RNA 5ʹ terminal nucleotide determines the strength of the RIG-I/IFN signaling pathway

Abstract

AbstractThe interferon (IFN) response is crucial for antiviral activity, but its overstimulation can lead to a wide range of autoimmune disorders. The cytoplasmic pattern recognition receptor RIG-I detects viral RNAs and endogenous polymerase III transcripts carrying a 5′-triphosphate (5′- ppp) or 5′-diphosphate (5′-pp) moiety, triggering an IFN immune response. While many viral RNAs initiate with 5′-ppp-adenosine (5′-pppA) and most endogenous Pol III transcripts in higher eukaryotes start with 5′-ppp-guanosine (5′-pppG), no apparent reason for this bias has been identified so far. Here we demonstrate that RNAs initiating with 5′-pppA trigger a much stronger RIG-I/IFN response than those starting with 5′-pppG. The structures of the matching RNA pairs have been confirmed to be similar, suggesting that functional differences in RIG-I/IFN pathway stimulation cannot be primarily explained by an altered conformation. We show that several GTP-binding proteins interact with 5′-pppG RNAs creating a steric hindrance and protecting these RNAs from activating RIG-I. Our findings suggest that 5′-pppG RNAs may allow some RNA viruses and Pol III transcripts to evade detection by cellular immune sensors. These results provide a new insight into the mechanism of sequence-dependent RIG-I/IFN pathway activation and have significant implications for understanding the antiviral response to RNA viruses and the contribution of Pol III-derived RNAs to autoimmune disorders.