Mechanism of ribosome recruitment by hepatitis CIRES RNA

Many viruses and certain cellular mRNAs initiate protein synthesis from a h ighly structured RNA sequence in the 5' untranslated region, called the int ernal ribosome entry site (IRES). In hepatitis C virus (HCV), the IRES RNA functionally replaces several large initiation factor proteins by directly recruiting the 43S particle. Using quantitative binding assays, modificatio n interference of binding, and chemical and enzymatic footprinting experime nts, we show that three independently folded tertiary structural domains in the IRES RNA make intimate contacts to two purified components of the 43S particle: the 40S ribosomal subunit and eukaryotic initiation factor 3 (eIF 3). We measure the affinity and demonstrate the specificity of these intera ctions for the first time and show that the high affinity interaction of IR ES RNA with the 40S subunit drives formation of the IRES RNA.40S.eIF3 terna ry complex. Thus, the HCV IRES RNA recruits 43S particles in a mode distinc t from both eukaryotic cap-dependent and prokaryotic ribosome recruitment s trategies, and is architecturally and functionally unique from other large folded RNAs that have been characterized to date.