N6-methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I

Abstract

Internal N6-methyladenosine (m6A) modification of RNA is one of the most abundant modifications in eukaryotic cells as well as in viruses. However, the biological role(s) of RNA m6A in virus-host interaction remains elusive. Using human metapneumovirus (hMPV), a medically important non-segmented negative-sense RNA virus as a model, we demonstrate that m6A serves as a molecular marker for innate immune discrimination of self from nonself RNAs. We show that hMPV RNAs are m6A methylated and that viral m6A methylation promotes hMPV replication and gene expression. Inactivating these m6A sites with synonymous mutations resulted in m6A deficient recombinant hMPVs that induced significantly higher expression of type I interferon (IFN) that restricted viral replication. Notably, the induction of type I IFN by m6A-deficient rhMPVs and virion RNA was dependent on the cytoplasmic RNA sensor RIG-I, not MDA5. Using RIG-I pull down and RIG-I limited digestion assay, we mechanistically demonstrated that m6A-deficient virion RNA exposed to cytoplasm has much high accessibility to the binding of RIG-I, which allows RIG-I’s translocation along the RNA strand and subsequential conformational change, oligomerization, activation of IFN signaling cascade, and then even higher RIG-I expression during anti-virus status. Furthermore, m6A-deficient rhMPVs triggered higher type I IFN in vivo and were significantly attenuated in the lower respiratory tract yet retained high immunogenicity in cotton rats. Collectively, our results highlight that (i) virus acquires m6A in their RNAs as a means of mimicking cellular RNA to avoid the detection by innate immunity; and (ii) viral m6A RNA can serve as a novel target to attenuate hMPV for vaccine purposes.

m6 RNA methylation: an emerging common target in the immune response to cancer and severe acute respiratory syndrome-coronavirus-2 infection

“…The study also reported that the SARS-CoV-2 genome contains m 6 A modifications enriched in the 3' region of RNA and that RIG-I binds to SARS-CoV-2 viral RNAs and is inhibited by m 6 A RNA modifications [30]. In patients with severe coronavirus disease 2019 (COVID-19), METTL3 is reduced and inflammatory genes are induced [30], which agrees with the findings in other viruses [29]. It has been shown that host m 6 A components interact with viral proteins to modulate SARS-CoV-2 replication [31].…”

“…Importantly, research on RNA modification has revealed that viruses acquire m 6 A in their RNA as a means of mimicking cellular RNA to avoid detection by innate immunity. This finding implies that the m 6 A modification enables viral RNA to evade RNA sensor RIG-I [29]. A study has suggested that viral m 6 A RNA modification can be used as a vaccine target to attenuate viral infections, such as those caused by human metapneumovirus [29].…”

“…This finding implies that the m 6 A modification enables viral RNA to evade RNA sensor RIG-I [29]. A study has suggested that viral m 6 A RNA modification can be used as a vaccine target to attenuate viral infections, such as those caused by human metapneumovirus [29]. Furthermore, a recent investigation has observed that METTL3 regulates viral m 6 A RNA modification and host cell innate immune responses during SARS-CoV-2 infection [30].…”

RBP–RNA interactions in the control of autoimmunity and autoinflammation

“…44 Given the role of 2′-O-methylation and m 6 A in marking RNA as self, targeting these modifications may serve as potential strategy to enhance mRNA vaccine efficacy. 45,46 Inflammasomes are large protein platforms triggered by various internal or external stimuli via NLR members, to promote caspase-1-dependent cleavage and maturation of inflammatory cytokines IL-1β and IL-18, as well as to induce gasdermin D-induced pyroptotic cell death. 47 Overactivation of inflammasome is closely related to a variety of inflammatory and autoimmune diseases, such as diabetes, 48 Alzheimer's disease 49 and atherosclerosis.…”