Translation and Protein Processing

Abstract

This chapter addresses the main features concerning picornavirus gene expression. Picornavirus genomes are tightly packed; the RNA encodes a single poly protein whose translation is governed by the internal ribosome entry site (IRES) element using a cap-independent mechanism that hijacks the translation machinery. Picornavirus IRES activity depends on the coordination of RNA structure and RNA-protein interactions. RNA probing of the entire element revealed long-distance interactions within the 5' untranslated region (UTR) of coxsackievirus B3 (CVB3), thereby providing information on overall IRES structure. Despite the fact that many IRES trans-acting factors (ITAFs) are promiscuous RNA-binding proteins, IRESs exhibit distinct requirements in terms of functional RNA-protein associations. Ribonucleoprotein complexes assembled on IRESs share various components with the spliceosome, as in the case of SRp20, polypyrimidine tract-binding protein (PTB), or hnRNP A1. Most of the knowledge on factors required for IRES activity comes from in vitro assays. The study of IRES-ribonucleoprotein complexes in living cells has been addressed using reagents that are permeable to the cell membrane and recognize RNA molecules in a structure-dependent manner. Picornaviral genome RNAs encode their proteins in a single, long open reading frame (ORF), translated into a single poly protein. The presence of 3C and 3C-like proteinase domains in a wide range of positive-stranded RNA virus poly proteins argues strongly that this proteolytic domain was acquired at an early stage in the evolution of these viruses.