Domain II of the HCV IRES is a potent activator of PKR

Abstract

The protein kinase PKR is an essential component of the human innate immune response. In the presence of certain RNAs, PKR is autophosphorylated, which enables it to phosphorylate its substrate, eIF2α, leading to shut down of cellular translation. Activators of PKR are typically long double‐stranded RNAs (≥33 bp) present during viral infection. Recent studies have indicated that the internal ribosome entry site (IRES) in the 5’‐UTR of hepatitis C virus (HCV) RNA can also activate PKR1. The HCV IRES has a complex secondary structure consisting of four distinct domains. While it has been shown that domains III and IV of the IRES activate1, we report that Domain II can also potently activate PKR independent of the other IRES domains. We present analysis of the structural elements of this domain and find that while the double‐stranded helical regions of the RNA are important for activation, the loop regions of Domain II are also important. PKR activation by Domain II of the IRES alone has implications for the cell's immune response when the other domains of the IRES may be inaccessible during various stages of the HCV life cycle. Supported by NIH GM 58709