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Huston NC, Tsao LH, Brackney DE, Pyle AM. The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles. Proc Natl Acad Sci U S A 2024; 121:e2312080121. [PMID: 38985757 PMCID: PMC11260092 DOI: 10.1073/pnas.2312080121] [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: 07/16/2023] [Accepted: 05/25/2024] [Indexed: 07/12/2024] Open
Abstract
West Nile virus (WNV) is an arthropod-borne, positive-sense RNA virus that poses an increasing global threat due to warming climates and lack of effective therapeutics. Like other enzootic viruses, little is known about how host context affects the structure of the full-length RNA genome. Here, we report a complete secondary structure of the entire WNV genome within infected mammalian and arthropod cell lines. Our analysis affords structural insights into multiple, conserved aspects of flaviviral biology. We show that the WNV genome folds with minimal host dependence, and we prioritize well-folded regions for functional validation using structural homology between hosts as a guide. Using structure-disrupting, antisense locked nucleic acids, we then demonstrate that the WNV genome contains riboregulatory structures with conserved and host-specific functional roles. These results reveal promising RNA drug targets within flaviviral genomes, and they highlight the therapeutic potential of ASO-LNAs as both WNV-specific and pan-flaviviral therapeutic agents.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511
| | - Lucille H. Tsao
- Department of Chemistry, Yale University, New Haven, CT06511
| | - Doug E. Brackney
- Department of Entomology, Connecticut Agricultural Experimental Station, New Haven, CT06511
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT06511
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- HHMI, Chevy Chase, MD20815
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2
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018. [PMID: 30564270 DOI: 10.3389/fgene.2018.00595/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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3
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Mazeaud C, Freppel W, Chatel-Chaix L. The Multiples Fates of the Flavivirus RNA Genome During Pathogenesis. Front Genet 2018; 9:595. [PMID: 30564270 PMCID: PMC6288177 DOI: 10.3389/fgene.2018.00595] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/15/2018] [Indexed: 12/11/2022] Open
Abstract
The Flavivirus genus comprises many viruses (including dengue, Zika, West Nile and yellow fever viruses) which constitute important public health concerns worldwide. For several of these pathogens, neither antivirals nor vaccines are currently available. In addition to this unmet medical need, flaviviruses are of particular interest since they constitute an excellent model for the study of spatiotemporal regulation of RNA metabolism. Indeed, with no DNA intermediate or nuclear step, the flaviviral life cycle entirely relies on the cytoplasmic fate of a single RNA species, namely the genomic viral RNA (vRNA) which contains all the genetic information necessary for optimal viral replication. From a single open reading frame, the vRNA encodes a polyprotein which is processed to generate the mature viral proteins. In addition to coding for the viral polyprotein, the vRNA serves as a template for RNA synthesis and is also selectively packaged into newly assembled viral particles. Notably, vRNA translation, replication and encapsidation must be tightly coordinated in time and space via a fine-tuned equilibrium as these processes cannot occur simultaneously and hence, are mutually exclusive. As such, these dynamic processes involve several vRNA secondary and tertiary structures as well as RNA modifications. Finally, the vRNA can be detected as a foreign molecule by cytosolic sensors which trigger upon activation antiviral signaling pathways and the production of antiviral factors such as interferons and interferon-stimulated genes. However, to create an environment favorable to infection, flaviviruses have evolved mechanisms to dampen these antiviral processes, notably through the production of a specific vRNA degradation product termed subgenomic flavivirus RNA (sfRNA). In this review, we discuss the current understanding of the fates of flavivirus vRNA and how this is regulated at the molecular level to achieve an optimal replication within infected cells.
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Affiliation(s)
- Clément Mazeaud
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre INRS-Institut Armand-Frappier, Laval, QC, Canada
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4
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Genomic changes in an attenuated genotype I Japanese encephalitis virus and comparison with virulent parental strain. Virus Genes 2018; 54:424-431. [PMID: 29605839 DOI: 10.1007/s11262-018-1559-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Genotype I Japanese encephalitis virus (JEV) strain SCYA201201 was previously isolated from brain tissues of aborted piglets. In this study, we obtained an attenuated SCYA201201-0901 strain by serial passage of strain SCYA201201-1 in Syrian baby hamster kidney cells, combined with multiple plaque purifications and selection for virulence in mice. We investigated the genetic changes associated with attenuation by comparing the entire genomes of SCYA201201-0901 and SCYA201201-1. Sequence comparisons identified 14 common amino acid substitutions in the coding region, with two nucleotide point mutations in the 5'-untranslated region (UTR) and another three in the 3'-UTR, which differed between the attenuated and virulent strains. In addition, a total of 13 silent nucleotide mutations were found after attenuation. These substitutions, alone or in combination, may be responsible for the attenuated phenotype of the SCYA201201-0901 strain in mice. This information will contribute to our understanding of attenuation and of the molecular basis of virulence in genotype I strains such as SCYA201201-0901, as well as aiding the development of safer JEV vaccines.
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Yokoyama S, Starmer WT. Possible Roles of New Mutations Shared by Asian and American Zika Viruses. Mol Biol Evol 2017; 34:525-534. [PMID: 28087772 PMCID: PMC5400385 DOI: 10.1093/molbev/msw270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930–1945 and, at that point, its mutation rate was probably less than 0.2 × 10−3/nucleotide site/year and subsequently increased significantly in most of its descendants. Sustaining a high mutation rate of 4 × 10−3/site/year throughout its evolution, the Ancestral Asian strain, which was sampled from a mosquito in Malaysia, accumulated 13 mutations in the 3′-untranslated region of RNA stem-loops prior to 1963, seven of which generate more stable stem-loop structures and are likely to inhibit cellular antiviral activities, including immune and RNA interference (RNAi) pathways. The seven mutations have been maintained in all Asian and American strains and may be responsible for serious medical problems we are facing today and offer testable hypotheses to examine their roles in molecular interactions during brain development.
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Ablation of Programmed -1 Ribosomal Frameshifting in Venezuelan Equine Encephalitis Virus Results in Attenuated Neuropathogenicity. J Virol 2017; 91:JVI.01766-16. [PMID: 27852852 DOI: 10.1128/jvi.01766-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/07/2016] [Indexed: 12/21/2022] Open
Abstract
The alphaviruses Venezuelan equine encephalitis virus (VEEV), eastern equine encephalitis virus (EEEV), and western equine encephalitis virus (WEEV) are arthropod-borne positive-strand RNA viruses that are capable of causing acute and fatal encephalitis in many mammals, including humans. VEEV was weaponized during the Cold War and is recognized as a select agent. Currently, there are no FDA-approved vaccines or therapeutics for these viruses. The spread of VEEV and other members of this family due to climate change-mediated vector range expansion underscores the need for research aimed at developing medical countermeasures. These viruses utilize programmed -1 ribosomal frameshifting (-1 PRF) to synthesize the viral trans-frame (TF) protein, which has previously been shown to be important for neuropathogenesis in the related Sindbis virus. Here, the alphavirus -1 PRF signals were characterized, revealing novel -1 PRF stimulatory structures. -1 PRF attenuation mildly affected the kinetics of VEEV accumulation in cultured cells but strongly inhibited its pathogenesis in an aerosol infection mouse model. Importantly, the decreased viral titers in the brains of mice infected with the mutant virus suggest that the alphavirus TF protein is important for passage through the blood-brain barrier and/or for neuroinvasiveness. These findings suggest a novel approach to the development of safe and effective live attenuated vaccines directed against VEEV and perhaps other closely related -1 PRF-utilizing viruses. IMPORTANCE Venezuelan equine encephalitis virus (VEEV) is a select agent that has been weaponized. This arthropod-borne positive-strand RNA virus causes acute and fatal encephalitis in many mammals, including humans. There is no vaccine or other approved therapeutic. VEEV and related alphaviruses utilize programmed -1 ribosomal frameshifting (-1 PRF) to synthesize the viral trans-frame (TF) protein, which is important for neuropathogenesis. -1 PRF attenuation strongly inhibited VEEV pathogenesis in mice, and viral replication analyses suggest that the TF protein is critical for neurological disease. These findings suggest a new approach to the development of safe and effective live attenuated vaccines directed against VEEV and other related viruses.
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Rastogi M, Sharma N, Singh SK. Flavivirus NS1: a multifaceted enigmatic viral protein. Virol J 2016; 13:131. [PMID: 27473856 PMCID: PMC4966872 DOI: 10.1186/s12985-016-0590-7] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/26/2016] [Indexed: 12/31/2022] Open
Abstract
Flaviviruses are emerging arthropod-borne viruses representing an immense global health problem. The prominent viruses of this group include dengue virus, yellow fever virus, Japanese encephalitis virus, West Nile virus tick borne encephalitis virus and Zika Virus. These are endemic in many parts of the world. They are responsible for the illness ranging from mild flu like symptoms to severe hemorrhagic, neurologic and cognitive manifestations leading to death. NS1 is a highly conserved non-structural protein among flaviviruses, which exist in diverse forms. The intracellular dimer form of NS1 plays role in genome replication, whereas, the secreted hexamer plays role in immune evasion. The secreted NS1 has been identified as a potential diagnostic marker for early detection of the infections caused by flaviviruses. In addition to the diagnostic marker, the importance of NS1 has been reported in the development of therapeutics. NS1 based subunit vaccines are at various stages of development. The structural details and diverse functions of NS1 have been discussed in detail in this review.
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Affiliation(s)
- Meghana Rastogi
- Institute of Medical Sciences (IMS), Laboratory of Human Molecular Virology & Immunology, Molecular Biology Unit, Faculty of Medicine, Banaras Hindu University, Varanasi, 221005, India
| | - Nikhil Sharma
- Laboratory of Neurovirology and Inflammation Biology, CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Sunit Kumar Singh
- Institute of Medical Sciences (IMS), Laboratory of Human Molecular Virology & Immunology, Molecular Biology Unit, Faculty of Medicine, Banaras Hindu University, Varanasi, 221005, India.
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Blazevic J, Rouha H, Bradt V, Heinz FX, Stiasny K. Membrane Anchors of the Structural Flavivirus Proteins and Their Role in Virus Assembly. J Virol 2016; 90:6365-6378. [PMID: 27147734 PMCID: PMC4936158 DOI: 10.1128/jvi.00447-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/22/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED The structural proteins of flaviviruses carry a unique set of transmembrane domains (TMDs) at their C termini that are derived from the mode of viral polyprotein processing. They function as internal signal and stop-transfer sequences during protein translation, but possible additional roles in protein interactions required during assembly and maturation of viral particles are ill defined. To shed light on the role of TMDs in these processes, we engineered a set of tick-borne encephalitis virus mutants in which these structural elements were replaced in different combinations by the homologous sequences of a distantly related flavivirus (Japanese encephalitis virus). The effects of these modifications were analyzed with respect to protein synthesis, viral particle secretion, specific infectivity, and acidic-pH-induced maturation processes. We provide evidence that interactions involving the double-membrane anchor of the envelope protein E (a unique feature compared to other viral fusion proteins) contribute substantially to particle assembly, stability, and maturation. Disturbances of the inter- and intra-TMD interactions of E resulted in the secretion of a larger proportion of capsidless subviral particles at the expense of whole virions, suggesting a possible role in the still incompletely understood mechanism of capsid integration during virus budding. In contrast, the TMD initially anchoring the C protein to the endoplasmic reticulum membrane does not appear to take part in envelope protein interactions. We also show that E TMDs are involved in the envelope protein rearrangements that are triggered by acidic pH in the trans-Golgi network and represent a hallmark of virus maturation. IMPORTANCE The assembly of flaviviruses occurs in the endoplasmic reticulum and leads to the formation of immature, noninfectious particles composed of an RNA-containing capsid surrounded by a lipid membrane, with the two integrated envelope proteins, prM and E, arranged in an icosahedral lattice. The mechanism by which the capsid is formed and integrated into the budding viral envelope is currently unknown. We provide evidence that the transmembrane domains (TMDs) of E are essential for the formation of capsid-containing particles and that disturbances of these interactions lead to the preferential formation of capsidless subviral particles at the expense of whole virions. E TMD interactions also appear to be essential for the envelope protein rearrangements required for virus maturation and for the generation of infectious virions. Our data thus provide new insights into the biological functions of E TMDs and extend their role during viral polyprotein processing to additional functions in particle assembly and maturation.
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Affiliation(s)
- Janja Blazevic
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Harald Rouha
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Victoria Bradt
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Franz X Heinz
- Department of Virology, Medical University of Vienna, Vienna, Austria
| | - Karin Stiasny
- Department of Virology, Medical University of Vienna, Vienna, Austria
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Wang J, Li X, Gu J, Fan Y, Zhao P, Cao R, Chen P. The A66G back mutation in NS2A of JEV SA14-14-2 strain contributes to production of NS1' protein and the secreted NS1' can be used for diagnostic biomarker for virulent virus infection. INFECTION GENETICS AND EVOLUTION 2015; 36:116-125. [PMID: 26384477 DOI: 10.1016/j.meegid.2015.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 08/18/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022]
Abstract
Japanese encephalitis virus (JEV) is the most common cause of the prevalent encephalitis in Asia-Pacific region and poses a serious risk to public health. Here, we developed a reliable reverse genetics system based on the JEV SA14-14-2 strain to further explore the mechanism for the synthesis of NS1' protein and to investigate the function of NS1' protein during virus infection. NS1' is an additional form of NS1 protein with 52 amino acid carboxy-terminal extension and is expressed by the members of the Japanese encephalitis (JE) serogroup due to the translation frameshift. A66G substitution in NS2A gene of JEV SA14-14-2 strain contributed to recover the GC-rich pseudoknot and resulted in the formation of the NS1'. The NS1' protein has no significant effect on the virus replication properties in BHK-21 cells. Animal experiments demonstrated that the NS1' protein had a rather minor effect on neurovirulence of JEV SA14-14-2 strain. But the NS1'-expressing virus (rA66G) could induce a higher humoral immune response than the NS1'-non-expressing virus (rSA14-14-2). NS1' protein can be detected in the serum of JEV rA66G infected animal and in the cultural media of that infected mammalian cells. Interesting, only the dimer of NS1' can be detected in the cultural media of the infected BHK-21 cells and the amount of the secreted NS1' was in agreement with that of the secreted virion. In comparison with the live-attenuated JE vaccine strain which is incapable of formation of NS1', most of the virulent JEV strains produce the NS1' protein. And the secreted NS1' may serve as an early surrogate biomarker for viremia to distinguish the field infection from the vaccine inoculation. In total, in the present study, we identified the nt 66 in the viral NS2A gene as one of the critical site for the -1 programmed ribosomal frameshift to produce the NS1' protein and demonstrated the secreted NS1' could be used for diagnostic biomarker during JEV infection.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Base Sequence
- Biomarkers
- Cell Line
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Disease Models, Animal
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis Virus, Japanese/metabolism
- Encephalitis Virus, Japanese/pathogenicity
- Encephalitis, Japanese/diagnosis
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/mortality
- Encephalitis, Japanese/virology
- Genes, Viral
- Genome, Viral
- Humans
- Immunity, Humoral
- Mice
- Molecular Sequence Data
- Mutation
- Viral Nonstructural Proteins/biosynthesis
- Viral Nonstructural Proteins/genetics
- Viral Nonstructural Proteins/immunology
- Virulence
- Virus Replication
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Affiliation(s)
- Jingman Wang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xinfeng Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jinyan Gu
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yu Fan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Peng Zhao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Ruibing Cao
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
| | - Puyan Chen
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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Two distinct sets of NS2A molecules are responsible for dengue virus RNA synthesis and virion assembly. J Virol 2014; 89:1298-313. [PMID: 25392211 DOI: 10.1128/jvi.02882-14] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Flavivirus nonstructural protein 2A (NS2A) plays important roles in both viral RNA synthesis and virion assembly. The molecular details of how the NS2A protein modulates the two distinct events have not been defined. To address this question, we have performed a systematic mutagenesis of NS2A using dengue virus (DENV) serotype 2 (DENV-2) as a model. We identified two sets of NS2A mutations with distinct defects during a viral infection cycle. One set of NS2A mutations (D125A and G200A) selectively abolished viral RNA synthesis. Mechanistically, the D125A mutation abolished viral RNA synthesis through blocking the N-terminal cleavage of the NS2A protein, leading to an unprocessed NS1-NS2A protein; this result suggests that amino acid D125 (far downstream of the N terminus of NS2A) may contribute to the recognition of host protease at the NS1-NS2A junction. The other set of NS2A mutations (G11A, E20A, E100A, Q187A, and K188A) specifically impaired virion assembly without significantly affecting viral RNA synthesis. Remarkably, mutants defective in virion assembly could be rescued by supplying in trans wild-type NS2A molecules expressed from a replicative replicon, by wild-type NS2A protein expressed alone, by a mutant NS2A (G200A) that is lethal for viral RNA synthesis, or by a different mutant NS2A that is defective in virion assembly. In contrast, none of the mutants defective in viral RNA synthesis could be rescued by trans-complementation. Collectively, the results indicate that two distinct sets of NS2A molecules are responsible for DENV RNA synthesis and virion assembly. IMPORTANCE Dengue virus (DENV) represents the most prevalent mosquito-borne human pathogen. Understanding the replication of DENV is essential for development of vaccines and therapeutics. Here we characterized the function of DENV-2 NS2A using a systematic mutagenesis approach. The mutagenesis results revealed two distinct sets of NS2A mutations: one set of mutations that result in defects in viral RNA synthesis and another set of mutations that result in defects in virion assembly. trans-Complementation analysis showed that mutants defective in viral RNA synthesis could not be rescued by wild-type NS2A; in contrast, mutants defective in virion assembly could be successfully rescued by wild-type NS2A or even by a mutant NS2A that is incompetent to support viral RNA synthesis. These results support a model in which two distinct sets of NS2A molecules are responsible for DENV RNA synthesis (located in the viral replication complex) and virion assembly (located in the virion assembly/budding site). The study confirms and extends our understanding of the two critical roles of flavivirus NS2A in viral RNA synthesis and virion assembly.
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Melian EB, Hall-Mendelin S, Du F, Owens N, Bosco-Lauth AM, Nagasaki T, Rudd S, Brault AC, Bowen RA, Hall RA, van den Hurk AF, Khromykh AA. Programmed ribosomal frameshift alters expression of west nile virus genes and facilitates virus replication in birds and mosquitoes. PLoS Pathog 2014; 10:e1004447. [PMID: 25375107 PMCID: PMC4223154 DOI: 10.1371/journal.ppat.1004447] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/04/2014] [Indexed: 01/28/2023] Open
Abstract
West Nile virus (WNV) is a human pathogen of significant medical importance with close to 40,000 cases of encephalitis and more than 1,600 deaths reported in the US alone since its first emergence in New York in 1999. Previous studies identified a motif in the beginning of non-structural gene NS2A of encephalitic flaviviruses including WNV which induces programmed −1 ribosomal frameshift (PRF) resulting in production of an additional NS protein NS1′. We have previously demonstrated that mutant WNV with abolished PRF was attenuated in mice. Here we have extended our previous observations by showing that PRF does not appear to have a significant role in virus replication, virion formation, and viral spread in several cell lines in vitro. However, we have also shown that PRF induces an over production of structural proteins over non-structural proteins in virus-infected cells and that mutation abolishing PRF is present in ∼11% of the wild type virus population. In vivo experiments in house sparrows using wild type and PRF mutant of New York 99 strain of WNV viruses showed some attenuation for the PRF mutant virus. Moreover, PRF mutant of Kunjin strain of WNV showed significant decrease compared to wild type virus infection in dissemination of the virus from the midgut through the haemocoel, and ultimately the capacity of infected mosquitoes to transmit virus. Thus our results demonstrate an important role for PRF in regulating expression of viral genes and consequently virus replication in avian and mosquito hosts. Programmed ribosomal frameshift (PRF) is a strategy used by some viruses to regulate expression of viral genes and/or generate additional gene products for the benefit of the virus. Encephalitic flaviruses from Japanese encephalitis virus serogroup encode PRF motif in the beginning of nonstructural gene NS2A that results in production of an additional nonstructural protein NS1′ which for West Nile virus (WNV) consists of NS1 protein with 52 amino acid addition at the C terminus. Our previous studies showed that abolishing PFR and NS1′ production attenuated WNV virulence in mice. Here we show by using wild type and PRF-deficient WNV mutant that PRF induces overproduction of structural proteins, which facilitates virus replication in birds and mosquitoes while having no advantage for virus replication in cell lines in vitro. Presence of PRF/NS1′ allowed more efficient virus dissemination in the body of mosquitoes after taking infected blood meal and subsequent accumulation of the virus in saliva to facilitate transmission. Combined with our previous data in mice, the results obtained in this study demonstrate that while having no advantage for WNV replication in vitro, PRF provides advantage for WNV replication in vivo in mammalian, avian and mosquito hosts most likely by overproducing viral structural proteins and generating NS1′.
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Affiliation(s)
- Ezequiel Balmori Melian
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Sonja Hall-Mendelin
- Virology, Public and Environmental Health, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, Queensland, Australia
| | - Fangyao Du
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Nick Owens
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Angela M. Bosco-Lauth
- Division of Vector-Borne Diseases, Centers for Disease Prevention and Control, Fort Collins, Colorado, United States of America
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Tomoko Nagasaki
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Stephen Rudd
- Queensland Facility for Advanced Bioinformatics (QFAB), University of Queensland, Brisbane, Queensland, Australia
| | - Aaron C. Brault
- Division of Vector-Borne Diseases, Centers for Disease Prevention and Control, Fort Collins, Colorado, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Roy A. Hall
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Andrew F. van den Hurk
- Virology, Public and Environmental Health, Forensic and Scientific Services, Department of Health, Queensland Government, Coopers Plains, Queensland, Australia
| | - Alexander A. Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
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Apte-Sengupta S, Sirohi D, Kuhn RJ. Coupling of replication and assembly in flaviviruses. Curr Opin Virol 2014; 9:134-42. [PMID: 25462445 DOI: 10.1016/j.coviro.2014.09.020] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 02/06/2023]
Abstract
Flaviviruses affect hundreds of millions of people each year causing tremendous morbidity and mortality worldwide. This genus includes significant human pathogens such as dengue, West Nile, yellow fever, tick-borne encephalitis and Japanese encephalitis virus among many others. The disease caused by these viruses can range from febrile illness to hemorrhagic fever and encephalitis. A deeper understanding of the virus life cycle is required to foster development of antivirals and vaccines, which are an urgent need for many flaviviruses, especially dengue. The focus of this review is to summarize our current knowledge of flaviviral replication and assembly, the proteins and lipids involved therein, and how these processes are coordinated for efficient virus production.
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Affiliation(s)
- Swapna Apte-Sengupta
- Markey Center for Structural Biology, Department of Biological Sciences and Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Devika Sirohi
- Markey Center for Structural Biology, Department of Biological Sciences and Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Sciences and Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA.
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13
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Takamatsu Y, Okamoto K, Dinh DT, Yu F, Hayasaka D, Uchida L, Nabeshima T, Buerano CC, Morita K. NS1' protein expression facilitates production of Japanese encephalitis virus in avian cells and embryonated chicken eggs. J Gen Virol 2014; 95:373-383. [PMID: 24443559 DOI: 10.1099/vir.0.057968-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Japanese encephalitis virus (JEV), which belongs to the genus Flavivirus of the family Flaviviridae, is a leading cause of meningo-encephalitis in Asian countries. The flavivirus non-structural protein 1 (NS1) plays a role in virus replication and in the elicitation of an immune response. The NS1' protein found among the members of the JEV subgroup is an extended form of NS1 and is generated by a -1 ribosomal frameshift. This protein is known to be involved in viral pathogenicity; however, its specific function is still unknown. Here, we describe an investigation of the molecular function of NS1' protein through the production of JEV NS1'-expressing and -non-expressing clones and their infection of avian and mammalian cells. Efficient NS1' protein expression was observed in avian cells and was found to facilitate JEV production in both avian cultured cells and embryonated chicken eggs. NS1' protein was observed to co-localize with NS5 protein and resulted in increased viral RNA levels in avian cells. These findings clearly indicate that NS1' enhances the production of JEV in avian cells and may facilitate the amplification/maintenance role of birds in the virus transmission cycle in nature.
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Affiliation(s)
- Yuki Takamatsu
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kenta Okamoto
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Duc Tuan Dinh
- Respiratory Viruses Laboratory, Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.,Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Fuxun Yu
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Daisuke Hayasaka
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Leo Uchida
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Takeshi Nabeshima
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Corazon C Buerano
- Department of Molecular Epidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.,Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kouichi Morita
- Department of Virology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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14
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Suzuki R, Ishikawa T, Konishi E, Matsuda M, Watashi K, Aizaki H, Takasaki T, Wakita T. Production of single-round infectious chimeric flaviviruses with DNA-based Japanese encephalitis virus replicon. J Gen Virol 2014; 95:60-65. [DOI: 10.1099/vir.0.058008-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A method for rapid production of single-round infectious particles (SRIPs) of flavivirus would be useful for viral mutagenesis studies. Here, we established a DNA-based production system for SRIPs of flavivirus. We constructed a Japanese encephalitis virus (JEV) subgenomic replicon plasmid, which lacked the C-prM-E (capsid–pre-membrane–envelope) coding region, under the control of the cytomegalovirus promoter. When the JEV replicon plasmid was transiently co-transfected with a JEV C-prM-E expression plasmid into 293T cells, SRIPs were produced, indicating successful trans-complementation with JEV structural proteins. Equivalent production levels were observed when C and prM–E proteins were provided separately. Furthermore, dengue types 1–4, West Nile, yellow fever or tick-borne encephalitis virus prM-E proteins could be utilized for production of chimaeric flavivirus SRIPs, although the production was less efficient for dengue and yellow fever viruses. These results indicated that our plasmid-based system is suitable for investigating the life cycles of flaviviruses, diagnostic applications and development of safer vaccine candidates.
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Affiliation(s)
- Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiro Ishikawa
- Department of Microbiology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun, Tochigi, 321-0293, Japan
| | - Eiji Konishi
- BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchahewi, Bangkok 10440, Thailand
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Hideki Aizaki
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tomohiko Takasaki
- Department of Virology I, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
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15
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Replication cycle and molecular biology of the West Nile virus. Viruses 2013; 6:13-53. [PMID: 24378320 PMCID: PMC3917430 DOI: 10.3390/v6010013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 12/27/2022] Open
Abstract
West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated.
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16
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Sangiambut S, Suphatrakul A, Sriburi R, Keelapang P, Puttikhunt C, Kasinrerk W, Malasit P, Sittisombut N. Sustained replication of dengue pseudoinfectious virus lacking the capsid gene by trans-complementation in capsid-producing mosquito cells. Virus Res 2013; 174:37-46. [DOI: 10.1016/j.virusres.2013.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 11/16/2022]
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17
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Ye Q, Li XF, Zhao H, Li SH, Deng YQ, Cao RY, Song KY, Wang HJ, Hua RH, Yu YX, Zhou X, Qin ED, Qin CF. A single nucleotide mutation in NS2A of Japanese encephalitis-live vaccine virus (SA14-14-2) ablates NS1' formation and contributes to attenuation. J Gen Virol 2012; 93:1959-1964. [PMID: 22739060 DOI: 10.1099/vir.0.043844-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Japanese encephalitis (JE) remains the leading cause of viral encephalitis in the Asia-Pacific region, and the live vaccine SA14-14-2 is currently recommended by WHO and widely used in Asian countries with a good safety and efficacy profile. In this study, we demonstrated that SA14-14-2 failed to produce NS1', the larger NS1-related protein, compared with its parental strain SA14 in various cells. Sequence analysis and secondary structure prediction identified a single silent mutation G66A in the NS2A-coding region of SA14-14-2 destabilized the conserved pseudoknot structure, which was associated with a -1 ribosomal frame shift event. Using reverse genetic technology and animal study, we provided solid evidence that this single silent mutation G66A in the NS2A gene abolished the production of NS1' in vitro and reduced neurovirulence and neuroinvasiveness in mice. These findings provide critical information in understanding the molecular mechanism of JE vaccine attenuation and is critical for JE vaccine quality control.
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Affiliation(s)
- Qing Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Hui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Shi-Hua Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Rui-Yuan Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Ke-Yu Song
- School of Medicine Jinan University, Guangzhou, 510632, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Hong-Jiang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Rong-Hong Hua
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, PR China
| | - Yong-Xin Yu
- National Institutes for Food and Drug Control, Beijing 100050, PR China
| | - Xi Zhou
- State Key Laboratory of Virology, Wuhan University, Wuhan 430072, PR China
| | - E-De Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, PR China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, PR China
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18
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Evidence for a genetic and physical interaction between nonstructural proteins NS1 and NS4B that modulates replication of West Nile virus. J Virol 2012; 86:7360-71. [PMID: 22553322 DOI: 10.1128/jvi.00157-12] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flavivirus NS1 is a nonstructural glycoprotein that is expressed on the cell surface and secreted into the extracellular space. Despite its transit through the secretory pathway, NS1 is an essential gene linked to early viral RNA replication. How this occurs has remained a mystery given the disparate localization of NS1 and the viral RNA replication complex, as the latter is present on the cytosolic face of the endoplasmic reticulum (ER). We recently identified an N-terminal di-amino acid motif in NS1 that modulates protein targeting and affected viral replication. Exchange of two amino acids at positions 10 and 11 from dengue virus (DENV) into West Nile virus (WNV) NS1 (RQ10NK) changed its relative surface expression and secretion and attenuated infectivity. However, the phenotype of WNV containing NS1 RQ10NK was unstable, as within two passages heterogeneous plaque variants were observed. Here, using a mutant WNV encoding the NS1 RQ10NK mutation, we identified a suppressor mutation (F86C) in NS4B, a virally encoded transmembrane protein with loops on both the luminal and cytoplasmic sides of the ER membrane. Introduction of NS4B F86C specifically rescued RNA replication of mutant WNV but did not affect the wild-type virus. Mass spectrometry and coimmunoprecipitation studies established a novel physical interaction between NS1 and NS4B, suggesting a mechanism for how luminal NS1 conveys signals to the cytoplasm to regulate RNA replication.
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