Comparative Analyses and Structural Modeling of RNAs Participating in Non-Canonical Initiation of Protein Synthesis

Abstract

Transfer-messenger RNA and the Internal Ribosomal Entry Site (IRES) RNAs of Foot and Mouth Disease Virus (FMDV) and Bovine Viral Diarrhea Virus (BVDV) play important roles in trans-translation and cap-independent protein synthesis. TmRNA sequences were examined using covariation analysis. Its secondary structure diagram was improved and three-dimensional molecular models were produced. These models were essential for a detailed interpretation of cryo-EM images of tmRNA as it binds to the ribosome. Subsequently, FMDV and BVDV IRES RNAs were investigated in silico and their secondary structures were determined. The modeling method for investigating tertiary structures of RNA molecules was expanded to include RNA-protein interactions captured in high resolution and then used to build biologically relevant structural models of FMDV and BVDV IRES RNAs both off and on the ribosome. Modeling of tmRNA and the IRES RNA structures provided important insights into non-canonical initiation of protein synthesis in prokaryotes and eukaryotes. Moreover, this project generated data essential for developing novel antiviral drugs that will be able to inhibit binding of IRES RNAs to the ribosome.