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1.
Int J Mol Sci ; 21(18)2020 Sep 22.
Article in English | MEDLINE | ID: mdl-32971876

ABSTRACT

Hepatitis C virus (HCV) infects liver cells and often causes chronic infection, also leading to liver cirrhosis and cancer. In the cytoplasm, the viral structural and non-structural (NS) proteins are directly translated from the plus strand HCV RNA genome. The viral proteins NS3 to NS5B proteins constitute the replication complex that is required for RNA genome replication via a minus strand antigenome. The most C-terminal protein in the genome is the NS5B replicase, which needs to initiate antigenome RNA synthesis at the very 3'-end of the plus strand. Using ribosome profiling of cells replicating full-length infectious HCV genomes, we uncovered that ribosomes accumulate at the HCV stop codon and about 30 nucleotides upstream of it. This pausing is due to the presence of conserved rare, inefficient Wobble codons upstream of the termination site. Synonymous substitution of these inefficient codons to efficient codons has negative consequences for viral RNA replication but not for viral protein synthesis. This pausing may allow the enzymatically active replicase core to find its genuine RNA template in cis, while the protein is still held in place by being stuck with its C-terminus in the exit tunnel of the paused ribosome.


Subject(s)
Codon , Genome, Viral , Hepacivirus/physiology , Open Reading Frames , RNA, Viral/biosynthesis , RNA-Dependent RNA Polymerase/biosynthesis , Ribosomes/metabolism , Virus Replication/physiology , Cell Line, Tumor , Humans , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Ribosomes/genetics
2.
J Virol ; 91(8)2017 04 15.
Article in English | MEDLINE | ID: mdl-28148800

ABSTRACT

Tobacco necrosis virus, strain D (TNV-D), is a positive-strand RNA virus in the genus Betanecrovirus and family Tombusviridae The production of its RNA-dependent RNA polymerase, p82, is achieved by translational readthrough. This process is stimulated by an RNA structure that is positioned immediately downstream of the recoding site, termed the readthrough stem-loop (RTSL), and a sequence in the 3' untranslated region of the TNV-D genome, called the distal readthrough element (DRTE). Notably, a base pairing interaction between the RTSL and the DRTE, spanning ∼3,000 nucleotides, is required for enhancement of readthrough. Here, some of the structural features of the RTSL, as well as RNA sequences and structures that flank either the RTSL or DRTE, were investigated for their involvement in translational readthrough and virus infectivity. The results revealed that (i) the RTSL-DRTE interaction cannot be functionally replaced by stabilizing the RTSL structure, (ii) a novel tertiary RNA structure positioned just 3' to the RTSL is required for optimal translational readthrough and virus infectivity, and (iii) these same activities also rely on an RNA stem-loop located immediately upstream of the DRTE. Functional counterparts for the RTSL-proximal structure may also be present in other tombusvirids. The identification of additional distinct RNA structures that modulate readthrough suggests that regulation of this process by genomic features may be more complex than previously appreciated. Possible roles for these novel RNA elements are discussed.IMPORTANCE The analysis of factors that affect recoding events in viruses is leading to an ever more complex picture of this important process. In this study, two new atypical RNA elements were shown to contribute to efficient translational readthrough of the TNV-D polymerase and to mediate robust viral genome accumulation in infections. One of the structures, located close to the recoding site, could have functional equivalents in related genera, while the other structure, positioned 3' proximally in the viral genome, is likely limited to betanecroviruses. Irrespective of their prevalence, the identification of these novel RNA elements adds to the current repertoire of viral genome-based modulators of translational readthrough and provides a notable example of the complexity of regulation of this process.


Subject(s)
Protein Biosynthesis , RNA, Messenger/genetics , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/biosynthesis , Tombusviridae/genetics , Cucumis/virology , DNA Mutational Analysis , Nucleic Acid Conformation , RNA, Messenger/chemistry , RNA, Viral/chemistry , RNA-Dependent RNA Polymerase/genetics , Tombusviridae/enzymology
3.
BMC Plant Biol ; 16: 15, 2016 Jan 13.
Article in English | MEDLINE | ID: mdl-26757721

ABSTRACT

BACKGROUND: Host RNA-dependent RNA polymerases (RDRs) 1 and 6 contribute to antiviral RNA silencing in plants. RDR6 is constitutively expressed and was previously shown to limit invasion of Nicotiana benthamiana meristem tissue by potato virus X and thereby inhibit disease development. RDR1 is inducible by salicylic acid (SA) and several other phytohormones. But although it contributes to basal resistance to tobacco mosaic virus (TMV) it is dispensable for SA-induced resistance in inoculated leaves. The laboratory accession of N. benthamiana is a natural rdr1 mutant and highly susceptible to TMV. However, TMV-induced symptoms are ameliorated in transgenic plants expressing Medicago truncatula RDR1. RESULTS: In MtRDR1-transgenic N. benthamiana plants the spread of TMV expressing the green fluorescent protein (TMV.GFP) into upper, non-inoculated, leaves was not inhibited. However, in these plants exclusion of TMV.GFP from the apical meristem and adjacent stem tissue was greater than in control plants and this exclusion effect was enhanced by SA. TMV normally kills N. benthamiana plants but although MtRDR1-transgenic plants initially displayed virus-induced necrosis they subsequently recovered. Recovery from disease was markedly enhanced by SA treatment in MtRDR1-transgenic plants whereas in control plants SA delayed but did not prevent systemic necrosis and death. Following SA treatment of MtRDR1-transgenic plants, extractable RDR enzyme activity was increased and Western blot analysis of RDR extracts revealed a band cross-reacting with an antibody raised against MtRDR1. Expression of MtRDR1 in the transgenic N. benthamiana plants was driven by a constitutive 35S promoter derived from cauliflower mosaic virus, confirmed to be non-responsive to SA. This suggests that the effects of SA on MtRDR1 are exerted at a post-transcriptional level. CONCLUSIONS: MtRDR1 inhibits severe symptom development by limiting spread of virus into the growing tips of infected plants. Thus, RDR1 may act in a similar fashion to RDR6. MtRDR1 and SA acted additively to further promote recovery from disease symptoms in MtRDR1-transgenic plants. Thus it is possible that SA promotes MtRDR1 activity and/or stability through post-transcriptional effects.


Subject(s)
Medicago truncatula/enzymology , Nicotiana/virology , Plant Diseases/virology , RNA-Dependent RNA Polymerase/biosynthesis , Salicylic Acid/pharmacology , Tobacco Mosaic Virus/physiology , Enzyme Induction , Gene Expression , Medicago truncatula/genetics , Meristem/virology , Plants, Genetically Modified , RNA-Dependent RNA Polymerase/metabolism , Nicotiana/genetics , Tobacco Mosaic Virus/drug effects
4.
PLoS Pathog ; 10(2): e1003921, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24516387

ABSTRACT

In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs) that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR ßC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV). Nbrgs-CaM expression is up-regulated by the ßC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of ßC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the ßC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that ßC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and highlight an essential role for RDR6 in RNA silencing defense response against geminivirus infection.


Subject(s)
Geminiviridae , Host-Parasite Interactions/physiology , Nicotiana/virology , Plant Proteins/metabolism , RNA Interference/physiology , RNA-Dependent RNA Polymerase/biosynthesis , Calmodulin/metabolism , DNA, Plant , Gene Expression Regulation/physiology , Immunoblotting , Plant Proteins/genetics , Polymerase Chain Reaction , RNA-Dependent RNA Polymerase/genetics , Nicotiana/genetics , Nicotiana/metabolism
5.
Virus Genes ; 51(3): 423-9, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26560706

ABSTRACT

The RNA-dependent RNA polymerase (RdRp) of rice stripe virus (RSV) is critical for both the transcription and replication of the viral genome. Despite its importance, little is known about how it functions in cells. In the present study, RSV RdRp was split into three pieces, since expression of the full protein could not be achieved. Then, the intracellular localization of these three RdRp fragments and their interactions with nucleocapsid protein (NP) were investigated, which is another viral protein required for viral RNA synthesis. The data showed that all three RdRp fragments displayed punctuate staining patterns in the cytoplasm, and the C-terminal fragment co-localized with NP in the perinuclear region. Both bimolecular fluorescence complementation and co-immunoprecipitation experiments demonstrated that of the three RdRp fragments, only the C-terminal fragment could interact with NP. Further analysis using a series of truncated NPs identified the N-terminal 50-amino-acid region within NP as the determinant for its interaction with the C-terminus of RdRp.


Subject(s)
Nucleocapsid Proteins/metabolism , RNA-Dependent RNA Polymerase/metabolism , Tenuivirus/metabolism , Animals , Coinfection/virology , Immunoprecipitation/methods , Mutation , Nuclear Localization Signals , Nucleocapsid Proteins/biosynthesis , Nucleocapsid Proteins/genetics , Oryza/virology , Plant Leaves/virology , Protein Binding , Protein Interaction Mapping , RNA, Viral/biosynthesis , RNA, Viral/metabolism , RNA-Dependent RNA Polymerase/biosynthesis , RNA-Dependent RNA Polymerase/genetics , Sf9 Cells/virology , Tenuivirus/genetics , Viral Proteins/biosynthesis , Viral Proteins/metabolism , Virus Replication
6.
Anal Biochem ; 418(1): 50-7, 2011 Nov 01.
Article in English | MEDLINE | ID: mdl-21782784

ABSTRACT

Hepatitis C virus (HCV) NS5B, an RNA-dependent RNA polymerase (RdRp), is an attractive target for antiviral agents. The in vitro RNA synthesis system based on radioisotopic readout is commonly used for polymerase inhibitor screening; however, this system generates large amounts of radioactive waste and is not amenable to high-throughput applications. To overcome this limitation, we generated pFLuc-(-)UTRΔC-RLuc, a bicistronic reporter vector, which allows effective and sensitive distinction of RdRp activity by using a cell-free coupled transcription/translation system. This reporter construct comprises the firefly luciferase (FLuc) and the Renilla luciferase (RLuc) genes in reverse orientation flanked by the two negative strands of the HCV 5'- and 3'-untranslated regions in which FLuc and RLuc reporter proteins are regulated by bacteriophage T7 polymerase and NS5B polymerase, respectively. The increase in RLuc activity was proportional to the amount of active RdRp. This cell-free dual reporter system was further validated using specific RdRp inhibitors. Hence, linear dose-response curves between RLuc activity and specific inhibitors were obtained, as was faster drug screening through real-time measurement of chemiluminescence. Moreover, this reporter system is suitable for robust in vitro screening because of a statistically acceptable Z' factor value of 0.79 under the antiviral screening condition in the 96-well format.


Subject(s)
Genes, Reporter , Hepacivirus/enzymology , Luciferases, Renilla/genetics , RNA-Dependent RNA Polymerase/genetics , Transcription, Genetic , Antiviral Agents/pharmacology , Coumarins/pharmacology , Hepacivirus/genetics , Luciferases, Renilla/metabolism , RNA, Viral/chemistry , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/biosynthesis , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , Virus Replication
7.
Nat Med ; 5(7): 823-7, 1999 Jul.
Article in English | MEDLINE | ID: mdl-10395329

ABSTRACT

'Naked' nucleic acid vaccines are potentially useful candidates for the treatment of patients with cancer, but their clinical efficacy has yet to be demonstrated. We sought to enhance the immunogenicity of a nucleic acid vaccine by making it 'self-replicating'. We accomplished this by using a gene encoding an RNA replicase polyprotein derived from the Semliki forest virus, in combination with a model antigen. A single intramuscular injection of a self-replicating RNA immunogen elicited antigen-specific antibody and CD8+ T-cell responses at doses as low as 0.1 microg. Pre-immunization with a self-replicating RNA vector protected mice from tumor challenge, and therapeutic immunization prolonged the survival of mice with established tumors. The self-replicating RNA vectors did not mediate the production of substantially more model antigen than a conventional DNA vaccine did in vitro. However, the enhanced efficacy in vivo correlated with a caspase-dependent apoptotic death in transfected cells. This death facilitated the uptake of apoptotic cells by dendritic cells, providing a potential mechanism for enhanced immunogenicity. Naked, non-infectious, self-replicating RNA may be an excellent candidate for the development of new cancer vaccines.


Subject(s)
B-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Cancer Vaccines/therapeutic use , Colonic Neoplasms/prevention & control , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/therapeutic use , Animals , Antibody Formation , Apoptosis , Colonic Neoplasms/immunology , Dendritic Cells/immunology , Enhancer Elements, Genetic , Injections, Intramuscular , Mice , Mice, Inbred BALB C , Plasmids , Promoter Regions, Genetic , RNA-Dependent RNA Polymerase/biosynthesis , Recombinant Proteins/biosynthesis , Reverse Transcriptase Polymerase Chain Reaction , Semliki forest virus/enzymology , Semliki forest virus/genetics , Transfection , Tumor Cells, Cultured
8.
Biochem Biophys Res Commun ; 391(1): 570-4, 2010 Jan 01.
Article in English | MEDLINE | ID: mdl-19932088

ABSTRACT

The influenza virus RNA polymerase (RdRp) was purified from insect cells (around 0.2mg/l). The RdRp catalyzed all the biochemical reactions of influenza virus transcription and replication in vitro; dinucleotide ApG and globin mRNA-primed transcription, de novo initiation (replication), and polyadenylation. The optimal Mg concentration, pH and temperature were 8mM, 8.0 and 25 degrees C, respectively, which were slightly different from those measured for RdRp of virions. This system is a single-round transcription system. K(m) (microM) were 10.74+/-0.26 (GTP), 33.22+/-3.37 (ATP), 28.93+/-0.48 (CTP) and 22.01+/-1.48 (UTP), and V(max) (fmol nucleotide/pmol RdRp/min) were 2.40+/-0.032 (GTP), 1.95+/-0.17 (ATP), 2.07+/-0.17 (CTP), and 1.52+/-0.38 (UTP), which agreed with high mutation of influenza viruses.


Subject(s)
Influenza A Virus, H1N1 Subtype/enzymology , Influenza A Virus, H5N1 Subtype/enzymology , RNA-Dependent RNA Polymerase/chemistry , Viral Proteins/chemistry , Animals , Cells, Cultured , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza A Virus, H5N1 Subtype/genetics , Influenza A Virus, H5N1 Subtype/isolation & purification , Insecta/cytology , Kinetics , RNA-Dependent RNA Polymerase/biosynthesis , RNA-Dependent RNA Polymerase/isolation & purification , Viral Proteins/biosynthesis , Viral Proteins/isolation & purification
9.
J Virol ; 83(23): 12279-89, 2009 Dec.
Article in English | MEDLINE | ID: mdl-19759133

ABSTRACT

The RNA-dependent RNA polymerase 3D(pol) is required for the elongation of positive- and negative-stranded picornavirus RNA. During the course of investigating the effect of the transgenic expression of viral genes on the host immune response, we evaluated the viral load present in the host after infection. To our surprise, we found that 3D transgenic expression in genetically susceptible FVB mice led to substantially lower viral loads after infection with Theiler's murine encephalomyelitis virus (TMEV). As a result, spinal cord damage caused by chronic viral infection in the central nervous system was reduced in FVB mice that expressed 3D. This led to the preservation of large-diameter axons and motor function in these mice. The 3D transgene also lowered early viral loads when expressed in FVB-D(b) mice resistant to persistent TMEV infection. The protective effect of 3D transgenic expression was not altered in FVB-Rag(-/-).3D mice that are deficient in T and B cells, thus ruling out a mechanism by which the overexpression of 3D enhanced the adaptive immune clearance of the virus. Understanding how endogenously overexpressed 3D polymerase inhibits viral replication may lead to new strategies for targeting therapies to all picornaviruses.


Subject(s)
Demyelinating Diseases/immunology , RNA-Dependent RNA Polymerase/biosynthesis , Theilovirus/immunology , Animals , Mice , Mice, Knockout , Mice, Transgenic , Motor Activity , RNA-Dependent RNA Polymerase/genetics , Spinal Cord/pathology , Viral Load
10.
Nucleic Acids Res ; 36(4): 1220-6, 2008 Mar.
Article in English | MEDLINE | ID: mdl-18160413

ABSTRACT

RNA-dependent RNA polymerase 6 (RDR6) catalyses dsRNA synthesis for post-transcriptional gene silencing (PTGS)-associated amplification and the generation of endogeneous siRNAs involved in developmental determinations or stress responses. The functional importance of RDR6 in PTGS led us to examine its connection to the cellular regulatory network by analyzing the hormonal responses of RDR6 gene expression in a cultured cell system. Delivery of dsRNA, prepared in vitro, into cultured rice (Oryza sativa cv. Japonica Dongjin) cells successfully silenced the target isocitrate lyase (ICL) transcripts. Silencing was transient in the absence of abscisic acid (ABA), while it became persistent in the presence of ABA in growth medium. A transcription assay of the OsRDR6 promoter showed that it was positively regulated by ABA. OsRDR6-dependent siRNA(ICL) generation was also significantly up-regulated by ABA. The results showed that, among the five rice OsRDR isogenes, only OsRDR6 was responsible for the observed ABA-mediated amplification and silencing of ICL transcripts. We propose that ABA modulates PTGS through the transcriptional control of the OsRDR6 gene.


Subject(s)
Abscisic Acid/pharmacology , Gene Expression Regulation, Plant , Oryza/genetics , Plant Growth Regulators/pharmacology , Plant Proteins/genetics , RNA Interference , RNA-Dependent RNA Polymerase/genetics , Isocitrate Lyase/biosynthesis , Isocitrate Lyase/genetics , Oryza/drug effects , Oryza/enzymology , Plant Proteins/biosynthesis , RNA-Dependent RNA Polymerase/biosynthesis
11.
Antiviral Res ; 165: 55-64, 2019 05.
Article in English | MEDLINE | ID: mdl-30885750

ABSTRACT

Influenza viruses are major respiratory pathogens responsible for both seasonal epidemics and occasional pandemics worldwide. The current available treatment options have limited efficacy and thus the development of new antivirals is highly needed. We previously reported the identification of a series of cycloheptathiophene-3-carboxamide compounds as influenza A virus inhibitors that act by targeting the protein-protein interactions between the PA-PB1 subunits of the viral polymerase. In this study, we characterized the antiviral properties of the most promising compounds as well as investigated their propensity to induce drug resistance. Our results show that some of the selected compounds possess potent, broad-spectrum anti-influenza activity as they efficiently inhibited the replication of several strains of influenza A and B viruses, including an oseltamivir-resistant clinical isolate, with nanomolar or low-micromolar potency. The most promising compounds specifically inhibited the PA-PB1 binding in vitro and interfered with the influenza A virus polymerase activity in a cellular context, without showing cytotoxicity. The most active PA-PB1 inhibitors showed to possess a drug resistance barrier higher than that of oseltamivir. Indeed, no viral variants with reduced susceptibility to the selected compounds emerged after serial passages of influenza A virus under drug selective pressure. Overall, our studies identified potent PA-PB1 inhibitors as promising candidates for the development of new anti-influenza drugs.


Subject(s)
Antiviral Agents/pharmacology , Orthomyxoviridae/drug effects , RNA-Dependent RNA Polymerase/drug effects , Animals , Drug Resistance, Viral , Humans , Influenza A virus/metabolism , Influenza B virus/metabolism , Oseltamivir/pharmacology , RNA-Dependent RNA Polymerase/biosynthesis , Viral Proteins/genetics , Virus Replication/drug effects
12.
Antiviral Res ; 76(1): 93-7, 2007 Oct.
Article in English | MEDLINE | ID: mdl-17561278

ABSTRACT

Compound A-837093, a non-nucleoside HCV RNA-dependent RNA polymerase inhibitor, displayed nanomolar potencies against HCV genotypes 1a and 1b replicons. It also exhibited an excellent metabolic profile and achieved high plasma and liver concentrations in animals. In order to characterize the development of resistance to this anti-HCV agent, HCV subgenomic 1b strain N replicon cells were cultured in the presence of A-837093 with G418. Mutations S368A, Y448H, G554D, Y555C, and D559G in the NS5B polymerase gene were identified that led to substantial decreases in the susceptibilities of 1b genotype replicons to the inhibitor A-837093. However, the resistant mutants remained susceptible to HCV protease inhibitor BILN-2061 and alpha interferon as well as to a different class of non-nucleoside HCV polymerase inhibitor. In addition, each single resistant mutation identified significantly reduced the replication capacity of mutant compared to wild-type replicon. These findings provide a strategic guide for the future development of non-nucleoside inhibitors of HCV NS5B polymerase.


Subject(s)
Enzyme Inhibitors/pharmacology , Hepacivirus/drug effects , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/genetics , Viral Proteins/genetics , Cell Line , Drug Resistance, Viral/genetics , Genes, Viral/drug effects , Hepacivirus/physiology , Humans , Models, Molecular , Mutation , RNA-Dependent RNA Polymerase/biosynthesis , RNA-Dependent RNA Polymerase/chemistry , Replicon/genetics , Viral Proteins/biosynthesis , Viral Proteins/chemistry , Virus Replication
13.
Article in English | MEDLINE | ID: mdl-17554171

ABSTRACT

The Picornaviridae virus family contains a large number of human pathogens such as poliovirus, hepatitis A virus and rhinoviruses. Amongst the viruses belonging to the genus Enterovirus, several serotypes of coxsackievirus coexist for which neither vaccine nor therapy is available. Coxsackievirus B3 is involved in the development of acute myocarditis and dilated cardiomyopathy and is thought to be an important cause of sudden death in young adults. Here, the first crystal of a coxsackievirus RNA-dependent RNA polymerase is reported. Standard crystallization methods yielded crystals that were poorly suited to X-ray diffraction studies, with one axis being completely disordered. Crystallization was improved by testing crystallization solutions from commercial screens as additives. This approach yielded crystals that diffracted to 2.1 A resolution and that were suitable for structure determination.


Subject(s)
Enterovirus B, Human/enzymology , RNA-Dependent RNA Polymerase/chemistry , Crystallization , Enterovirus B, Human/genetics , Gene Expression Regulation, Bacterial/physiology , RNA-Dependent RNA Polymerase/biosynthesis , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/isolation & purification
14.
Nucleic Acids Res ; 33(7): 2239-47, 2005.
Article in English | MEDLINE | ID: mdl-15843686

ABSTRACT

The ratio between proteins P27 and replicase of Cocksfoot mottle virus (CfMV) is regulated via a -1 programmed ribosomal frameshift (-1 PRF). A minimal frameshift signal with a slippery U UUA AAC heptamer and a downstream stem-loop structure was inserted into a dual reporter vector and directed -1 PRF with an efficiency of 14.4 +/- 1.9% in yeast and 2.4 +/- 0.7% in bacteria. P27-encoding CfMV sequence flanking the minimal frameshift signal caused approximately 2-fold increase in the -1 PRF efficiencies both in yeast and in bacteria. In addition to the expected fusion proteins, termination products ending putatively at the frameshift site were found in yeast cells. We propose that the amount of premature translation termination from control mRNAs played a role in determining the calculated -1PRF efficiency. Co-expression of CfMV P27 with the dual reporter vector containing the minimal frameshift signal reduced the production of the downstream reporter, whereas replicase co-expression had no pronounced effect. This finding allows us to propose that CfMV protein P27 may influence translation at the frameshift site but the mechanism needs to be elucidated.


Subject(s)
Frameshifting, Ribosomal , Gene Expression Regulation, Viral , Plant Viruses/genetics , RNA Viruses/genetics , Escherichia coli/genetics , Genes, Reporter , RNA, Viral/chemistry , RNA-Dependent RNA Polymerase/biosynthesis , RNA-Dependent RNA Polymerase/genetics , Saccharomyces cerevisiae/genetics , Viral Proteins/biosynthesis , Viral Proteins/genetics , Viral Proteins/metabolism
15.
Acta Virol ; 51(3): 195-201, 2007.
Article in English | MEDLINE | ID: mdl-18076310

ABSTRACT

The RNA-dependent RNA polymerase (RdRp) in viruses of the family Flaviviridae plays an important role in the viral replication process and in the forming of a replicase complex. We used small interfering RNAs (siRNAs) corresponding to the highly conservative Motif V of RdRp gene of different viruses to examine their role in modulating the expression of RdRp. Evaluation of the expression of RdRps was performed by the fluorescence, flow cytometry, Western blotting, and real-time PCR. We found that Classical swine fever virus (CSFV) siRNA could completely block the transcription and expression of RdRp. Additionally, Hepatitis C virus (HCV) siRNA could cause effective inhibition of RdRp, whereas Japanese encephalitis virus siRNA did not show significant repression of corresponding RdRp. These results demonstrated that siRNAs inhibited the expression of tested RdRps at the transcription level or at the posttranscriptional processing to a different extent.


Subject(s)
Classical Swine Fever Virus/genetics , Encephalitis Virus, Japanese/genetics , Gene Silencing , Hepacivirus/genetics , RNA-Dependent RNA Polymerase/biosynthesis , Viral Proteins/biosynthesis , Animals , Artificial Gene Fusion , Blotting, Western , Cell Line , Conserved Sequence/genetics , Flow Cytometry , Gene Expression , Genes, Reporter , Green Fluorescent Proteins/biosynthesis , Green Fluorescent Proteins/genetics , RNA, Small Interfering/genetics , RNA, Viral/biosynthesis , RNA-Dependent RNA Polymerase/genetics , Reverse Transcriptase Polymerase Chain Reaction , Swine , Viral Proteins/genetics
16.
Biochim Biophys Acta ; 656(2): 134-9, 1981 Dec 28.
Article in English | MEDLINE | ID: mdl-7032595

ABSTRACT

The effect of polyamines on Q beta and MS2 phage RNA-directed synthesis of three kinds of protein in an Escherichia coli cell-free system has been studied. With both phage RNAs, the degree of stimulation of protein synthesis by spermidine was in the order RNA replicase greater than A protein, while the synthesis of coat protein was not stimulated significantly by spermidine. The synthesis of RNA replicase was stimulated by 1 mM spermidine approx. 8-fold. From the results of Q beta RNA direct alanyl-tRNA and seryl-tRNA binding to ribosomes and initiation dipeptide synthesis, it is suggested that the preferential stimulation of the synthesis of RNA replicase by spermidine is due at least partially to the stimulation of the initiation of RNA replicase synthesis.


Subject(s)
Bacteriophages/metabolism , Polyamines/pharmacology , Protein Biosynthesis/drug effects , RNA, Viral/metabolism , Viral Proteins/biosynthesis , Dipeptides/biosynthesis , Escherichia coli , Formaldehyde/pharmacology , Molecular Weight , Peptide Chain Initiation, Translational/drug effects , RNA, Transfer, Amino Acyl/metabolism , RNA-Dependent RNA Polymerase/biosynthesis , Ribosomes/metabolism
17.
Virus Res ; 53(2): 141-9, 1998 Feb.
Article in English | MEDLINE | ID: mdl-9620206

ABSTRACT

The hepatitis C virus (HCV) represents a major public health problem that can produce liver failure and hepatocellular carcinoma in chronically infected patients. Our goal was to express the HCV non-structural protein 5B (NS5B) protein of HCV genotype 1a in Escherichia coli and initiate studies of its role in HCV genomic replication. In this report we demonstrate that a recombinant NS5B protein with an amino terminal sequence of ASMSYSWTG has RNA-dependent RNA polymerase (RDRP) activity. This recombinant enzyme was active in poly(U) polymerase assays and produced template-sized RNA products when globin mRNA was used as a template. The polymerase activity of recombinant NS5B was primer-dependent and was active for at least 60 min of incubation at 30 degrees C. Deletion of the carboxyl terminal region of HCV NS5B resulted in a loss of RDRP activity indicating that the enzymatic activity observed was due to the full-length recombinant enzyme. Recombinant NS5B (RDRP) should assist in understanding the mechanism of HCV replication and the identification of specific enzyme inhibitors.


Subject(s)
Escherichia coli/metabolism , Hepacivirus/enzymology , RNA-Dependent RNA Polymerase/biosynthesis , Viral Nonstructural Proteins/biosynthesis , Gene Expression , Globins/genetics , Hepacivirus/genetics , Humans , Mutagenesis , Poly U/metabolism , RNA, Messenger/metabolism , RNA-Dependent RNA Polymerase/genetics , Recombinant Fusion Proteins/biosynthesis , Recombinant Fusion Proteins/genetics , Templates, Genetic , Viral Nonstructural Proteins/genetics
18.
Adv Exp Med Biol ; 380: 399-404, 1995.
Article in English | MEDLINE | ID: mdl-8830515

ABSTRACT

Two hammerhead ribozymes targeted against the polymerase gene of mouse hepatitis virus (MHV), which consisted of 22-nucleotide (nt) ribozyme core sequences and antisense sequences of different lengths, 243-nt (S-ribozyme) and 926-nt (L-ribozyme), were tested for their++ inhibitory effects on viral multiplication. Vectors that expressed the ribozymes were transfected into mouse DBT cells and several resulting cell lines constitutively expressing the ribozymes were selected and examined for intracellular MHV multiplication in acute and chronic stages of infection. The production of infectious progeny viral particles was significantly reduced in the transfected cell lines expressing either the S-ribozyme or L-ribozyme in acute infection. Although the in vitro cleavage process of the L-ribozyme was slower than that of the S-ribozyme, no difference was observed in inhibitory effects on MHV multiplication between S- and L-ribozymes in the transfected cells. In the transfected cells expressing L-ribozymes, production of viral particles was also inhibited in the chronic stage of MHV infection.


Subject(s)
Antiviral Agents/pharmacology , Murine hepatitis virus/physiology , Oligonucleotides, Antisense/pharmacology , RNA, Catalytic/genetics , RNA-Dependent RNA Polymerase/biosynthesis , Virus Replication/drug effects , Animals , Astrocytoma , Base Sequence , Cell Line , DNA Primers , Genes, Viral , Mice , Molecular Sequence Data , Murine hepatitis virus/drug effects , Murine hepatitis virus/genetics , Promoter Regions, Genetic , RNA, Catalytic/biosynthesis , RNA-Dependent RNA Polymerase/genetics , Transfection , Tumor Cells, Cultured , Virus Replication/physiology
19.
PLoS One ; 8(9): e76090, 2013.
Article in English | MEDLINE | ID: mdl-24098767

ABSTRACT

Plant RNA-dependent RNA Polymerase 1 (RDR1) is an important element of the RNA silencing pathway in the plant defense against viruses. RDR1 expression can be elicited by viral infection and salicylic acid (SA), but the mechanisms of signaling during this process remains undefined. The involvement of hydrogen peroxide (H2O2) and nitric oxide (NO) in RDR1 induction in the compatible interactions between Tobacco mosaic tobamovirus (TMV) and Nicotiana tabacum, Nicotiana benthamiana, and Arabidopsis thaliana was examined. TMV inoculation onto the lower leaves of N. tabacum induced the rapid accumulation of H2O2 and NO followed by the increased accumulation of RDR1 transcripts in the non-inoculated upper leaves. Pretreatment with exogenous H2O2 and NO on upper leaf led to increased RDR1 expression and systemic TMV resistance. Conversely, dimethylthiourea (an H2O2 scavenger) and 2-(4-carboxyphenyl)- 4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (an NO scavenger) partly blocked TMV- and SA-induced RDR1 expression and increased TMV susceptibility, whereas pretreatment with exogenous H2O2 and NO failed to diminish TMV infection in N. benthamiana plants with naturally occurring RDR1 loss-of-function. Furthermore, in N. tabacum and A. thaliana, TMV-induced H2O2 accumulation was NO-dependent, whereas NO generation was not affected by H2O2. These results suggest that, in response to TMV infection, H2O2 acts downstream of NO to mediate induction of RDR1, which plays a critical role in strengthening RNA silencing to restrict systemic viral infection.


Subject(s)
Arabidopsis/immunology , Hydrogen Peroxide/metabolism , Nicotiana/immunology , Nitric Oxide/metabolism , Plant Diseases/immunology , RNA-Dependent RNA Polymerase/biosynthesis , Tobacco Mosaic Virus , Arabidopsis/virology , Enzyme Induction/physiology , Fluorescence , Plant Diseases/virology , Plant Leaves/metabolism , RNA Interference , Real-Time Polymerase Chain Reaction , Time Factors , Nicotiana/virology
20.
J Med Chem ; 56(24): 10118-31, 2013 Dec 27.
Article in English | MEDLINE | ID: mdl-24313730

ABSTRACT

The limited number of drug classes licensed for treatment of influenza virus (Flu), together with the continuous emergence of viral variants and drug resistant mutants, highlights the urgent need to find antivirals with novel mechanisms of action. In this context, the viral RNA-dependent RNA polymerase (RdRP) subunits assembly has emerged as an attractive target. Starting from a cycloheptathiophene-3-carboxamide derivative recently identified by us for its ability to disrupt the interaction between the PA and PB1 subunits of RdRP, we have designed and synthesized a series of analogues. Their biological evaluation led to the identification of more potent protein-protein interaction inhibitors, endowed with antiviral activity that also encompassed a number of clinical isolates of FluA, including an oseltamivir-resistant strain, and FluB, without showing appreciable toxicity. From this study, the cycloheptathiophene-3-carboxamide scaffold emerged as being particularly suitable to impart anti-Flu activity.


Subject(s)
Antiviral Agents/pharmacology , Benzamides/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Orthomyxoviridae/drug effects , Orthomyxoviridae/enzymology , RNA-Dependent RNA Polymerase/biosynthesis , Thiophenes/pharmacology , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Benzamides/chemical synthesis , Benzamides/chemistry , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Models, Molecular , Molecular Structure , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , Structure-Activity Relationship , Thiophenes/chemical synthesis , Thiophenes/chemistry
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