RIG-I-like receptors: their regulation and roles in RNA sensing

Abstract

Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are key sensors of virus infection, mediating the transcriptional induction of type I interferons and other genes that collectively establish an antiviral host response. Recent studies have revealed that both viral and host-derived RNAs can trigger RLR activation; this can lead to an effective antiviral response but also immunopathology if RLR activities are uncontrolled. In this Review, we discuss recent advances in our understanding of the types of RNA sensed by RLRs in the contexts of viral infection, malignancies and autoimmune diseases. We further describe how the activity of RLRs is controlled by host regulatory mechanisms, including RLR-interacting proteins, post-translational modifications and non-coding RNAs. Finally, we discuss key outstanding questions in the RLR field, including how our knowledge of RLR biology could be translated into new therapeutics.

Fig. 1. The type I interferon system.

Nucleic acid sensors of the innate immune system recognize unusual DNA and RNA molecules, for example, viral genomes. This results in the triggering of an intracellular signalling cascade that transcriptionally induces the genes encoding type I interferons, which are subsequently secreted. Type I interferons act in an autocrine (not shown) and paracrine manner by binding to their receptor, interferon-α/β receptor (IFNAR), which activates the Janus kinases (JAKs). These in turn activate the transcription factors signal transducer and activator of transcription 1 (STAT1) and STAT2, leading to expression of interferon-stimulated genes (ISGs). Several ISGs have direct antiviral effects. Type I interferons and ISGs also play important roles in bacterial infections and cancer; these effects can be both beneficial and detrimental, depending on the setting. Finally, production of type I interferons and ISGs over extended periods of time can lead to autoinflammatory and autoimmune diseases.

Fig. 2. RIG-I-like receptors.

a | Domain architecture of retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) and mitochondrial antiviral-signalling protein (MAVS). The three members of the RLR family have a central helicase domain and form a subfamily of SF2 helicases. An additional RNA-binding fold, called the carboxy-terminal domain (CTD), is also found in all RLRs. RIG-I and melanoma differentiation-associated protein 5 (MDA5) contain two caspase activation and recruitment domains (CARDs) in tandem orientation at their N termini. The signalling adaptor protein MAVS also has a CARD as well as a C-terminal transmembrane domain (TM). b | RLR signalling pathway. RIG-I and MDA5 are activated by immunostimulatory RNA, for example, viral RNAs. They then undergo conformational changes that expose and multimerize their CARDs (not shown for simplicity), which allows homotypic CARD–CARD interactions with MAVS. MAVS is anchored with its TM into mitochondria, mitochondrial-associated membranes (MAMs) and peroxisomes, and relays the signal to TANK-binding kinase 1 (TBK1) and IκB kinase-ε (IKKε). These in turn activate interferon regulatory factor 3 (IRF3) and IRF7, which together with the transcription factor nuclear factor-κB (NF-κB) induce the expression of type I interferons and other genes. c | RIG-I is shown in its active conformation, bound to an immunostimulatory RNA. The molecular features of RIG-I-stimulatory RNAs are also illustrated; please see text for details. B, nucleobase; IFNα/β, interferon-α/β; LGP2, laboratory of genetics and physiology 2; P, phosphate; PP, diphosphate; PPP, triphosphate; R, ribose.

Fig. 3. Post-translational modifications of RIG-I and MDA5 and responsible enzymes.

RIG-I (retinoic acid-inducible gene I) and MDA5 (melanoma differentiation-associated protein 5) are regulated by acetylation, deamidation, phosphorylation, SUMOylation, modification with FAT10 and several types of polyubiquitylation, in particular K63-linked and K48-linked polyubiquitin-linkage types (illustrated in green and red, respectively). Activating regulatory post-translational modifications (PTMs) are illustrated on the left, and those that inhibit RIG-I-like receptor (RLR) activation are depicted on the right, as well as the respective enzymes that synthesize, or remove, these PTMs. Enzymes that ultimately lead to RLR activation are shown in green; those that lead to RLR signal inhibition are shown in red. Furthermore, key modified amino acid residues in human RIG-I and MDA5 are illustrated, if known. Ac, acetylation; CARD, caspase activation and recruitment domain; CKII, casein kinase II; CTD, carboxy-terminal domain; CYLD, CYLD lysine 63 deubiquitinase; HDAC6, histone deacetylase 6; MEX3C, Mex-3 RNA binding family member C; P, phosphorylation; PFAS, phosphoribosyl-formylglycinamide synthase; PKC, protein kinase C; PP1, protein phosphatase 1; RIOK3, RIO kinase 3; RNF, ring finger protein; SENP2, sentrin/SUMO-specific protease 2; Su, SUMOylation; TRIM, tripartite motif; Ub, ubiquitin; USP, ubiquitin specific peptidase.

Fig. 4. Regulation of RIG-I and MDA5 activity by interacting proteins and non-coding RNAs.

The activities of retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5) are regulated by interacting proteins that modulate their RNA-binding ability, oligomerization, tripartite motif-containing 25 (TRIM25)-mediated K63-linked ubiquitylation or subcellular localization. Furthermore, several cellular long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) regulate RIG-I-mediated and MDA5-mediated innate immune signalling. Conceptually, these RNAs promote or diminish RIG-I-like receptor (RLR) signalling by regulating the gene expression of these sensors or regulatory proteins in the RLR pathway, or they modulate the activity of RLRs or TRIM25 through a direct physical interaction. CARD, caspase activation and recruitment domain; CTD, carboxy-terminal domain; CYLD, CYLD lysine 63 deubiquitinase; DDX60, DExD/H-box helicase 60; DHX15, DEAH-box helicase 15; dsRNA, double-stranded RNA; IKKε, IκB kinase-ε; IRF, interferon regulatory factor; ISG, interferon-stimulated gene; K48-(Ub)n, K48-linked ubiquitylation; K63-(Ub)n, K63-linked ubiquitylation; LGP2, laboratory of genetics and physiology 2; lncRNA, long non-coding RNA; MAVS, mitochondrial antiviral-signalling protein; NDR2, nuclear dbf2-related 2; NLRP12, NLR family pyrin domain-containing 12; OASL, oligoadenylate synthetase-like; P, phosphorylation; (P)PP, (tri)diphosphate; RNF, ring finger protein; SFPQ, splicing factor proline and glutamine rich; TBK1, TANK-binding kinase 1; Ub, ubiquitin; ZCCHC3, zinc finger CCHC-type-containing 3.