RNA-dependent RNA polymerase encoded by hepatitis C virus: biomedical applications

The hepatitis C viruses (HCVs) are a group of small enveloped RNA viruses that have been viewed as a leading cause of chronic hepatitis in humans. Infections by HCV represent a serious global health problem, because millions of people worldwide are infected and no efficient treatment is available at the present time. Since HCV was identified in 1989, considerable effort has been devoted to the discovery and development of novel molecules to treat HCV-related diseases. One of the approaches is the development of novel inhibitors that interrupt the normal functions of HCV NS5B, an RNA-dependent RNA polymerase essential to HCV replication. This review summarizes recent advances in the biochemical and structural understanding of HCV NS5B polymerase as well as in the development of antiviral agents targeting this important enzyme. Received 19 March 2002; received after revision 23 April 2002; accepted 23 April 2002     

Structure and function of Zika virus NS5 protein: perspectives for drug design

Zika virus (ZIKV) belongs to the positive-sense single-stranded RNA-containing Flaviviridae family. Its recent outbreak and association with human diseases (e.g. neurological disorders) have raised global health concerns, and an urgency to develop a therapeutic strategy against ZIKV infection. However, there is no currently approved antiviral against ZIKV. Here we present a comprehensive overview on recent progress in structure–function investigation of ZIKV NS5 protein, the largest non-structural protein of ZIKV, which is responsible for replication of the viral genome, RNA capping and suppression of host interferon responses. Structural comparison of the N-terminal methyltransferase domain and C-terminal RNA-dependent RNA polymerase domain of ZIKV NS5 with their counterparts from related viruses provides mechanistic insights into ZIKV NS5-mediated RNA replication, and identifies residues critical for its enzymatic activities. Finally, a collection of recently identified small molecule inhibitors against ZIKV NS5 or its closely related flavivirus homologues are also discussed.     

Purfication and molecular weight of an RNA-dependant RNA polymerase from Brassicae oleracea var. Botrytis]

An RNA-dependent RNA polymerase has been completely purified from Cauliflower inflorescences. Analysis of the purified enzyme on SDS-polyacrylamide gels showed one polypeptide chain with a molecular weight of 140,000 dalton. The enzyme is monomeric in its native state. The in vitro activity was completely dependent on added RNA, the most efficient templates being poly (U), poly (U, C), poly (I) and viral RNA.     

High salt effect on RNA synthesis in Krebs ascites tumor cells

The incubation of Krebs ascites tumor cells in medium with a high salt concentration resulted in a partial inhibition of nuclear RNA synthesis. The residual RNA polymerase activity in such nuclei was only slightly inhibited by low concentrations (50 nM) of alpha-amanitin. This finding suggested an inhibition of RNA polymerase II activity under conditions of medium hypertonicity. Indeed, RNA polymerase II, isolated from the nuclei of cells exposed to hypertonicity, revealed only half of the control activity. On the other hand, RNA polymerase I was not affected by hypertonicity. Moreover, chromatin fractions isolated from cells incubated in hypertonic or isotonic medium were equally template-active in RNA synthesis.     

Organization and expression of the poxvirus genome

Summary Poxviruses comprise a large group of very complex animal DNA viruses which replicate in the cytoplasm of infected cells. Vaccinia virus, the most studied poxvirus, has a linear, double stranded DNA genome with an approximate molecular weight of 120×10⁶ (180 kilobase pairs). The two strands of the DNA molecule are naturally cross-linked at both termini. In addition, the vaccinia virus genome contains very long inverted terminal repetitions of approximately 10 kilobase pairs which are further characterized by the presence of direct tandem repeats of a 70-base-pair sequence arranged in two blocks of 13 and 17 copies, respectively. A central region of the genome is highly conserved between different orthopoxviruses. In contrast, the ends are hypervariable and may contain extensive deletions and complex, symmetrical sequences rearrangements. Vaccinia virus gene expression is divided into two stages. Early in infection, RNA complementary to one half of one strand-equivalent of the genome is transcribed within subviral particles by the virion-associated RNA polymerase. Later in infection, after DNA replication, RNA complementary to one entire strand-equivalent is transcribed. RNA made late in infection is very heterogeneous in length and a large fraction of it contains self-complementary sequences. Late genes are clustered near the central region of the genome. Vaccinia virus mRNAs do not appear to be synthesized by a splicing mechanism.     

High salt effect on RNA synthesis in Krebs ascites tumor cells

Summary The incubation of Krebs ascites tumor cells in medium with a high salt concentration resulted in a partial inhibition of nuclear RNA synthesis. The residual RNA polymerase activity in such nuclei was only slightly inhibited by low concentrations (50 nM) of -amanitin. This finding suggested an inhibition of RNA polymerase II activity under conditions of medium hypertonicity. Indeed, RNA polymerase II, isolated from the nuclei of cells exposed to hypertonicity, revealed only half of the control activity. On the other hand, RNA polymerase I was not affected by hypertonicity. Moreover, chromatin fractions isolated from cells incubated in hypertonic or isotonic medium were equally template-active in RNA synthesis.This investigation was supported by the Turkish Scientific and Technical Research Council (TÜBITAK), Project No. TAG 339.     

Arabinose nucleoside triphosphates are no inhibitors for DNA-dependent RNA polymerases.

1-Beta-D-arabinofuranosylcytosine-5' -triphosphate and 9-beta-D-arabinofuranosyladenosine-5' -triphosphate were found to have no inhibitory potency for both mammalian DNA-dependent RNA polymerase II and E. coli DNA-dependent RNA polymerase.     

Inhibitory effect of flavonoids on DNA-dependent DNA and RNA polymerases

Flavonoids, (-)-epigallocatechin (1), myricetin (2) and quercetin (3), were investigated for inhibitory effects on E. coli DNA polymerase I and T7 bacteriophage RNA polymerase. In both DNA and RNA synthesis, 1 and 3 inhibited enzyme reactions by non-competitive and mixed type inhibition respectively, with regard to template DNAs. Myricetin (2) inhibited DNA and RNA polymerase reactions by mixed type and competitive type inhibition, respectively, with template DNAs. It was suggested that 2 interacts with covalently closed circular DNA.     

The role of proteolytic processing in the morphogenesis of virus particles

Proteinases are encoded by many RNA viruses, all retroviruses and several DNA viruses. They play essential roles at various stages in viral replication, including the coordinated assembly and maturation of virions. Most of these enzymes belong to one of three (Ser, Cys or Asp) of the four major classes of proteinases, and have highly substrate-selective and cleavage specific activities. They can be thought of as playing one of two general roles in viral morphogenesis. Structural proteins are encoded by retroviruses and many RNA viruses as part of large polyproteins. Their proteolytic release is a prerequisite to particle assembly; consequent structural rearrangement of the capsid domains serves to regulate and direct association and assembly of capsid subunits. The second general role of proteolysis is in assembly-dependent maturation of virus particles, which is accompanied by the acquisition of infectivity.     

The role of proteolytic processing in the morphogenesis of virus particles.

Proteinases are encoded by many RNA viruses, all retroviruses and several DNA viruses. They play essential roles at various stages in viral replication, including the coordinated assembly and maturation of virions. Most of these enzymes belong to one of three (Ser, Cys or Asp) of the four major classes of proteinases, and have highly substrate-selective and cleavage specific activities. They can be thought of as playing one of two general roles in viral morphogenesis. Structural proteins are encoded by retroviruses and many RNA viruses as part of large polyproteins. Their proteolytic release is a prerequisite to particle assembly; consequent structural rearrangement of the capsid domains serves to regulate and direct association and assembly of capsid subunits. The second general role of proteolysis is in assembly-dependent maturation of virus particles, which is accompanied by the acquisition of infectivity.     

Susceptibility of chick neural retina to viral multiplication in vitro during embryonic development

Decrease in the susceptibility of embryonic chick neural retina cultures to the multiplication of various viruses was observed with increasing age of the embryo. In contrast the retinal cells supported the multiplication of Sindbis virus irrespective of the age when they were infected with the viral RNA. These results suggest that the restricted multiplication of the viruses observed is due to the modulated inability of the cell to process the adsorbed viruses for subsequent replication.     

Susceptibility of chick neural retina to viral multiplication in vitro during embryonic development

Summary Decrease in the susceptibility of embryonic chick neural retina cultures to the multiplication of various viruses was observed with increasing age of the embryo. In contrast the retinal cells supported the multiplication of Sindbis virus irrespective of the age when they were infected with the viral RNA. These results suggest that the restricted multiplication of the viruses observed is due to the modulated inability of the cell to process the adsorbed viruses for subsequent replication.     

The spread of Tobacco mosaic virus infection: insights into the cellular mechanism of RNA transport

Interactions of plant cells with pathogens or other biotic or abiotic environmental factors can give rise to systemic defense responses that rely upon the cell-to-cell and systemic transport of specific signals. A novel type of systemic signaling was revealed by recent evidence indicating the existence of RNA species that travel cell to cell and through the vasculature. The most compelling evidence for intercellular and systemic transport of RNA in plants is provided by viroids and viruses that apparently use the endogenous transport machinery to spread infection. The cell to cell movement of plant viruses occurs through small pores in the cell wall known as plasmodesmata and depends on virus-encoded 'movement proteins'. This review summarizes current knowledge of Tobacco mosaic virus infection with emphasis on the mechanism by which this virus targets its RNA genome from sites of replication to plasmodesmata to achieve intercellular spread.     

Inhibitory effect of halocyamine,an antimicrobial substance from ascidian hemocytes,on the growth of fish viruses and marine bacteria

Summary Halocyamine A, an antimicrobial substance isolated from hemocytes of the solitary ascidianHalocynthia roretzi, inhibited in vitro the growth of fish RNA viruses (infectious hematopoietic necrosis virus and infectious pancreatic necrosis virus). Pretreatment of RNA virus with halocyamine A reduced the infectivity of the virus toward host cells. The growth of marine bacteria,Achromobacter aquamarinus andPseudomonas perfectomarinus, was also inhibited by halocyamine A but that ofAlteromonas putrefaciens andVibrio anguillarum was not. These results suggest that halocyamine may have a role in the defense mechanisms ofH. roretzi against marine viruses and bacteria.     

Regulation of microRNA biogenesis and turnover by animals and their viruses

MicroRNAs (miRNAs) are a ubiquitous component of gene regulatory networks that modulate the precise amounts of proteins expressed in a cell. Despite their small size, miRNA genes contain various recognition elements that enable specificity in when, where and to what extent they are expressed. The importance of precise control of miRNA expression is underscored by functional studies in model organisms and by the association between miRNA mis-expression and disease. In the last decade, identification of the pathways by which miRNAs are produced, matured and turned-over has revealed many aspects of their biogenesis that are subject to regulation. Studies in viral systems have revealed a range of mechanisms by which viruses target these pathways through viral proteins or non-coding RNAs in order to regulate cellular gene expression. In parallel, a field of study has evolved around the activation and suppression of antiviral RNA interference (RNAi) by viruses. Virus encoded suppressors of RNAi can impact miRNA biogenesis in cases where miRNA and small interfering RNA pathways converge. Here we review the literature on the mechanisms by which miRNA biogenesis and turnover are regulated in animals and the diverse strategies that viruses use to subvert or inhibit these processes.     

Morphological evidence for the presence of the endogenous guinea-pig retravirus in the lymphoblasts of L2C leukemia.

Peripheral blood samples of a transplantable guinea-pig leukemia revealed that, only during the terminal stages of the disease, leukemic cells produce virus particles indistinguishable from the RNA tumor viruses of the Retraviridae family genus Oncorna virus B.