Targeting the viral Achilles' heel: recognition of 5'-triphosphate RNA in innate anti-viral defence

Abstract

Some RNA virus genomes bear 5'-triphosphates, which can be recognized in the cytoplasm of infected cells by host proteins that mediate anti-viral immunity. Both the innate sensor RIG-I and the interferon-induced IFIT proteins bind to 5'-triphosphate viral RNAs. RIG-I signals for induction of interferons during RNA virus infection while IFITs sequester viral RNAs to exert an anti-viral effect. Notably, the structures of these proteins reveal both similarities and differences, which are suggestive of independent evolution towards ligand binding. 5'-triphosphates, which are absent from most RNAs in the cytosol of uninfected cells, are thus a marker of virus infection that is targeted by the innate immune system for both induction and execution of the anti-viral response.

Figure 1

Induction and effects of IFN during virus infection. Virus infection delivers nucleic acids into the cytosol or endosomal compartment. Innate nucleic acid sensors including TLRs, RLRs and the poorly characterized cytosolic DNA receptors (CDRs) detect these DNAs and RNAs and then trigger a signal transduction cascade that induces IFN. Adaptor proteins, kinases and transcription factors mediate signalling. Note that additional proteins have been implicated and that the figure only shows some selected key components. IFN signals via IFNAR resulting in the induction of ISGs that have direct and indirect anti-viral effects.

Figure 2

Model of RIG-I activation and signalling. (a) The most potent RIG-I agonists are characterized by a 5PPP moiety and by base-pairing to a complementary stretch of RNA. This base-pairing can either be provided by a second molecule of RNA or by complementarity of the 5′-end and 3′-end of the 5PPP bearing RNA. As such, RIG-I agonists can be double-stranded (ds) and single-stranded (ss) RNAs. (b) The domain architecture of RIG-I and MAVS is shown schematically. CARD, caspase recruitment domain; CTD, C-terminal domain; TM, transmembrane domain; Hel-1, Hel-2i and Hel-2, subdomains of the RIG-I helicase domain; K63-ub, K63-linked polyubiquitin. The RIG-I pincer domain (also called bridging helices) is shown as a red line connecting the helicase domain and CTD. (c) In the autorepressed conformation, the CTD is flexibly connected to the helicase domain and this allows for binding of 5PPP groups of viral RNA genomes to the CTD. (d) Upon RNA binding to the CTD, the helicase domain makes contacts with the RNA and RIG-I undergoes a conformational change that exposes the CARDs. (e) RIG-I is then ubiquitylated or binds to free ubiquitin chains. (f and g) This facilitates RIG-I tetramerization and interaction with MAVS. Upon initial oligomerization of MAVS, a prion-like mechanism recruits additional MAVS molecules into the complex (red arrow) and signal transduction is initiated via TBK1 activation.

Figure 3

RIG-I and IFITs recognize 5PPP RNA. (a) Several RNA viruses generate 5PPP RNAs, such as viral genomic RNAs. These RNAs are recognized by RIG-I that induces IFN production (green). IFNs then induce the expression of IFITs that bind and sequester 5PPP viral RNAs, preventing their translation, replication and/or packaging (red). Note that IFITs can also be induced directly by RIG-I/MAVS (dashed arrow) [43]. (b) The top row shows overall structures of RIG-I and IFIT5 in complex with 5PPP RNA; the bottom row zooms in on the 5PPP binding sites. The RIG-I structure is the RIG-I ΔCARD plus 5PPP RNA hairpin complex described in [33^•] (PDB code 4AY2). IFIT5 is shown in complex with 5PPP-oligo-C [8^••] (PDB code 4HOR). Amino acid residues contacting the 5PPP are shown in stick format and dashed lines indicate hydrogen-bonding interactions.