Antiviral DExD/H-box helicase 60 selectively inhibits translation from type II internal ribosome entry sites

During viral infection, competition ensues between viruses and their host cells to control the protein synthesis machinery. In response, certain host defense proteins globally limit mRNA translation. However, this is also detrimental for host protein synthesis. Here we describe an interferon-stimulated helicase, DDX60, that specifically inhibits translation from type II viral internal ribosome entry sites (IRESs). IRESs are RNA structures that enable mRNAs to recruit ribosomes directly, bypassing translation initiation using a 5’ cap. DDX60 was previously observed to inhibit replication of a reporter hepatitis C virus (HCV). We show that DDX60 likely does not inhibit HCV replication, but surprisingly, inhibits the type II IRES used in the reporter HCV genomic RNA. Using firefly luciferase mRNAs translationally driven by different viral IRESs or a 5’ cap analog, we show that DDX60 selectively reduces translation driven by type II IRESs of encephalomyocarditis virus (EMCV) and foot and mouth disease virus (FMDV), but not other IRES types or a 5’ cap analog. Correspondingly, DDX60 reduces EMCV and FMDV (type II IRES) replication, but not poliovirus or bovine enterovirus 1 (type I IRES) replication. Furthermore, replacing the IRES of poliovirus with a type II IRES is sufficient for DDX60 to inhibit poliovirus replication. Finally, we demonstrate that DDX60 specifically reduces polysome binding on type II IRES mRNA, but not 5’ cap-dependent mRNA. Our data demonstrate that the cellular defense factor DDX60 counteracts viral takeover of host translation by blocking ribosome access to type II IRES elements specifically.