Initiation of Translation of Picornavirus RNAs: Structure and Function of the Internal Ribosome Entry Site

By the late 1970s, a skeleton of the translation mechanism utilized by the bulk of cellular mRNAs had been elucidated. More elegant proof of utilization of an internal ribosome entry site (IRES) on the viral RNA was provided by analysis of translation of bicistronic constructs engineered to encode two tandem protein sequences, separated by a viral 5' untranslated region (UTR). The RNA sequences that constitute an IRES extend through several hundred nucleotides and fold into complex, multidomain structures. To identify the nucleotide sequences and structures in the picornavirus 5' UTRs that contribute to IRES function, mutations were introduced into cDNAs to generate transcripts whose translation could be evaluated in vitro or in transfected cells. For the picornavirus RNAs, a relatively relaxed structure is predicted, with a long, central axis of shifting base pairs, with relatively stable stems, loops, helices, and branch points extending from the central backbone. The conserved motifs in the secondary structure elements that are essential for IRES activity are likely to facilitate RNA-RNA or RNA-protein interactions required to maintain a higher order structure needed for proper recognition of the IRES element by the translational machinery. The picornavirus IRES elements represent relatively large complex domains composed of multiple subdomains that require correct spatial orientation and interactions to carry out IRES function. Efficient translation of capped mRNAs in eukaryotic cells involves a synergistic dependence on the 5--terminal cap structure and the 3--terminal poly(A) tail.