MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA

Qin Yu,Yorgo Modis,Alba Herrero del Valle,Rahul Singh

doi:10.1038/s41467-021-27062-5

Qin Yu, Yorgo Modis + Show 2 more

Open Access

https://doi.org/10.1038/s41467-021-27062-5

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Abstract

Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease.

Highlights

Our innate immune responses to viral RNA are vital defenses
Cryogenic electron microscopy structures of MDA5-double-stranded RNA (dsRNA) filaments at different stages of the ATPase cycle—bound to ATP, transition-state analog atomic displacement parameter (ADP)-AlF4, or no nucleotide—showed that ATP hydrolysis by MDA5 is coupled to conformational changes in MDA5-dsRNA filaments[14]
This is consistent with the reported upregulation of type I interferon signaling in a patient harboring the M854K mutation, in the absence of viral infection[28]

Summary

Introduction

Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The M854K mutation inhibits ATPdependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease. DsRNA is recognized in the cytosol by the innate immune receptors RIG-I, MDA5, and LGP2. We proposed the ATPase cycle performs a mechanical proofreading function by testing the interactions with the bound RNA, promoting dissociation of MDA5 from loosely-bound endogenous RΝΑs while allowing it to remain bound to viral RNAs long enough to activate signaling[14]. Mutations that alter the parameters governing MDA5-dsRNA filament dynamics can cause inappropriate activation of the antiviral innate response. MDA5 gain-of-function mutations and ADAR1 loss-of-function can cause PKR-mediated translational shutdown and severe autoinflammatory disorders[19,20,23,24]

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