RACK1 mediates rewiring of intracellular networks induced by hepatitis C virus infection

Abstract

Hepatitis C virus (HCV) is a positive-strand RNA virus replicating in a membranous replication organelle composed primarily of double-membrane vesicles (DMVs) having morphological resemblance to autophagosomes. To define the mechanism of DMV formation and the possible link to autophagy, we conducted a yeast two-hybrid screening revealing 32 cellular proteins potentially interacting with HCV proteins. Among these was the Receptor for Activated Protein C Kinase 1 (RACK1), a scaffolding protein involved in many cellular processes, including autophagy. Depletion of RACK1 strongly inhibits HCV RNA replication without affecting HCV internal ribosome entry site (IRES) activity. RACK1 is required for the rewiring of subcellular membranous structures and for the induction of autophagy. RACK1 binds to HCV nonstructural protein 5A (NS5A), which induces DMV formation. NS5A interacts with ATG14L in a RACK1 dependent manner, and with the ATG14L-Beclin1-Vps34-Vps15 complex that is required for autophagosome formation. Both RACK1 and ATG14L are required for HCV DMV formation and viral RNA replication. These results indicate that NS5A participates in the formation of the HCV replication organelle through interactions with RACK1 and ATG14L. Author summary All positive-strand RNA viruses replicate their genomes in distinct membrane-associated compartments designated replication organelles. The compartmentalization of viral replication machinery allows the enrichment and coordination of cellular and viral factors required for RNA replication and the evasion from innate host defense systems. Hepatitis C virus (HCV), a prototype member of the Flaviviridae family, rearranges intracellular membranes to construct replication organelles composed primarily of double-membrane vesicles (DMVs) which are morphologically similar to autophagosomes. Nonstructural protein 5A (NS5A), which is essential for HCV replication, induces DMV formation. Here, we report that NS5A triggers DMV formation through interactions with RACK1 and components of the vesicle nucleation complex acting at the early stage of autophagy. These results illustrate how a virus skews cellular machineries to utilize them for its replication by hijacking cellular proteins through protein-protein interactions. This research sheds light on the molecular basis of replication organelle formation by HCV and possibly other viruses employing organelles with DMV morphology.