ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA

Abstract

The cytosolic antiviral innate immune sensor RIG-I distinguishes 5′ tri- or diphosphate containing viral double-stranded (ds) RNA from self-RNA by an incompletely understood mechanism that involves ATP hydrolysis by RIG-I's RNA translocase domain. Recently discovered mutations in ATPase motifs can lead to the multi-system disorder Singleton-Merten Syndrome (SMS) and increased interferon levels, suggesting misregulated signaling by RIG-I. Here we report that SMS mutations phenocopy a mutation that allows ATP binding but prevents hydrolysis. ATPase deficient RIG-I constitutively signals through endogenous RNA and co-purifies with self-RNA even from virus infected cells. Biochemical studies and cryo-electron microscopy identify a 60S ribosomal expansion segment as a dominant self-RNA that is stably bound by ATPase deficient RIG-I. ATP hydrolysis displaces wild-type RIG-I from this self-RNA but not from 5' triphosphate dsRNA. Our results indicate that ATP-hydrolysis prevents recognition of self-RNA and suggest that SMS mutations lead to unintentional signaling through prolonged RNA binding.

DOI: http://dx.doi.org/10.7554/eLife.10859.001

eLife digest

Living cells produce long, strand-like molecules of RNA that carry the instructions needed to make proteins. Viruses also make use of RNA molecules to hijack an infected cell’s protein-production machinery and create new copies of the virus. RNA molecules from viruses have a number of features that distinguish them from a cell’s own RNAs, and human cells contain receptors called RLRs that can start an immune response whenever they detect viral RNAs. All of these receptors break down molecules of ATP, a process that releases useable energy. However, so far it is not understood how this activity helps the receptors to distinguish viral RNA from the cell’s own RNA molecules (called self-RNA).

Recently, some autoimmune diseases (including Singleton-Merten Syndrome) were linked to mutations in the parts of RLRs that allow the receptors to break down ATP. Now, Lässig et al. have studied the effects of specific mutations in an RLR called RIG-I in human cells. The experiments showed that mutations that disrupt RIG-I’s ability to bind to ATP also prevented the receptor from becoming activated. However, mutations linked to Singleton-Merten Syndrome don’t stop ATP from binding but instead slow its breakdown; this effectively locks the receptor in an ATP-bound state. Lässig et al. found that similar mutations in RIG-I caused human cells to trigger a constant immune response against the self-RNAs.

Further experiments then suggested that the breakdown of ATP helps to remove RIG-I that has bound to double-stranded sections of self-RNAs. This activity frees the receptor, making it more able to detect double-stranded viral RNAs and preventing unintentional signaling. Lässig et al. also identified a specific double-stranded section of a human RNA that may be recognized by the mutated version of RIG-I in people with Singleton-Merten Syndrome.

The next steps following on from this work are to extend the analysis to also include other RLRs and further explore the underlying mutations within the three-dimensional structures of the receptors and RNA molecules involved.

DOI: http://dx.doi.org/10.7554/eLife.10859.002