Extensive editing of cellular and viral double-stranded RNA structures accounts for innate immunity suppression and the proviral activity of ADAR1 p150

摘要

The interferon (IFN)-mediated innate immune response is the first line of defense against viruses. However, an IFN-stimulated gene, the adenosine deaminase acting on RNA 1 (ADAR1), favors the replication of several viruses. ADAR1 binds double-stranded RNA and converts adenosine to inosine by deamination. This form of editing makes duplex RNA unstable, thereby preventing IFN induction. To better understand how ADAR1 works at the cellular level, we generated cell lines that express exclusively either the IFN-inducible, cytoplasmic isoform ADAR1 ~(p150), the constitutively expressed nuclear isoform ADAR1 ~(p110), or no isoform. By comparing the transcriptome of these cell lines, we identified more than 150 polymerase II transcripts that are extensively edited, and we attributed most editing events to ADAR1 ~(p150). Editing is focused on inverted transposable elements, located mainly within introns and untranslated regions, and predicted to form duplex RNA structures. Editing of these elements occurs also in primary human samples, and there is evidence for cross-species evolutionary conservation of editing patterns in primates and, to a lesser extent, in rodents. Whereas ADAR1 ~(p150) rarely edits tightly encapsidated standard measles virus (MeV) genomes, it efficiently edits genomes with inverted repeats accidentally generated by a mutant MeV. We also show that immune activation occurs in fully ADAR1-deficient (ADAR1 ~(KO)) cells, restricting virus growth, and that complementation of these cells with ADAR1 ~(p150) rescues virus growth and suppresses innate immunity activation. Finally, by knocking out either protein kinase R (PKR) or mitochondrial antiviral signaling protein (MAVS)—another protein controlling the response to duplex RNA—in ADAR1 ~(KO) cells, we show that PKR activation elicits a stronger antiviral response. Thus, ADAR1 prevents innate immunity activation by cellular transcripts that include extensive duplex RNA structures. The trade-off is that viruses take advantage of ADAR1 to elude innate immunity control. Author summary The innate immune response is a double-edged sword. It must protect the host from pathogens while avoiding accidental recognition of “self” molecular patterns, which can lead to autoimmune reactions. Double-stranded RNA is among the most potent inducers of cellular stress and interferon responses. We characterize here a mechanism that prevents autoimmune activation and show that an RNA virus, measles virus, can exploit it to elude innate immune responses. This mechanism relies on the enzyme adenosine deaminase acting on RNA 1 (ADAR1), which converts adenosine residues within duplex RNA structures to inosine. We identify duplex RNA structures in the 3′ untranslated regions of over 150 cellular transcripts and show that they are heavily edited in ADAR1-expressing cells. We detect the same type of editing in duplex RNA–forming defective genomes accidentally generated by measles virus. Loss of RNA editing causes strong innate immune responses and is detrimental to viral replication. Thus, by keeping the amount of duplex RNA in cells below an immune activation threshold, ADAR1 prevents autoimmunity while also favoring pathogens.