Kinetic discrimination of self/non-self RNA by the ATPase activity of RIG-I and MDA5

By Jade Louber, J. Brunel, E. Uchikawa, Stephen Cusack, D. Gerlier. 2015

56 citations recorded by the source corpus.

The cytoplasmic RIG-like receptors are responsible for the early detection of viruses and other intracellular microbes by activating the innate immune response mediated by type I interferons (IFNs). RIG-I and MDA5 detect virus-specific RNA motifs with short 5′-tri/diphosphorylated, blunt-end double-stranded RNA (dsRNA) and >0.5–2 kb long dsRNA as canonical agonists, respectively. However, in vitro, they can bind to many RNA species, while in cells there is an activation threshold. As SF2 helicase/ATPase family members, ATP hydrolysis is dependent on co-operative RNA and ATP binding. Whereas simultaneous ATP and cognate RNA binding is sufficient to activate RIG-I by releasing autoinhibition of the signaling domains, the physiological role of the ATPase activity of RIG-I and MDA5 remains controversial. A cross-analysis of a rationally designed panel of RNA binding and ATPase mutants and truncated receptors, using type I IFN promoter activation as readout, allows us to refine our understanding of the structure-function relationships of RIG-I and MDA5. RNA activation of RIG-I depends on multiple critical RNA binding sites in its helicase domain as confirmed by functional evidence using novel mutations. We found that RIG-I or MDA5 mutants with low ATP hydrolysis activity exhibit constitutive activity but this was fully reverted when associated with mutations preventing RNA binding to the helicase domain. We propose that the turnover kinetics of the ATPase domain enables the discrimination of self/non-self RNA by both RIG-I and MDA5. Non-cognate, possibly self, RNA binding would lead to fast ATP turnover and RNA disassociation and thus insufficient time for the caspase activation and recruitment domains (CARDs) to promote downstream signaling, whereas tighter cognate RNA binding provides a longer time window for downstream events to be engaged. The exquisite fine-tuning of RIG-I and MDA5 RNA-dependent ATPase activity coupled to CARD release allows a robust IFN response from a minor subset of non-self RNAs within a sea of cellular self RNAs. This avoids the eventuality of deleterious autoimmunity effects as have been recently described to arise from natural gain-of-function alleles of RIG-I and MDA5.

Subfields: Immunology, Molecular Biology

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Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, neutral): “These appear to have a negligible impact on IFN levels unless the concentration of host dsRNAs becomes extraordinarily high or mutations in RIG-I result in long-lived complexes with host dsRNA (L€ assig et al., 2018, 2015; Louber et al., 2015; Manivannan et al., 2020; Yang et al., 2014).”
ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA (2015, background): “DOI: 10.7554/eLife.10859.001”
Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants (2018, background): “Since an intact SF2 ATPase domain of RIG-I is needed so that signaling only occurs when foreign RNA molecules are recognized (Louber et al., 2015; Rawling et al., 2015), we further analyzed the ATP binding and hydrolysis properties of RIG-I C268F in vitro.”
RIG-I uses an ATPase-powered translocation-throttling mechanism for kinetic proofreading of RNAs and oligomerization (2018, background): “Another model proposes that ATP hydrolysis offers this proofreading function (Lassig et al., 2015; Louber et al., 2015).”
RNA binding activates RIG-I by releasing an autorepressed signaling domain (2019, background): “For example, patients with SMS have mutations in RIG-I that block its ATPase activity, preventing dissociation of RIG-I from self-RNA (5, 18, 22, 36).”
Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding (2016, background): “It has been suggested that SMS mutants are defective in proofreading (29), however, the physical basis for this apparent loss of RIG-I specificity and the mechanism of activation by off-target RNAs is not known (30).”