Structural Basis of RNA Recognition and Activation by Innate Immune Receptor RIG-I

By F. Jiang, Anand Ramanathan, Matthew T. Miller, G. Tang, M. Gale, Smita S. Patel, J. Marcotrigiano. 2011

440 citations recorded by the source corpus.

Retinoic-acid-inducible gene-I (RIG-I; also known as DDX58) is a cytoplasmic pathogen recognition receptor that recognizes pathogen-associated molecular pattern (PAMP) motifs to differentiate between viral and cellular RNAs. RIG-I is activated by blunt-ended double-stranded (ds)RNA with or without a 5′-triphosphate (ppp), by single-stranded RNA marked by a 5′-ppp and by polyuridine sequences. Upon binding to such PAMP motifs, RIG-I initiates a signalling cascade that induces innate immune defences and inflammatory cytokines to establish an antiviral state. The RIG-I pathway is highly regulated and aberrant signalling leads to apoptosis, altered cell differentiation, inflammation, autoimmune diseases and cancer. The helicase and repressor domains (RD) of RIG-I recognize dsRNA and 5′-ppp RNA to activate the two amino-terminal caspase recruitment domains (CARDs) for signalling. Here, to understand the synergy between the helicase and the RD for RNA binding, and the contribution of ATP hydrolysis to RIG-I activation, we determined the structure of human RIG-I helicase-RD in complex with dsRNA and an ATP analogue. The helicase-RD organizes into a ring around dsRNA, capping one end, while contacting both strands using previously uncharacterized motifs to recognize dsRNA. Small-angle X-ray scattering, limited proteolysis and differential scanning fluorimetry indicate that RIG-I is in an extended and flexible conformation that compacts upon binding RNA. These results provide a detailed view of the role of helicase in dsRNA recognition, the synergy between the RD and the helicase for RNA binding and the organization of full-length RIG-I bound to dsRNA, and provide evidence of a conformational change upon RNA binding. The RIG-I helicase-RD structure is consistent with dsRNA translocation without unwinding and cooperative binding to RNA. The structure yields unprecedented insight into innate immunity and has a broader impact on other areas of biology, including RNA interference and DNA repair, which utilize homologous helicase domains within DICER and FANCM.

Subfields: Immunology, Molecular Biology

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Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, methodology): “…reveal a familiar ring-like structure in which the domains of RIG-I are wrapped around dsRNA and the blunt duplex terminus is capped by stacking and hydrogen-bonding networks with the protein (Figures 1, S6, and S7) (Jiang et al., 2011; Kohlway et al., 2013; Luo et al., 2011; Luo et al., 2012).”
A structure-based model of RIG-I activation. (2012, methodology): “This is consistent with the 24-fold weaker binding of dsRNA to full-length RIG-I than to RIG-IDCARDs (Jiang et al. 2011).”
RIG-I uses an ATPase-powered translocation-throttling mechanism for kinetic proofreading of RNAs and oligomerization (2018, background): “However, a key mechanism for limiting non-specific RNA binding is a structurally encoded autoinhibition mechanism (Jiang et al., 2011; Kowalinski et al., 2011; Lu et al., 2011; Luo et al., 2011; Wang et al., 2010).”
Structural basis for m7G recognition and 2′-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I (2016, neutral): “The proteins were expressed and purified from recombinant Rosetta DE3 Escherichia coli cell line, as described (3).”
ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA (2015, methodology): “In this conformation, the 2CARD module is sterically displaced from its auto-inhibited state (Jiang et al., 2011; Kowalinski et al., 2011; Luo et al., 2011) and can be K63-linked poly-ubiquitinated (Gack et al., 2007).”
How RNA binding proteins interact with RNA: molecules and mechanisms (2020, background): “VdW interactions generally share the same preferences for amino acids that are observed for hydrogen bonds (Ellis et al., 2007; Han and Nepal, 2007; Jones et al., 2001; Treger and Westhof, 2001).”
Defining the functional determinants for RNA surveillance by RIG-I (2013, positive): “Furthermore, the RIG-I helicase domain exhibits weak, micromolar affinity for blunt-ended duplex RNA that is terminated either by a 5 0 triphosphate or 5 0 hydroxyl [19,21], suggesting that internal duplex stem binding has a lesser role in RIG-I stimulation.”
Kinetic discrimination of self/non-self RNA by the ATPase activity of RIG-I and MDA5 (2015, positive): “Upon viral infection, RIG-I CTD selectively traps non-self dsRNA ectopically present in the cytosol with high affinity (nM range [31, 32, 60]) (Fig.”
Pattern recognition receptors in health and diseases (2021, background): “The Nterminus of the RIG-I protein is composed of two caspase activation and recruitment domains in series,(109) which are responsible for transmitting signals downstream.(110) The Cterminus is composed of the repressor domain (RD) and the Cterminal domain (CTD), which can regulate its own state.”
Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants (2018, background): “Intriguingly, despite an overall high structural similarity to wtRIG-I D2CARD bound to dsRNA (Jiang et al., 2011), the SMS mutant shows crucial amino acid side chain rearrangements in the active site that stabilize the protein in an activated state but prevent binding and co-crystalization of a nucl”
Establishing the role of ATP for the function of the RIG-I innate immune sensor (2015, background): “DOI: 10.7554/eLife.09391 11 of 21 derives from a complex network of specific interactions with the 5′ triphosphate moiety and stacking interactions with the terminal base pair of an RNA duplex (Lu et al., 2010; Jiang et al., 2011; Kowalinski et al., 2011; Luo et al., 2011, 2012b).”