A conserved isoleucine in the binding pocket of RIG-I controls immune tolerance to mitochondrial RNA

Abstract

RIG-I is a cytosolic receptor of viral RNA essential for the immune response to numerous RNA viruses. Accordingly, RIG-I must sensitively detect viral RNA yet tolerate abundant self-RNA species. The basic binding cleft and an aromatic amino acid of the RIG-I C-terminal domain(CTD) mediate high-affinity recognition of 5triphosphorylated and 5base-paired RNA(dsRNA). Here, we found that, while 5unmodified hydroxyl(OH)-dsRNA demonstrated residual activation potential, 5-monophosphate(5p)-termini, present on most cellular RNAs, prevented RIG-I activation. Determination of CTD/dsRNA co-crystal structures and mutant activation studies revealed that the evolutionarily conserved I875 within the CTD sterically inhibits 5p-dsRNA binding. RIG-I(I875A) was activated by both synthetic 5p-dsRNA and endogenous long dsRNA within the polyA-rich fraction of total cellular RNA. RIG-I(I875A) specifically interacted with a long, highly structured, polyA-bearing, non-coding mitochondrial(mt) RNA, and depletion of mtRNA from total RNA abolished its activation. Altogether, our study demonstrates that avoidance of 5p-RNA recognition is crucial to preventing mtRNA-triggered RIG-I-mediated autoinflammation.