Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I

Abstract

RIG-I is a cytosolic helicase that senses 5’-ppp-RNA contained in negative strand RNA viruses and triggers innate antiviral immune responses. Calorimetric binding studies establish that the RIG-I C-terminal regulatory domain (CTD) binds to blunt-end double-stranded 5’-ppp-RNA a factor of 17 more tightly than to its single-stranded counterpart. Here we report on the crystal structure of RIG-I CTD domain bound to both blunt-ends of a self-complementary 5’-ppp-dsRNA 12-mer, with interactions involving 5’-pp clearly visible in the complex. The structure, supported by mutation studies, defines how a lysine-rich basic cleft within the RIG-I CTD domain sequesters the observable 5’-pp of the bound RNA, with a stacked Phe capping the terminal base pair. Key intermolecular interactions observed in the crystalline state are retained in the complex of 5’-ppp-dsRNA 24-mer and full-length RIG-I under in vivo conditions, as evaluated from the impact of binding pocket RIG-I mutations and 2’-OCH3 RNA modifications on the interferon response.

Function of HNRNPC in breast cancer cells by controlling the dsRNA‐induced interferon response

“…RIG‐I, but not MDA5, primarily recognizes RNA targets with triphosphorylated 5′ end (5′ppp) (Wang et al 2010; Baum et al 2010; Peisley et al 2012), and recent studies reported that RNA with diphosphorylated 5′ end (5′pp) are substrates of RIG‐I as well (Goubau et al , 2014). Therefore, we have performed enrichment of 5′ppp RNA followed by RNA sequencing to query the dsRNA species identified with J2 dsRNA‐seq and to quantify the percentage of the dsRNAs that have 5′ppp.…”

Toward a crystal-clear view of the viral RNA sensing and response by RIG-I-like receptors

“…1). 28,29 The 5′triphosphate of the RNA establishes strong electrostatic interactions with the conserved positively charged residues of RIG-I. This provides the structural basis for the high affinity and specificity of RIG-I for the duplex RNAs bearing 5′ triphosphates that are generated during viral replication, as opposed to host RNAs generated during normal cellular metabolism ( Fig.…”

Mouse Embryonic Stem Cells Have Underdeveloped Antiviral Mechanisms That Can Be Exploited for the Development of mRNA-Mediated Gene Expression Strategy

“…The length and the 5¢-triphosphate (3p) group of RNA are considered to be the most important factors in eliciting antiviral responses, while the sequence seems to be less critical [35][36][37]. We synthesized a panel of short 3p-ssRNA that have 20, 40, 60, and 80 nt with a random sequence of A, U, C, and G, each of which was detected as a single band with expected size by PAGE analysis (Fig.…”