The RNA secondary structural variation in the cyclization elements of the dengue genome and the possible implications in pathogenicity

Abstract

Dengue virus (DENV), the causative agent of dengue fever and severe dengue, exists as four antigenically different serotypes. These serotypes are further classified into genotypes and have varying degrees of pathogenicity. The 5' and 3' ends of the genomic RNA play a critical role in the viral life cycle. A global scale study of the RNA structural variation among the sero- and genotypes was carried out to correlate RNA structure with pathogenicity. We found that the GC rich stem and rigid loop structure of the 5' end of the genomic RNA of DENV 2 differs significantly from the others. The observed variation in base composition and base pairing may confer structural and functional advantage in highly virulent strains. This variation in the structure may influence the ease of cyclization and recruitment of viral RNA polymerase, NS5 RdRp, thereby affecting the pathogenicity of these strains.

Keywords: Dengue virus; Genotypes; Pathogenicity; RNA secondary structure; Serotypes; UTRs.

Fig. 1

The RNA secondary structures of the 5′ and 3′ regions of the DENV 2 genomic RNA encompassing the cyclization elements (top) and the pan handle structure (cyclic form) of the RNA genome (below). The cyclization elements: Upstream AUG region (UAR); Downstream AUG region (DAR), and cyclization sequence (CS) in both 5′ and 3′ CE (genomic RNA sequence encompassing cyclization elements) are in italics and colored in red, blue, and green respectively. The start codon AUG is underlined. The structural elements present in the 5′ CE: SLA: Stem loop A; UFS: UAR flanking stem; SLB: Stem loop B; cHP: capsid hairpin. The various structural elements present in the SLA: stem 1 (S1); U bulge; stem 2 (S2); stem 3 (S3); top loop (TL) and side stem loop (SSL) are labeled. The 3′ CE consists of the terminal stem loop (SL) and short hairpin (sHP) (color figure online)

Fig. 2

RNA secondary structural variation among DENV serotypes and genotypes: a DENV 1, b DENV 2, c DENV 3 and d DENV 4. The UAR, DAR, and CS regions in blue and the start codon AUG underlined. The various structural components are also labelled (see text). The serotype specific differences are shown with double headed arrows. The acronyms used for genotypes and the accession number of the reference sequence and the genotype it belongs to is mentioned in the inset. Differences among the genotypes are mapped onto the reference structure labelled with an arrow and coloured in red. For example, in DENV 2 Cosmopolitan (CP) genotype there is a change of GC base pair to AU base pair at the bottom of the side stem loop (color figure online)