Essential Role of Cyclization Sequences in Flavivirus RNA Replication

A possible role in RNA replication for interactions between conserved complementary (cyclization) sequences in the 5'- and 3'-terminal regions of Flavivirus RNA was previously suggested but never tested in vivo. Using the M-fold program for RNA secondary-structure predictions, we examined for the first time the base-pairing interactions between the covalently linked 5' genomic region (first ~160 nucleotides) and the 3' untranslated region (last ~115 nucleotides) for a range of mosquito-borne Flavivirus species. Base-pairing occurred as predicted for the previously proposed conserved cyclization sequences. In order to obtain experimental evidence of the predicted interactions, the putative cyclization sequences (5' or 3') in the replicon RNA of the mosquito-borne Kunjin virus were mutated either separately, to destroy base-pairing, or simultaneously, to restore the complementarity. None of the RNAs with separate mutations in only the 5' or only the 3' cyclization sequences was able to replicate after transfection into BHK cells, while replicon RNA with simultaneous compensatory mutations in both cyclization sequences was replication competent. This was detected by immunofluorescence for expression of the major nonstructural protein NS3 and by Northern blot analysis for amplification and accumulation of replicon RNA. We then used the M-fold program to analyze RNA secondary structure of the covalently linked 5'- and 3'-terminal regions of three tick-borne virus species and identified a previously undescribed additional pair of conserved complementary sequences in locations similar to those of the mosquito-borne species. They base-paired with DeltaG values of approximately -20 kcal, equivalent or greater in stability than those calculated for the originally proposed cyclization sequences. The results show that the base-pairing between 5' and 3' complementary sequences, rather than the nucleotide sequence per se, is essential for the replication of mosquito-borne Kunjin virus RNA and that more than one pair of cyclization sequences might be involved in the replication of the tick-borne Flavivirus species.     

Cytogenetic analysis of chromosome segments containing radiosensitivity genes in Drosophila. Radiation mutagenesis in the 44-45 region of chromosome 2 of Drosophila melanogaster

The first step of cytogenetic analysis of Drosophila melanogaster chromosome 2 44F-45D containing the radiosensitivity gene rad(2)201 is described. Using various mutation selection systems as well as lines of different origin and two kinds of ionizing radiation--gamma-rays and neutrons--the mutagenesis in the region of interest is characterized at the cytogenetic level. 85 gamma-induced mutations affecting viability were isolated in the 44F 2-4; 45C6-7 interval, 27% of mutations being chromosomal aberrations. 15 radiation-induced aberrations were obtained by selecting mutations at the white gene inserted into the 45D region by P-mediated transformation. The 44F-45D region is characterized by relatively low frequency of deficiency formation and by significant predomination of heterochromatic aberrations in the spectrum of rearrangements. In these regions, the existence of hot spots for heterochromatic aberrations was discovered. As low deletion frequency is not connected with the presence of haplolethal and haplosterile loci in the region studied, the unusual character of radiation mutagenesis reflects possibly the peculiarities in sequence organization of the chromosomal region mentioned or the packaging in the sperm nuclei.     

The naturally attenuated Kunjin strain of West Nile virus shows enhanced sensitivity to the host type I interferon response

The host determinants that contribute to attenuation of the naturally occurring nonpathogenic strain of West Nile virus (WNV), the Kunjin strain (WNV(KUN)), remain unknown. Here, we show that compared to a highly pathogenic North American strain, WNV(KUN) exhibited an enhanced sensitivity to the antiviral effects of type I interferon. Our studies establish that the virulence of WNV(KUN) can be restored in cells and mice deficient in specific interferon regulatory factors (IRFs) or the common type I interferon receptor. Thus, WNV(KUN) is attenuated primarily through its enhanced restriction by type I interferon- and IRF-3-dependent mechanisms.     

Effect of chitosan on the electrophoretic motility of thymocytes

An increase of contact interaction between macrophages and thymocytes in the presence of polysaccharide chitosan was suggested to be due to the change of surface charge of interacting cells. It was found that incubation of thymocytes in the presence of chitosan leads to the change of their charge in the positive direction. The measurement of electrophoretic mobility of the cells was carried out on " Parmoquant 2" (Carl Zeiss Jena, DDR). The change of electrophoretic mobility increases with decrease of pH, increase of chitosan concentration and decrease of the cell concentration in the medium. This phenomenon is probably due to absorption of positively charged molecules of chitosan on negatively charged cell surface.     

Role of nonstructural protein NS2A in flavivirus assembly

Flavivirus nonstructural (NS) proteins are involved in RNA replication and modulation of the host antiviral response; however, evidence is mounting that some NS proteins also have essential roles in virus assembly. Kunjin virus (KUN) NS2A is a small, hydrophobic, transmembrane protein that is part of the replication complex and inhibits interferon induction. Previously, we have shown that an isoleucine (I)-to-asparagine (N) substitution at position 59 of the NS2A protein blocked the production of secreted virus particles in cells electroporated with viral RNA carrying this mutation. We now show that prolonged incubation of mutant KUN NS2A-I59N replicon RNA, in an inducible BHK-derived packaging cell line (expressing KUN structural proteins C, prM, and E), generated escape mutants that rescued the secretion of infectious virus-like particles. Sequencing identified three groups of revertants that included (i) reversions to wild-type, hydrophobic Ile, (ii) pseudorevertants to more hydrophobic residues (Ser, Thr, and Tyr) at codon 59, and (iii) pseudorevertants retaining Asn at NS2A codon 59 but containing a compensatory mutation (Thr-to-Pro) at NS2A codon 149. Engineering hydrophobic residues at NS2A position 59 or the compensatory T149P mutation into NS2A-I59N replicon RNA restored the assembly of secreted virus-like particles in packaging cells. T149P mutation also rescued virus production when introduced into the full-length KUN RNA containing an NS2A-I59N mutation. Immunofluorescence and electron microscopy analyses of NS2A-I59N replicon-expressing cells showed a distinct lack of virus-induced membranes normally present in cells expressing wild-type replicon RNA. The compensatory mutation NS2A-T149P restored the induction of membrane structures to a level similar to those observed during wild-type replication. The results further confirm the role of NS2A in virus assembly, demonstrate the importance of hydrophobic residues at codon 59 in this process, implicate the involvement of NS2A in the biogenesis of virus-induced membranes, and suggest a vital role for the virus-induced membranes in virus assembly.     

West Nile virus noncoding subgenomic RNA contributes to viral evasion of the type I interferon-mediated antiviral response

We previously showed that a noncoding subgenomic flavivirus RNA (sfRNA) is required for viral pathogenicity, as a mutant West Nile virus (WNV) deficient in sfRNA production replicated poorly in wild-type mice. To investigate the possible immunomodulatory or immune evasive functions of sfRNA, we utilized mice and cells deficient in elements of the type I interferon (IFN) response. Replication of the sfRNA mutant WNV was rescued in mice and cells lacking interferon regulatory factor 3 (IRF-3) and IRF-7 and in mice lacking the type I alpha/beta interferon receptor (IFNAR), suggesting a contribution for sfRNA in overcoming the antiviral response mediated by type I IFN. This was confirmed by demonstrating rescue of mutant virus replication in the presence of IFNAR neutralizing antibodies, greater sensitivity of mutant virus replication to IFN-α pretreatment, partial rescue of its infectivity in cells deficient in RNase L, and direct effects of transfected sfRNA on rescuing replication of unrelated Semliki Forest virus in cells pretreated with IFN-α. The results define a novel function of sfRNA in flavivirus pathogenesis via its contribution to viral evasion of the type I interferon response.