection, whereas no virus progeny could be detected after transfection of non-complementing cells. Infection of bovine cell cultures with rescued viruses resulted in one cycle of replication without release of infectious virus particles, and no genetic reversion of the generated viruses was detected. Packaged replicons with a deletion within the capsid-coding region were characterized in vivo in immunization and challenge trials. Following immunization of calves with the replication-deficient virus, neither virus shedding nor viremia was detected. After challenge infection with virulent BVDV, all vaccinates were completely protected from disease as measured by the absence of viremia and shedding of challenge virus, which indicated that a 'sterilizing immunity' could be induced with the generated replication-deficient packaged replicons.
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Affiliation(s)
- Ilona Reimann
- Institute of Molecular Biology, Friedrich-Loeffler-Institut, Boddenblick 5a, 17493 Greifswald-Insel Riems, Germany
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27
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Garmashova N, Gorchakov R, Volkova E, Paessler S, Frolova E, Frolov I. The Old World and New World alphaviruses use different virus-specific proteins for induction of transcriptional shutoff. J Virol 2006; 81:2472-84. [PMID: 17108023 PMCID: PMC1865960 DOI: 10.1128/jvi.02073-06] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Alphaviruses are widely distributed throughout the world. During the last few thousand years, the New World viruses, including Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV), evolved separately from those of the Old World, i.e., Sindbis virus (SINV) and Semliki Forest virus (SFV). Nevertheless, the results of our study indicate that both groups have developed the same characteristic: their replication efficiently interferes with cellular transcription and the cell response to virus replication. Transcriptional shutoff caused by at least two of the Old World alphaviruses, SINV and SFV, which belong to different serological complexes, depends on nsP2, but not on the capsid protein, functioning. Our data suggest that the New World alphaviruses VEEV and EEEV developed an alternative mechanism of transcription inhibition that is mainly determined by their capsid protein, but not by the nsP2. The ability of the VEEV capsid to inhibit cellular transcription appears to be controlled by the amino-terminal fragment of the protein, but not by its protease activity or by the positively charged RNA-binding domain. These data provide new insights into alphavirus evolution and present a plausible explanation for the particular recombination events that led to the formation of western equine encephalitis virus (WEEV) from SINV- and EEEV-like ancestors. The recombination allowed WEEV to acquire capsid protein functioning in transcription inhibition from EEEV-like virus. Identification of the new functions in the New World alphavirus-derived capsids opens an opportunity for developing new, safer alphavirus-based gene expression systems and designing new types of attenuated vaccine strains of VEEV and EEEV.
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MESH Headings
- Alphavirus/classification
- Alphavirus/genetics
- Alphavirus/pathogenicity
- Alphavirus/physiology
- Alphavirus Infections/genetics
- Alphavirus Infections/metabolism
- Alphavirus Infections/virology
- Amino Acid Sequence
- Animals
- Capsid Proteins/genetics
- Capsid Proteins/metabolism
- Cell Line
- Cell Survival
- Cricetinae
- Cysteine Endopeptidases/metabolism
- Encephalitis Virus, Eastern Equine/classification
- Encephalitis Virus, Eastern Equine/genetics
- Encephalitis Virus, Eastern Equine/pathogenicity
- Encephalitis Virus, Eastern Equine/physiology
- Encephalitis Virus, Venezuelan Equine/classification
- Encephalitis Virus, Venezuelan Equine/genetics
- Encephalitis Virus, Venezuelan Equine/pathogenicity
- Encephalitis Virus, Venezuelan Equine/physiology
- Evolution, Molecular
- Mice
- Molecular Sequence Data
- NIH 3T3 Cells
- Replicon
- Semliki forest virus/classification
- Semliki forest virus/genetics
- Semliki forest virus/pathogenicity
- Semliki forest virus/physiology
- Sequence Homology, Amino Acid
- Sindbis Virus/classification
- Sindbis Virus/genetics
- Sindbis Virus/pathogenicity
- Sindbis Virus/physiology
- Species Specificity
- Transcription, Genetic
- Viral Proteins/genetics
- Viral Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Natalia Garmashova
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-1019, USA
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28
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Wierzchoslawski R, Bujarski JJ. Efficient in vitro system of homologous recombination in brome mosaic bromovirus. J Virol 2006; 80:6182-7. [PMID: 16731958 PMCID: PMC1472593 DOI: 10.1128/jvi.02447-05] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 03/26/2006] [Indexed: 12/26/2022] Open
Abstract
Recent in vivo studies have revealed that the subgenomic promoter (sgp) in brome mosaic bromovirus (BMV) RNA3 supports frequent homologous recombination events (R. Wierzchoslawski, A. Dzianott, and J. Bujarski, J. Virol. 78:8552-8564, 2004). In this paper, we describe an sgp-driven in vitro system that supports efficient RNA3 crossovers. A 1:1 mixture of two (-)-sense RNA3 templates was copied with either a BMV replicase (RdRp) preparation or recombinant BMV protein 2a. The BMV replicase enzyme supported a lower recombination frequency than 2a, demonstrating a role of other viral and/or host factors. The described in vitro system will allow us to study the mechanism of homologous RNA recombination.
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Affiliation(s)
- Rafal Wierzchoslawski
- Plant Molecular Biology Center, Department of Biological Sciences, Northern Illinois University, De Kalb, IL 60115, USA
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29
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Cayabyab MJ, Hovav AH, Hsu T, Krivulka GR, Lifton MA, Gorgone DA, Fennelly GJ, Haynes BF, Jacobs WR, Letvin NL. Generation of CD8+ T-cell responses by a recombinant nonpathogenic Mycobacterium smegmatis vaccine vector expressing human immunodeficiency virus type 1 Env. J Virol 2006; 80:1645-52. [PMID: 16439521 PMCID: PMC1367151 DOI: 10.1128/jvi.80.4.1645-1652.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Because the vaccine vectors currently being evaluated in human populations all have significant limitations in their immunogenicity, novel vaccine strategies are needed for the elicitation of cell-mediated immunity. The nonpathogenic, rapidly growing mycobacterium Mycobacterium smegmatis was engineered as a vector expressing full-length human immunodeficiency virus type 1 (HIV-1) HXBc2 envelope protein. Immunization of mice with recombinant M. smegmatis led to the expansion of major histocompatibility complex class I-restricted HIV-1 epitope-specific CD8(+) T cells that were cytolytic and secreted gamma interferon. Effector and memory T lymphocytes were elicited, and repeated immunization generated a stable central memory pool of virus-specific cells. Importantly, preexisting immunity to Mycobacterium bovis BCG had only a marginal effect on the immunogenicity of recombinant M. smegmatis. This mycobacterium may therefore be a useful vaccine vector.
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Affiliation(s)
- Mark J Cayabyab
- Department of Medicine, Division of Viral Pathogenesis, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02130, USA
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30
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Gallei A, Orlich M, Thiel HJ, Becher P. Noncytopathogenic pestivirus strains generated by nonhomologous RNA recombination: alterations in the NS4A/NS4B coding region. J Virol 2006; 79:14261-70. [PMID: 16254361 PMCID: PMC1280241 DOI: 10.1128/jvi.79.22.14261-14270.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several studies have demonstrated that cytopathogenic (cp) pestivirus strains evolve from noncytopathogenic (noncp) viruses by nonhomologous RNA recombination. In addition, two recent reports showed the rapid emergence of noncp Bovine viral diarrhea virus (BVDV) after a few cell culture passages of cp BVDV strains by homologous recombination between identical duplicated viral sequences. To allow the identification of recombination sites from noncp BVDV strains that evolve from cp viruses, we constructed the cp BVDV strains CP442 and CP552. Both harbor duplicated viral sequences of different origin flanking the cellular insertion Nedd8*; the latter is a prerequisite for their cytopathogenicity. In contrast to the previous studies, isolation of noncp strains was possible only after extensive cell culture passages of CP442 and CP552. Sequence analysis of 15 isolated noncp BVDVs confirmed that all recombinant strains lack at least most of Nedd8*. Interestingly, only one strain resulted from homologous recombination while the other 14 strains were generated by nonhomologous recombination. Accordingly, our data suggest that the extent of sequence identity between participating sequences influences both frequency and mode (homologous versus nonhomologous) of RNA recombination in pestiviruses. Further analyses of the noncp recombinant strains revealed that a duplication of 14 codons in the BVDV nonstructural protein 4B (NS4B) gene does not interfere with efficient viral replication. Moreover, an insertion of viral sequences between the NS4A and NS4B genes was well tolerated. These findings thus led to the identification of two genomic loci which appear to be suited for the insertion of heterologous sequences into the genomes of pestiviruses and related viruses.
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Affiliation(s)
- Andreas Gallei
- Institut für Virologie, Justus-Liebig-Universität, Frankfurter Strasse 107, D-35392 Giessen, Germany
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Rhême C, Ehrengruber MU, Grandgirard D. Alphaviral cytotoxicity and its implication in vector development. Exp Physiol 2004; 90:45-52. [PMID: 15542620 DOI: 10.1113/expphysiol.2004.028142] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A great variety of viruses have been engineered to serve as expression vectors. Among them, the alphaviruses Semliki Forest virus and Sindbis virus represent promising tools for heterologous gene expression in a wide variety of host cells. Several applications have already been described in neurobiological studies, in gene therapy, for vaccine development and in cancer therapy. Both viruses trigger stress pathways in the cells they infect, sometimes culminating in the death of the host. This inherent property is either an advantage or a drawback, depending on the type of application. This review covers the development and applications of alphavirus vectors and, as our work has been mainly with Semliki Forest virus, we have focused on this virus with special emphasis on how the understanding of Semliki Forest virus cytotoxicity enables it to be manipulated and used.
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Affiliation(s)
- Céline Rhême
- Institute of Molecular Medicine and Cell Research, Albert Ludwigs University, Stephan-Meier Strasse 17, D-79106 Freiburg im Breisgau, Germany.
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Chetverin AB, Kopein DS, Chetverina HV, Demidenko AA, Ugarov VI. Viral RNA-directed RNA polymerases use diverse mechanisms to promote recombination between RNA molecules. J Biol Chem 2004; 280:8748-55. [PMID: 15611043 DOI: 10.1074/jbc.m412684200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An earlier developed purified cell-free system was used to explore the potential of two RNA-directed RNA polymerases (RdRps), Qbeta phage replicase and the poliovirus 3Dpol protein, to promote RNA recombination through a primer extension mechanism. The substrates of recombination were fragments of complementary strands of a Qbeta phage-derived RNA, such that if aligned at complementary 3'-termini and extended using one another as a template, they would produce replicable molecules detectable as RNA colonies grown in a Qbeta replicase-containing agarose. The results show that while 3Dpol efficiently extends the aligned fragments to produce the expected homologous recombinant sequences, only nonhomologous recombinants are generated by Qbeta replicase at a much lower yield and through a mechanism not involving the extension of RNA primers. It follows that the mechanisms of RNA recombination by poliovirus and Qbeta RdRps are quite different. The data favor an RNA transesterification reaction catalyzed by a conformation acquired by Qbeta replicase during RNA synthesis and provide a likely explanation for the very low frequency of homologous recombination in Qbeta phage.
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Affiliation(s)
- Alexander B Chetverin
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
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33
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Panaviene Z, Nagy PD. Mutations in the RNA-binding domains of tombusvirus replicase proteins affect RNA recombination in vivo. Virology 2004; 317:359-72. [PMID: 14698673 DOI: 10.1016/j.virol.2003.08.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
RNA recombination, which is thought to occur due to replicase errors during viral replication, is one of the major driving forces of virus evolution. In this article, we show evidence that the replicase proteins of Cucumber necrosis virus, a tombusvirus, are directly involved in RNA recombination in vivo. Mutations within the RNA-binding domains of the replicase proteins affected the frequency of recombination observed with a prototypical defective-interfering (DI) RNA, a model template for recombination studies. Five of the 17 replicase mutants tested showed delay in the formation of recombinants when compared to the wild-type helper virus. Interestingly, two replicase mutants accelerated recombinant formation and, in addition, these mutants also increased the level of subgenomic RNA synthesis (Virology 308 (2003), 191-205). A trans-complementation system was used to demonstrate that mutation in the p33 replicase protein resulted in altered recombination rate. Isolated recombinants were mostly imprecise (nonhomologous), with the recombination sites clustered around a replication enhancer region and a putative cis-acting element, respectively. These RNA elements might facilitate the proposed template switching events by the tombusvirus replicase. Together with data in the article cited above, results presented here firmly establish that the conserved RNA-binding motif of the replicase proteins is involved in RNA replication, subgenomic RNA synthesis, and RNA recombination.
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Affiliation(s)
- Zivile Panaviene
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
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Cheng CP, Nagy PD. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. J Virol 2003; 77:12033-47. [PMID: 14581540 PMCID: PMC254248 DOI: 10.1128/jvi.77.22.12033-12047.2003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
RNA recombination occurs frequently during replication of tombusviruses and carmoviruses, which are related small plus-sense RNA viruses of plants. The most common recombinants generated by these viruses are either defective interfering (DI) RNAs or chimeric satellite RNAs, which are thought to be generated by template switching of the viral RNA-dependent RNA polymerase (RdRp) during the viral replication process. To test if RNA recombination is mediated by the viral RdRp, we used either a purified recombinant RdRp of Turnip crinkle carmovirus or a partially purified RdRp preparation of Cucumber necrosis tombusvirus. We demonstrated that these RdRp preparations generated RNA recombinants in vitro. The RdRp-driven template switching events occurred between either identical templates or two different RNA templates. The template containing a replication enhancer recombined more efficiently than templates containing artificial sequences. We also observed that AU-rich sequences promote recombination more efficiently than GC-rich sequences. Cloning and sequencing of the generated recombinants revealed that the junction sites were located frequently at the ends of the templates (end-to-end template switching). We also found several recombinants that were generated by template switching involving internal positions in the RNA templates. In contrast, RNA ligation-based RNA recombination was not detected in vitro. Demonstration of the ability of carmo- and tombusvirus RdRps to switch RNA templates in vitro supports the copy-choice models of RNA recombination and DI RNA formation for these viruses.
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Affiliation(s)
- Chi-Ping Cheng
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546, USA
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35
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Vasilakis N, Falvey D, Gangolli SS, Coleman J, Kowalski J, Udem SA, Zamb TJ, Kovacs GR. Transfection-independent production of alphavirus replicon particles based on poxvirus expression vectors. Nat Biotechnol 2003; 21:932-5. [PMID: 12845329 DOI: 10.1038/nbt845] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2002] [Accepted: 04/24/2003] [Indexed: 11/08/2022]
Abstract
This report describes a transfection-independent system for packaging alphavirus replicon vectors using modified vaccinia virus Ankara (MVA) vectors to express all of the RNA components necessary for the production of Venezuelan equine encephalitis (VEE) virus replicon particles (VRP). Infection of mammalian cells with these recombinant MVA vectors resulted in robust expression of VEE structural genes, replication of the alphavirus vector and high titers of VRP. In addition, VRP packaging was achieved in a cell type (fetal rhesus lung) that has been approved for the manufacturing of vaccines destined for human use.
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Affiliation(s)
- Nikos Vasilakis
- Viral Vaccine Discovery, Wyeth Vaccines Research, Pearl River, New York 10965, USA
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36
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Abstract
To investigate whether rubella virus (RUB) undergoes intermolecular RNA-RNA recombination, cells were cotransfected with pairs of in vitro transcripts from genomic cDNA plasmid vectors engineered to contain nonoverlapping deletions: the replicative transcript maintained the 5'-proximal nonstructural (NS) ORF (which contained the replicase, making it RNA replication competent), had a deletion in the 3'-proximal structural protein (SP) ORF, and maintained the 3' end of the genome, including the putative 3' cis-acting elements (CSE), while the nonreplicative transcript consisted of the 3' half of the genome including the SP-ORF and 3' CSE. Cotransfection yielded plaque-forming virus that synthesized the standard genomic and subgenomic RNAs and thus was generated by RNA-RNA recombination. Using transcripts tagged with a 3'-terminal deletion, it was found that recombinants contained the 3' end derived from the replicative strand, indicating a cis-preference for initiation of negative-strand synthesis. In cotransfections in which the replicative transcript lacked the 3' CSE, recombination occurred, albeit at lower efficiency, indicating that initiation in trans from the NS-ORF can occur. The 3' CSE was sufficient as a nonreplicative transcript, showing that it can serve as a promoter for negative-strand RNA synthesis. While deletion mutagenesis showed that the presence of the junction untranslated region (J-UTR) between the ORFs appeared to be necessary on both transcripts for recombination in this region of the genome, analysis with transcripts tagged with restriction sites showed that the J-UTR was not a hot spot for recombination compared to neighboring regions in both ORFs. Sequence analysis of recombinants revealed that both precise (homologous) and imprecise recombination (aberrant, homologous resulting in duplications) occurred; however, imprecise recombination only involved the J-UTR or the 3' end of the NS-ORF and the J-UTR (maintaining the NS-ORF), indicating selection pressure against duplications in other regions of the genome.
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Affiliation(s)
- Sandra D Adams
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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37
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Abstract
Alphaviruses are positive-stranded RNA viruses that have a broad host range and therefore are capable of replicating in many vertebrate and invertebrate cells. The single-stranded alphavirus genome is divided into two ORFs. The first ORF encodes the nonstructural proteins that are translated upon entry of the virus into the cytoplasm and are responsible for transcription and replication of viral RNA. The second ORF is under the control of a subgenomic promoter and normally encodes the structural proteins, which are responsible for encapsidation of viral RNA and final assembly into enveloped particles. Expression vectors have been engineered from at least three alphaviruses in which the structural protein gene region has been replaced by heterologous genes and have been shown to express high levels of the heterologous protein in cultured cells. These RNA vectors, known as replicons, are capable of replicating on their own but are not packaged into virus-like particles unless the structural proteins are provided in trans. Thus, replicons are single cycle vectors incapable of spreading from infected to noninfected cells. Because of these features, alphavirus replicon vectors are being developed as a platform vaccine technology for numerous viral, bacterial, protozoan and tumour antigens where they have been shown to be efficient inducers of both humoral and T cell responses. In addition, as the alphavirus structural proteins are not expressed in vaccine recipients, antivector immune responses are generally minimal, allowing for multiple effective immunisations of the same individual.
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Affiliation(s)
- Jonathan O Rayner
- AlphaVax, Inc., P.O. Box 110307, Research Triangle Park, NC 27709-0307, USA.
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38
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Katayama K, Shirato-Horikoshi H, Kojima S, Kageyama T, Oka T, Hoshino F, Fukushi S, Shinohara M, Uchida K, Suzuki Y, Gojobori T, Takeda N. Phylogenetic analysis of the complete genome of 18 Norwalk-like viruses. Virology 2002; 299:225-239. [PMID: 12202225 DOI: 10.1006/viro.2002.1568] [Citation(s) in RCA: 241] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
"Norwalk-like viruses" (NLV), a member of the family Caliciviridae, are the major causative agents of acute gastroenteritis and are genetically divided into two groups, genogroup I (GI) and genogroup II (GII). We have determined the complete nucleotide sequences of 10 new NLV strains. Using this information together with eight known NLV sequences, the criteria to further classify genotypes of NLV were investigated. Validation of the topological error based on the bootstrap value and the branch length (distance) allowed us to identify two potential subgenomic regions suitable for the genotyping. They were the putative 3D-like RNA-dependent RNA polymerase (polymerase) and the capsid N-terminal/Shell domains (capsid N/S domain). When the distance distribution analysis was performed, the polymerase-based classification did not separate the strains into internal clusters within the genogroup. Furthermore, a diversity plot analysis of the complete nucleotide sequences of WUG1, a NLV GI strain, and Saitama U1, a NLV GII strain, indicated that the genotype was different between the polymerase and capsid N/S domain, suggesting that these strains are the genetic recombinants. Therefore, polymerase is not suitable for genotyping. On the other hand, the clustering based on the capsid N/S domain successfully distinguished the NLV as well as the grouping based on the antigenicity, as determined by both antigen and antibody ELISAs with recombinant virus-like particles. As the nucleotide sequences of the primers for the capsid N/S domain are highly conserved among the NLV, the amplification of the unknown genotype can be easily performed. This method will facilitate global surveying as well as epidemiologic study on NLV.
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Affiliation(s)
- Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan.
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39
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Lee JS, Pushko P, Parker MD, Dertzbaugh MT, Smith LA, Smith JF. Candidate vaccine against botulinum neurotoxin serotype A derived from a Venezuelan equine encephalitis virus vector system. Infect Immun 2001; 69:5709-15. [PMID: 11500447 PMCID: PMC98687 DOI: 10.1128/iai.69.9.5709-5715.2001] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A candidate vaccine against botulinum neurotoxin serotype A (BoNT/A) was developed by using a Venezuelan equine encephalitis (VEE) virus replicon vector. This vaccine vector is composed of a self-replicating RNA containing all of the VEE nonstructural genes and cis-acting elements and also a heterologous immunogen gene placed downstream of the subgenomic 26S promoter in place of the viral structural genes. In this study, the nontoxic 50-kDa carboxy-terminal fragment (H(C)) of the BoNT/A heavy chain was cloned into the replicon vector (H(C)-replicon). Cotransfection of BHK cells in vitro with the H(C)-replicon and two helper RNA molecules, the latter encoding all of the VEE structural proteins, resulted in the assembly and release of propagation-deficient, H(C) VEE replicon particles (H(C)-VRP). Cells infected with H(C)-VRP efficiently expressed this protein when analyzed by either immunofluorescence or by Western blot. To evaluate the immunogenicity of H(C)-VRP, mice were vaccinated with various doses of H(C)-VRP at different intervals. Mice inoculated subcutaneously with H(C)-VRP were protected from an intraperitoneal challenge of up to 100,000 50% lethal dose units of BoNT/A. Protection correlated directly with serum enzyme-linked immunosorbent assay titers to BoNT/A. The duration of the immunity achieved was tested at 6 months and at 1 year postvaccination, and mice challenged at these times remained refractory to challenge with BoNT/A.
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Affiliation(s)
- J S Lee
- Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702-5011, USA.
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40
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Koller D, Ruedl C, Loetscher M, Vlach J, Oehen S, Oertle K, Schirinzi M, Deneuve E, Moser R, Kopf M, Bailey JE, Renner W, Bachmann MF. A high-throughput alphavirus-based expression cloning system for mammalian cells. Nat Biotechnol 2001; 19:851-5. [PMID: 11533644 DOI: 10.1038/nbt0901-851] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have developed a widely applicable functional genomics strategy based on alphavirus expression vectors. The technology allows for rapid identification of genes encoding a functional activity such as binding of a defined ligand. Complementary DNA (cDNA) libraries were expressed in mammalian cells following infection with recombinant Sindbis virus (SIN replicon particles), a member of the Alphavirus genus. Virus-infected cells that specifically bound a ligand of choice were isolated using fluorescence-activated cell sorting (FACS). Replication-competent, infective SIN replicon particles harboring the corresponding cDNA were amplified in a next step. Within one round of selection, viral clones encoding proteins recognized by monoclonal antibodies or Fc-fusion molecules could be isolated and sequenced. Moreover, using the same viral libraries, a plaque-lift assay was established that allowed the identification of secreted, intracellular, and membrane proteins.
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Affiliation(s)
- D Koller
- Cytos Biotechnology AG, Wagistr. 21, CH-8952 Schlieren-Zürich, Switzerland
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41
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George J, Raju R. Alphavirus RNA genome repair and evolution: molecular characterization of infectious sindbis virus isolates lacking a known conserved motif at the 3' end of the genome. J Virol 2000; 74:9776-85. [PMID: 11000254 PMCID: PMC112414 DOI: 10.1128/jvi.74.20.9776-9785.2000] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 3' nontranslated region of the genomes of Sindbis virus (SIN) and other alphaviruses carries several repeat sequence elements (RSEs) as well as a 19-nucleotide (nt) conserved sequence element (3'CSE). The 3'CSE and the adjoining poly(A) tail of the SIN genome are thought to act as viral promoters for negative-sense RNA synthesis and genome replication. Eight different SIN isolates that carry altered 3'CSEs were studied in detail to evaluate the role of the 3'CSE in genome replication. The salient findings of this study as it applies to SIN infection of BHK cells are as follows: i) the classical 19-nt 3'CSE of the SIN genome is not essential for genome replication, long-term stability, or packaging; ii) compensatory amino acid or nucleotide changes within the SIN genomes are not required to counteract base changes in the 3' terminal motifs of the SIN genome; iii) the 5' 1-kb regions of all SIN genomes, regardless of the differences in 3' terminal motifs, do not undergo any base changes even after 18 passages; iv) although extensive addition of AU-rich motifs occurs in the SIN genomes carrying defective 3'CSE, these are not essential for genome viability or function; and v) the newly added AU-rich motifs are composed predominantly of RSEs. These findings are consistent with the idea that the 3' terminal AU-rich motifs of the SIN genomes do not bind directly to the viral polymerase and that cellular proteins with broad AU-rich binding specificity may mediate this interaction. In addition to the classical 3'CSE, other RNA motifs located elsewhere in the SIN genome must play a major role in template selection by the SIN RNA polymerase.
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Affiliation(s)
- J George
- Department of Microbiology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208, USA
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42
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Annaert W, De Strooper B. Neuronal models to study amyloid precursor protein expression and processing in vitro. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1502:53-62. [PMID: 10899431 DOI: 10.1016/s0925-4439(00)00032-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- W Annaert
- Neuronal Cell Biology and Gene Transfer Laboratory, Centre for Human Genetics, Flanders Interuniversitary Institute for Biotechnology, Gasthuisberg, KU Leuven, Belgium
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43
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Abstract
For more than three decades, RNA recombination remained a puzzle and has only begun to be solved in the last few years. The available data provide evidence for a variety of RNA recombination mechanisms. Non-homologous recombination seems to be the most common for RNA. Recent experiments in both the in vitro and the in vivo systems indicate that this type of recombination may result from various transesterification reactions which are either performed by RNA molecules themselves or are promoted by some proteins. The high frequency of homologous recombination manifested by some RNA viruses can be easier explained by a replicative template switch.
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Affiliation(s)
- A B Chetverin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino.
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44
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Nagy PD, Pogany J, Simon AE. RNA elements required for RNA recombination function as replication enhancers in vitro and in vivo in a plus-strand RNA virus. EMBO J 1999; 18:5653-65. [PMID: 10523308 PMCID: PMC1171632 DOI: 10.1093/emboj/18.20.5653] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
RNA replication requires cis-acting elements to recruit the viral RNA-dependent RNA polymerase (RdRp) and facilitate de novo initiation of complementary strand synthesis. Hairpins that are hot spots for recombination in the genomic RNA of turnip crinkle virus (TCV) and satellite (sat)-RNA C, a parasitic RNA associated with TCV infections, stimulate RNA synthesis 10-fold from a downstream promoter sequence in an in vitro assay using partially purified TCV RdRp. Artificial hairpins had an inhibitory effect on transcription. RNA accumulation in single cells was enhanced 5- to 10-fold when the natural stem-loop structures were inserted into a poorly accumulating sat-RNA. The effect of the stem-loop structures on RNA replication was additive, with insertion of three stem-loop RNA elements increasing sat-RNA accumulation to the greatest extent (25-fold). These stem-loop structures do not influence the stability of the RNAs in vivo, but may serve to recruit the RdRp to the template.
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Affiliation(s)
- P D Nagy
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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45
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Affiliation(s)
- Michael Worobey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK1
| | - Edward C Holmes
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK1
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46
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Herrmann A, Müller G, Gödecke A, Schrader J. Recombination of nonreplicative RNA precursors of Sindbis virus in infected cells overexpressing murine-inducible nitric oxide synthase. Biochem Biophys Res Commun 1998; 253:524-31. [PMID: 9878569 DOI: 10.1006/bbrc.1998.9608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Sindbis virus-based SINrep5 expression system is one of the most efficient vectors for gene transfer leading to fast and high expression of the gene of interest. This system was used to transfect vascular endothelial and smooth muscle cells using murine inducible nitric oxide synthase (miNOS) as a reporter gene. Infection of both cell types leads to high expression levels of miNOS. In addition, the harvested supernatant of these infected cells was used for further rounds of infections, demonstrating that recombination of the parental RNA with the helper RNA takes place and results in the production of infectious particles. As shown by RT-PCR, after recombination the miNOS gene is located in between the nonstructural and structural viral genes. This study demonstrates that despite claims in other publications, the Sindbis virus-based SINrep5 expression system leads to recombination and is thus not a safe system for in vitro and in vivo applications.
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Affiliation(s)
- A Herrmann
- Department of Physiology, Heinrich-Heine-University Düsseldorf, Germany
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47
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Nagy PD, Simon AE. In vitro characterization of late steps of RNA recombination in turnip crinkle virus. I. Role of motif1-hairpin structure. Virology 1998; 249:379-92. [PMID: 9791029 DOI: 10.1006/viro.1998.9341] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular mechanisms of RNA recombination were studied in turnip crinkle carmovirus (TCV), which has a uniquely high recombination frequency and nonrandom crossover site distribution among the recombining TCV-associated satellite RNAs. An in vitro system has been developed that includes a partially purified TCV replicase preparation (RdRp) and chimeric RNAs that resemble the putative in vivo recombination intermediates (Nagy, P. D., Zhang, C., and Simon, A. E. EMBO J. 17, 2392-2403, 1998). This system generates 3'-terminal extension products, which are analogous to the recombination end products. Efficient generation of 3'-terminal extension products depends on the presence of a hairpin structure (termed the motif1-hairpin) that possibly binds to the RdRp. Replacement of the motif1-hairpin with two separate randomized sequences resulted in a basal level of 3'-terminal extension. By using three separate constructs, each carrying similar mutations in the motif1-hairpin, we demonstrate that the role of the motif1-hairpin in 3'-terminal extension is complex and its function is influenced by flanking sequences. In addition to the mutagenesis approach, competition experiments between wild-type and mutated motif1-hairpin constructs suggest that the TCV RdRp likely recognizes the secondary and/or tertiary structure of the motif1-hairpin, while individual nucleotides play a less important role. Overall, the data shed new light into the mechanism of 3'-terminal extension by a viral RdRp that is analogous to the late steps of RNA recombination in TCV.
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Affiliation(s)
- P D Nagy
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, 01003, USA
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48
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DiCiommo DP, Bremner R. Rapid, high level protein production using DNA-based Semliki Forest virus vectors. J Biol Chem 1998; 273:18060-6. [PMID: 9660762 DOI: 10.1074/jbc.273.29.18060] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Semliki Forest virus (SFV) vectors can be produced faster, and have a wider host range, than baculovirus vectors. However, the original SFV system requires in vitro manipulation of RNA. We have generated a system that is wholly DNA-based. Both the replicon vector, encoding SFV polymerase and the protein of interest, and the helper vector, encoding viral structural proteins, were modified so that expression was RNA polymerase II-dependent. Transfection of the modified replicon plasmid alone generated 20-30-fold more protein than obtained from a simple expression vector. Expression required the SFV replicase, which amplifies replicon RNA. The SFV-based vector generated 10-20-fold more protein than a plasmid based on Sindbis virus. Cotransfection of SFV replicon and helper vectors generated viral titers of around 10(6) infectious particles/ml. A single electroporation, plated on one 10-cm plate, generated enough virus (10(7) particles) to produce >500 microg of protein. Wild type, replication proficient virus was not detected in three tests utilizing almost 10(8) viral particles, a distinct advantage over a DNA Sindbis-based system in which over half the virus particles generated are fully infectious. The new SFV vectors significantly enhance the utility of this expression system.
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Affiliation(s)
- D P DiCiommo
- Eye Research Institute of Canada, Toronto, Ontario M5T 2S8
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49
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Nagy PD, Zhang C, Simon AE. Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase. EMBO J 1998; 17:2392-403. [PMID: 9545250 PMCID: PMC1170582 DOI: 10.1093/emboj/17.8.2392] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Molecular mechanisms of RNA recombination were studied in turnip crinkle carmovirus (TCV), which has a uniquely high recombination frequency and non-random crossover site distribution among the recombining TCV-associated satellite RNAs. To test the previously proposed replicase-driven template-switching mechanism for recombination, a partially purified TCV replicase preparation (RdRp) was programed with RNAs resembling the putative in vivo recombination intermediates. Analysis of the in vitro RdRp products revealed efficient generation of 3'-terminal extension products. Initiation of 3'-terminal extension occurred at or close to the base of a hairpin that was a recombination hotspot in vivo. Efficient generation of the 3'-terminal extension products depended on two factors: (i) a hairpin structure in the acceptor RNA region and (ii) a short base-paired region formed between the acceptor RNA and the nascent RNA synthesized from the donor RNA template. The hairpin structure bound to the RdRp, and thus is probably involved in its recruitment. The probable role of the base-paired region is to hold the 3' terminus near the RdRp bound to the hairpin structure to facilitate 3'-terminal extension. These regions were also required for in vivo RNA recombination between TCV-associated sat-RNA C and sat-RNA D, giving crucial and direct support for a replicase-driven template-switching mechanism of RNA recombination.
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Affiliation(s)
- P D Nagy
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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Pushko P, Parker M, Ludwig GV, Davis NL, Johnston RE, Smith JF. Replicon-helper systems from attenuated Venezuelan equine encephalitis virus: expression of heterologous genes in vitro and immunization against heterologous pathogens in vivo. Virology 1997; 239:389-401. [PMID: 9434729 DOI: 10.1006/viro.1997.8878] [Citation(s) in RCA: 340] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A replicon vaccine vector system was developed from an attenuated strain of Venezuelan equine encephalitis virus (VEE). The replicon RNA consists of the cis-acting 5' and 3' ends of the VEE genome, the complete nonstructural protein gene region, and the subgenomic 26S promoter. The genes encoding the VEE structural proteins were replaced with the influenza virus hemagglutinin (HA) or the Lassa virus nucleocapsid (N) gene, and upon transfection into eukaryotic cells by electroporation, these replicon RNAs directed the efficient, high-level synthesis of the HA or N proteins. For packaging of replicon RNAs into VEE replicon particles (VRP), the VEE capsid and glycoproteins were supplied in trans by expression from helper RNA(s) coelectroporated with the replicon. A number of different helper constructs, expressing the VEE structural proteins from a single or two separate helper RNAs, were derived from attenuated VEE strains Regeneration of infectious virus was not detected when replicons were packaged using a bipartite helper system encoding the VEE capsid protein and glycoproteins on two separate RNAs. Subcutaneous immunization of BALB/c mice with VRP expressing the influenza HA or Lassa virus N gene (HA-VRP or N-VRP, respectively) induced antibody responses to the expressed protein. After two inoculations of HA-VRP, complete protection against intranasal challenge with influenza was observed. Furthermore, sequential immunization of mice with two inoculations of N-VRP prior to two inoculations of HA-VRP induced an immune response to both HA and N equivalent to immunization with either VRP construct alone. Protection against influenza challenge was unaffected by previous N-VRP immunization. Therefore, the VEE replicon system was characterized by high-level expression of heterologous genes in cultured cells, little or no regeneration of plaque-forming virus particles, the capability for sequential immunization to multiple pathogens in the same host, and induction of protective immunity against a mucosal pathogen.
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MESH Headings
- Animals
- Antibodies, Viral/biosynthesis
- Antibodies, Viral/immunology
- Antibody Specificity
- Capsid/biosynthesis
- Capsid/genetics
- Capsid/immunology
- Capsid Proteins
- Cell Line
- Chick Embryo
- Chlorocebus aethiops
- Cricetinae
- Defective Viruses/physiology
- Ducks
- Encephalitis Virus, Venezuelan Equine/genetics
- Encephalitis Virus, Venezuelan Equine/immunology
- Encephalitis Virus, Venezuelan Equine/physiology
- Fibroblasts
- Gene Expression Regulation, Viral
- Genetic Vectors/genetics
- Helper Viruses/physiology
- Hemagglutinin Glycoproteins, Influenza Virus/biosynthesis
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Influenza A virus/genetics
- Influenza A virus/immunology
- Lassa virus/genetics
- Lassa virus/immunology
- Mesocricetus
- Mice
- Mice, Inbred BALB C
- Orthomyxoviridae Infections/prevention & control
- RNA/genetics
- RNA, Viral/genetics
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/immunology
- Replicon
- Vaccination
- Vaccines, Attenuated/immunology
- Vaccines, Combined/genetics
- Vaccines, Combined/immunology
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- Vero Cells
- Viral Structural Proteins/biosynthesis
- Viral Structural Proteins/genetics
- Viral Vaccines/genetics
- Viral Vaccines/immunology
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Affiliation(s)
- P Pushko
- Virology Division, U.S. Army Medical Research Institute for Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA
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