Understanding the potential of hepatitis C virus internal ribosome entry site domains to modulate translation initiation via their structure and function

Abstract

Translation initiation in the hepatitis C virus (HCV) occurs through a cap-independent mechanism that involves an internal ribosome entry site (IRES) capable of interacting with and utilizing the eukaryotic translational machinery. In this review, we focus on the structural configuration of the different HCV IRES domains and the impact of IRES primary sequence variations on secondary structure conservation and function. In some cases, multiple mutations, even those scattered across different domains, led to restoration of the translational activity of the HCV IRES, although the individual occurrences of these mutations were found to be deleterious. We propose that such observation may be attributed to probable long-range inter- and/or intra-domain functional interactions. The precise functioning of the HCV IRES requires the specific interaction of its domains with ribosomal subunits and a subset of eukaryotic translation initiation factors (eIFs). The structural conformation, sequence preservation and variability, and translational machinery association with the HCV IRES regions are also thoroughly discussed, along with other factors that can affect and influence the formation of translation initiation complexes.

Figure 1

A stepwise demonstration of the hepatitis C virus internal ribosome entry site (HCV IRES) translation initiation pathway. The specified arrangement of the HCV IRES domains and ribosomal subunits along with the particular placement of a subset of canonical eukaryotic translation initiation factors (eIFs) required to assemble the pre-initiation 48S and 80S complexes are depicted. The red arrows indicate eIF2-GTP-independent translation under stress (upon eIF2α phosphorylation), when protein synthesis continues with eIF5B or other reported factors (eIF2A, eIF2D). Mutations in different HCV IRES domains that may inhibit particular stages of translation complex formation are shown under the arrows.

Figure 2

The proposed secondary structure of the hepatitis C virus internal ribosome entry site (HCV IRES),, with three-dimensional structures of domains II-IV resolved by NMR and X-ray crystallography.– The domains of the HCV IRES are labeled. Nucleotides colored in cyan indicate the highly conserved regions of the IRES, whereas nucleotides in red denote mutations in the domains involved in a proposed long-range inter or intra-domain interaction or an unusual translational activity. The colors in the secondary structure correspond to the 3D structure. The PDB entries for the HCV IRES domains are domains II (1P5P), IIIb (1KP7), IIIc (1IDV), IIIabc (1KH6), IIId (1F84), IIIe (1 F85), and IIIef (3T4B).