Mismatches in the Influenza A Virus RNA Panhandle Prevent Retinoic Acid-Inducible Gene I (RIG-I) Sensing by Impairing RNA/RIG-I Complex Formation

Abstract

Influenza virus RNA (vRNA) promoter panhandle structures are believed to be sensed by retinoic acid-inducible gene I (RIG-I). The occurrence of mismatches in this double-stranded RNA structure raises questions about their effect on innate sensing. Our results suggest that mismatches in vRNA promoters decrease binding to RIG-I in vivo, affecting RNA/RIG-I complex formation and preventing RIG-I activation. These results can be inferred to apply to other viruses and suggest that mismatches may represent a general viral strategy to escape RIG-I sensing. Detection of viral infections at the cellular level is crucial for the establishment of an innate immune response. Accordingly, viruses have developed strategies to circumvent this response. They can actively block the pathways involved or prevent the formation of viral molecular patterns sensed by specific cellular receptors, such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5, that recognize viral RNA patterns. For RIG-I, this pattern consists of double-stranded RNA (dsRNA) structures of various lengths, with 5= tri-or diphosphate (5= ppp or 5= pp, respectively) base-paired ribonucleotides (1, 2). For segmented negative-strand RNA viruses, dsRNA structures are found in panhandles formed by base pairing of conserved and complementary 5= and 3= genome ends, which activate RIG-I

Antiviral activity of double‐stranded RNA‐binding protein PACT against influenza A virus mediated via suppression of viral RNA polymerase

“…As a multifunctional dsRNA-binding protein, PACT has the potential to exert direct antiviral activity by targeting vRNA or viral RNP, as in the case of the IAV polymerase. This resembles RIG-I, which suppresses IAV and hepatitis B virus replication by not only activating IFN response, but also targeting the panhandle on the IAV nucleocapsid (54,(60)(61)(62) and the e element in the hepatitis B virus pregenomic RNA (63). Of interest, RIG-I and MDA5 are also thought to perform an IFN-independent antiviral effector function via an ATP-dependent displacement of viral proteins from vRNA (64,65).…”

Standing on three legs: antiviral activities of RIG-I against influenza viruses

“…Although the panhandle is not a perfect dsRNA, it was shown to act as RIG-I agonist [13,14 ]. However, the mismatches in the genome decrease RIG-I efficiency, indicating a viral escape mechanism [15]. In addition, U/A-rich ssRNA sequences in the 3 0 untranslated region (UTR) of the genome can activate RIG-I in a 5 0 ppp-independent manner [16].…”

Embracing proteins: structural themes in aptamer–protein complexes

“…RIG-I and MDA-5 can bind short and long dsRNA, with shorter dsRNA acting as better activators for RIG-I [22 ,39] and longer RNA are better activators of MDA-5 [9,40,41 ,42 ]. Additional studies point to the stability of the dsRNA stem region suggesting stable double stranded RNA is necessary for persistent signaling during viral infections [43,44], but not sufficient as a dumbbell RNA lacking blunt ends can bind RIG-I yet display attenuated signaling [22 ]. A recent study used mass spectrometry to assess how RIG-I domains change conformation upon RNA ligand and ATP binding [45 ].…”