DEAD-box RNA helicase DDX6 modulates hepatitis C virus replication and RNA stability
Text by Cara Pager
Hepatitis C virus (HCV) interfaces with host RNA metabolism pathways at different steps in the infectious cycle. These include the translation machinery required for synthesis of viral proteins, and several host components associated with the microRNA pathways, and localized in RNA granules, that promote replication of the genome and virus assembly.
Virus-host interactions are critical for HCV infection. These are not only limited to protein-protein and protein-RNA interactions but also RNA-RNA interactions. In particular, a liver-specific microRNA miR-122 has been shown to bind the HCV RNA genome at two separate sites. This interaction protects the viral RNA from destruction by cellular RNA-degrading enyzmes, and is thought to help the virus switch between HCV translation and replication. We are fascinated by how these processes are controlled during HCV infection.
Our earlier work showed that HCV subverts different proteins localized in RNA granules. One particular protein DDX6 when depleted dramatically changed the levels of HCV proteins and RNA. DDX6 is a DEAD-box RNA helicase that functions within mRNA decapping and deadenylation, and micro-RNA induced silencing complexes. Because of the important role of both miR-122 and DDX6 during HCV infection, and the mutual connection to regulation of cellular mRNAs, in this study we wanted to determine whether the functions of miR-122 and DDX6 were linked.
Depleting DDX6 did not appear to hamper the translation of the viral genome, but the decreased amount of DDX6 did reduce the amount of newly replicated viral RNA. Similar to sequestering miR-122, we found that the stability of HCV RNA stability was diminished when DDX6 levels were decreased. We were however very surprised, when we observed that DDX6 affected the interaction of miR-122 with the HCV RNA. In particular our data showed that DDX6 regulated the association of miR-122 binding site 2, but not site 1. This was an unexpected result that suggested that the interactions between host and viral components are more complicated and perhaps also more specific then we had previously considered. Overall, our findings lead us to conclude that DDX6 plays a role in mediating the interaction between miR-122 and HCV RNA, and that when this interaction was disrupted, the HCV RNA was destroyed. We propose that the HCV 5’ untranslated region (UTR) may function as a riboswitch that is flipped from translation to replication by DDX6 directing the specific binding of miR-122 to the second binding site in the 5’ UTR.
A model for the transition from translation to replication during HCV infection
Once the HCV virion has entered the cell its positive-sense RNA genome is released and immediately recruits host components including ribosomes to translate the viral genome (40S complex in light green and 60S complex is in dark green). Poly(RC) binding protein 2 (PCBP2) binds to sites within 5’ and 3’ untranslated regions (UTRs), and has been shown to facilitate HCV RNA circularization, translation, and replication. In this model we propose that the transition from active translation of the viral genome to replication requires miR-122 and at least some components of the microRNA induced silencing complex (miRISC) including argonaut 2 (Ago2) and the DEAD-box RNA helicase (DDX6). The ability of DDX6 to bind the viral RNA may be necessary to displace PCBP2, and help the loading of miR-122-Ago2 complexes, thus helping facilitate the switch from translation to replication of HCV.
Introducing the authors
Pictured are Cara Pager and Jason Biegel, Department of Biological Sciences, The RNA Institute, University at Albany, SUNY.
About the research
Jason M. Biegel, Eric Henderson, Erica M. Cox, Gaston Bonenfant, Rachel Netzband, Samantha Kahn, Rachel Eager, Cara T. Pager
Virology, Volume 507, July 2017, Pages 231–241