Internal ribosome entry site-mediated translation in hepatitis C virus replication

Abstract

Although internal ribosome entry results in the cap-independent initiation of translation on a number of different viral and cellular RNAs, the extent to which the responsible IRES elements share a common mechanism of translation initiation remains to be defined. The flaviviral IRES superficially resembles the type 2 picornavirus IRES in that there does not appear to be any scanning of the 40S subunit for the initiation codon (LEMON and HONDA 1997; WIMMER et al. 1993). Nonetheless, there are a number of differences between these IRESs that suggest significantly different mechanisms of translation initiation: (1) The flavivirus IRES is generally only half the length of the picornavirus IRES elements, and it assumes a completely different secondary and tertiary structure. (2) There is no conserved pYxxxAUG element in the flaviviral IRES, in contrast to the picornavirus IRES (EHRENFELD and SEMLER 1995; HELLEN and WIMMER 1995). (3) Despite the evidence described above for cell-specific differences in HCV IRES activity (Lerat et al., in preparation), the flaviviral IRES is remarkably versatile in its ability to drive efficient cap-independent translation in a variety of different cell lines. In contrast, picornaviral IRES elements appear to have much greater cell specificity (BORMAN et al. 1997). (4) The HCV IRES has no strict requirement for PTB, La, or any of the canonical translation initiation factors other than eIF2 and eIF3. This is in stark contrast to picornavirus IRES elements (PESTOVA et al. 1996). (5) Translation initiation occurs in the absence of a canonical AUG codon in some mutated HCV RNAs, a feature that has not been described for either type I or II picornavirus IRES elements. (6) The 40S ribosome subunit is directly positioned on top of the AUG codon after forming a complex with the flaviviral IRES, and there is little or no ability of the 40S subunit to scan for distally located AUG codons. At least with the type I picornavirus IRES elements, there is good evidence for scanning (BELSHAM 1992; HELLEN et al. 1994; PILIPENKO et al. 1994). These differences make it clear that the HCV IRES and related IRES elements in pestiviruses and GBV-B should be classified as a separate group (type III) of virus IRES elements as proposed by LEMON and HONDA (1997). There are also similarities and differences with cellular IRES elements. Unlike picornaviral IRESs, initiation of translation occurs at non-AUG codons in some cellular IRES elements. Cellular IRESs control translation on mRNAs encoding both c-myc and fibroblast growth factor (FGF- 2), and translation is initiated at CUG codons (NANBRU et al. 1997; VAGNER et al. 1995). It is not known how the ribosome selects for the translation initiation site, but the recognition of CUG codons is efficient (VAGNER et al. 1995). Scanning as well as a second IRES element may be involved in the recognition of the four initiation sites in the FGF-2 message (VAGNER et al. 1995). Scanning also appears to be involved in recognition of the initiation sites on eIF4E and c-myc mRNAs as well (GAN et al. 1998; NANBU et al. 1997; VAGNER et al. 1995). Thus, the mechanism of internal entry on HCV RNA may be significantly different from that occurring on these cellular RNAs. A great deal of effort has gone into the analysis of the flaviviral IRES element. However, there is much that remains to be done in order to arrive at a satisfactory understanding of the structure and function of this RNA element. Biophysical approaches to determining the structure of the 5'NTR, including NMR and X-ray crystallography, are very likely to provide a new view of the three dimensional structure of this unique RNA element. The interactions of viral and cellular proteins with the IRES require further investigation, as a better understanding of these interactions is certain to provide valuable insights into the translation mechanism and its regulation. The process of ribosome entry on the viral RNA is an attractive target for the development of effective anti-viral compounds.