Search for the putative RNA thermometers in the genome of Hepatitis E virus

Abstract

Currently, some temperature-sensitive elements in bacteria are known. Structurally and functionally different RNA thermometers control a variety of cellular processes in bacteria including virulence. Up-to-date experimental confirmation of RNA thermometers functioning in viruses was obtained only for West Nile virus. But other, unknown yet, types of RNA thermometers may exist in nature. The goal of this study was the determination of conservative stem-loop structures in the swine, wild boars’ hepatitis E virus (HEV) genome which may act as RNA thermometers. The search for putative RNA thermometers in the swine HEV which is a common pathogen in the pig population worldwide was executed. Bioinformatics analysis was used to predict the secondary structure of the linear RNA fragments and to determine the melting temperature of the potential hairpins in the HEV genome. 108 swine, wild boars genotype 3 and genotype 4 HEV isolates with complete genomes from the GenBank database were analyzed for the availability of stem-loop structures. Conservative hairpin with the putative thermoregulating function was found in genotype 3 HEV isolates from pig and wild boar for 64 HEV isolates from 108 analyzed ones. The stem of the hairpin with a length of 37 nt contains two AUG start codons of translation initiation and the melting temperature of the hairpin is equal to 38–42 °С for ionic strength of 0.165 M Na+. These hairpins contain a metastable element (one or two bulges) in the stem. Conservative secondary stem-loop structures with putative thermoregulating function for genomic RNA of 64 HEV isolates with complete genome were found by bioinformatics analysis. These hairpins contain a metastable element (one or two bulges) in the stem like an RNA thermometer of West Nile virus and satisfy the necessary and sufficient conditions of RNA thermometer formation. Determined stem-loop structures are proposed as putative thermoregulator elements because they are highly conservative uncanonical structures that are present in the genomes of 64 HEV isolates from 108 analyzed ones