Identification of a new class of picornavirus internal ribosome entry site.

The picornaviruses are a family of positive sense, single-stranded RNA viruses that initiate translation of their genome using an internal ribosome entry site (IRES), which is typically around 450 nt in length. Currently, three classes of picornavirus IRES element exist, based on structural similarities and biological properties. A novel picornavirus IRES element was identified within the 5' untranslated regions of porcine teschovirus-1 (PTV-1), porcine enterovirus-8 (PEV-8) and simian virus-2 (SV2). These related elements are considerably shorter than other picornavirus IRES elements and surprisingly formation of 48S pre-initiation complexes on the PTV-1 IRES is achieved in the absence of the translation initiation complex eIF4F. Indeed, toeprinting analysis with the PTV-1 IRES indicated that it is able to directly interact with the 40S ribosomal subunit. These properties are unusual for picornavirus IRES elements but are remarkably similar to those of the Flaviviridae IRES elements. Secondary structure models for the PTV-1, PEV-8 and SV2 IRES elements have been derived and key structural features verified through mutagenesis and functional assays. These studies have suggested that a fourth type of IRES element exists within the Picornaviridae, which is structurally and functionally related to the hepatitis C virus (HCV) and pestivirus IRES elements. Picornavirus IRES elements require accessory proteins for their activity. The availability of these proteins may provide insight into the tissue tropism of the viruses. To assess the binding of accessory proteins to the FMDV IRES in cells, a system was designed that could allow the capture of RNA transcripts containing the FMDV IRES and attached proteins from cells. This system made use of a specific protein-RNA interaction between the iron response protein and iron response element, which was placed at the 3' end of the FMDV IRES. Functional assays indicated that key features of this system were operational as expected, but currently no proteins have been identified as FMDV IRES binding proteins using this system.