New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome.

Mariola Dutkiewicz,Jakub Kuczynski,Agata Swiatkowska,Michal Jarzab,Aleksandra Stachowiak

doi:10.3390/v12111232

Mariola Dutkiewicz, Jakub Kuczynski + Show 3 more

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https://doi.org/10.3390/v12111232

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Abstract

Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the cis-acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb2+, were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3′-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA–protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation.

Highlights

Over the last decade the importance of the secondary structure of the RNA of viral genomes has become apparent, which has led to the mapping of the RNA of whole viral genomes, and transcriptomes isolated from simple organisms [1,2,3,4,5]
Stable RNA secondary structures in the coding part may affect the proper folding of viral proteins by slowing the ribosome, as proposed for HIV [1], or play a role in an immune response against hepatitis C virus (HCV) [20]
We investigated the possibility of genome dimerization and Ribonuclease L (RNase L) digestion in the region of the coxsackievirus B3 (CVB3) genome

Summary

Introduction

Over the last decade the importance of the secondary structure of the RNA of viral genomes has become apparent, which has led to the mapping of the RNA of whole viral genomes, and transcriptomes isolated from simple organisms [1,2,3,4,5]. Protein-coding RNA sequences can fold into functional structural motifs, similar to those found in non-protein-coding RNA sequences, though it appears to be less common [1,6]. By using global analysis of viral genomes in search of secondary structures, it was possible to identify new structural patterns and motifs present in both the coding and non-coding regions [7,8]. Numerous structures present in viral genomes play important roles, including at the stages of replication, translation, and stabilization of RNA transcripts or translocation. The complex structures in the coding region are Viruses 2020, 12, 1232; doi:10.3390/v12111232 www.mdpi.com/journal/viruses

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