Identification and analysis of conserved structures in RNA viruses

• Main Author: Hershan, Almonther A
• Format: Dissertation
• Language: English
• Published: University of Essex 2012

The family Picornaviridae includes many important human pathogens. RNA structures play important roles in picornavirus molecular biology and recent evidence suggests that these are more extensive than previously thought. In this project we identified a number of potential RNA structures in picornavirus genomes and started to analyse one of these structures. The work focussed on human parechoviruses (HPe V). The structure of the HPe V 5' untranslated region (UTR) was analysed by obtaining several new sequences and using an alignment of 60 sequences to identify covariant changes. This allowed the previously predicted structure to be confirmed and refined. Aligned sequences representing most picornavirus species were then analysed for suppression of synonymous codon variation (SSCV). Strong SSCV was seen in several cases and this was often related to the presence of RNA structures including the Cre and novel potential structures. Patterns of conserved dinucleotides were also used to identify regions of importance in the picornavirus genome. A new program, Dinucleotider (1.0) was developed and used, which allows a graphical output of conserved dinucleotides in aligned sequences. CG was found to be the most informative dinucleotide and could be used to identify regions of the picornavirus genome, which corresponded to the 5'UTR, 3'UTR and Cre, as well as further new structures. Genetic analysis of a predicted structure in the 3D-encoding region of HPe V s, was carried out by making two mutants, with 3 or 6 mutations in one of the structural domains. Both sets of mutations had little effect on virus growth in cultured cells, suggesting that the structure does not play a critical role in replication and other possible roles need to be identified. Overall, this project has allowed several RNA structures to be identified in picornaviruses. These are conserved between related viruses and presumably play important roles in the biology of picornaviruses. They need to be studied further in order to improve understanding of how picornaviruses infect cells, which is required to improve diagnosis and control of these pathogens.