Regulation of signaling mediated by nucleic acid sensors for innate interferon-mediated responses during viral infection

Abstract

Type I and type III interferons are important anti-viral cytokines that are massively induced during viral infection. This dynamic process is regulated by many executors and regulators for efficient eradication of invading viruses and protection from harmful, excessive responses. An array of innate sensors recognizes virus-derived nucleic acids to activate their downstream signaling to evoke cytokine responses including interferons. In particular, a cytoplasmic RNA sensor RIG-I (retinoic acid-inducible gene I) is involved in the detection of multiple types of not only RNA viruses but also DNA viruses. Accumulating findings have revealed that activation of nucleic acid sensors and the related signaling mediators is regulated on the basis of post-translational modification such as ubiquitination, phosphorylation and ADP-ribosylation. In addition, long non-coding RNAs (lncRNAs) have been implicated as a new class of regulators in innate signaling. A comprehensive understanding of the regulatory mechanisms of innate sensor activation and its signaling in host-virus interaction will provide a better therapeutic strategy to efficiently control viral infection and maintain immune homeostasis.

Keywords: RIG-I; interferon; pattern-recognition receptors; signal transduction; virus infection.

Fig. 1.

Nucleic acid sensors inducing type I and type III interferons. During viral infection, virus-derived nucleic acids (RNA and DNA) are mainly targeted by host nucleic acid sensors triggering the gene expression of type I and III interferons to induce anti-viral activities. As RNA sensors, TLR3 and TLR7/TLR8 sense viral RNAs on the endosomal or lysosomal membrane. RIG-I and MDA5 are ubiquitously expressed and recognize viral RNAs in the cytoplasmic space. Other RNA helicases DDX1, DDX21 and DHX36 form an RNA sensor complex in mDCs. The Nod-like receptor (NLR) NOD2 also detects the RSV-derived ssRNA genome to activate the MAVS/IPS-1 pathway. In the cases of DNA sensing, TLR9 detects DNA containing the unmethylated CpG motif. DAI (DLM-1/ZBP1) interacts with dsDNA and activates TBK1 and IRF-3 as a cytoplasmic DNA sensor. Cytoplasmic AT-rich dsDNA (B-DNA) is transcribed by host RNA polymerase III (RNA pol III) into 5′-triphosphate RNA (3pRNA), which becomes a RIG-I ligand. DHX36 and DHX9 intracellularly sense CpG class A and B, respectively, in mDCs. DNA-stimulated DDX41 and the ALR IFI16 interact with their adaptor protein STING. STING itself also serves as a sensor of CDNs such as bacterium-derived c-di-GMP as well as host-derived cGAMP generated by cGAS in response to microbe- and host-derived cytosolic DNAs. cGAS is a critical cytoplasmic sensor for the detection of both microbial and host DNAs. The cGAS–cGAMP–STING pathway is now recognized as a major intracellular dsDNA sensing pathway. DNA-PK, Ku70 and extrachromosomal histone H2B are also reported to function as cytosolic DNA sensors. As for Ku70, only type III interferon is induced. LRRFIP1 functions possibly as a cytosolic nucleic acid sensor that dually detects both RNA and DNA. HMGBs also bind to both double-stranded and single-stranded immunogenic RNAs and function as universal sensors for nucleic acid-mediated innate immune responses during viral infection.

Fig. 2.

Regulatory mechanisms of RIG-I activation and its signaling. (a) Ubiquitination-based regulatory mechanisms. The RING-finger E3 Ub ligase TRIM25 positively mediates the RIG-I pathway by its K63-linked ubiquitination of the N-terminal CARDs of RIG-I. Riplet/RNF135 promotes K63-linked polyubiquitination of the C-terminal region of RIG-I. MEX3C/RNF193 mediates K63-linked polyubiquitination of the CARDs of RIG-I for its activation. Caspase-12 is physically associated with RIG-I and up-regulates TRIM25-mediated ubiquitination of RIG-I, leading to the enhancement of type I interferon responses. Non-covalent binding of K63-Ub_n to the RIG-I CARDs induces its tetramer formation for downstream signal activation. Ube2D3/Ubc5c and Ube2N/Ubc13 were also identified as essential Ub-conjugating enzymes (E2) for RIG-I activation. The Ube2D3/Ubc5c–Riplet pair promotes covalent conjugation of polyubiquitin chains to RIG-I, whereas Ube2N/Ubc13 preferentially facilitates production of unanchored polyubiquitin chains. On the contrary, K48-linked ubiquitination of RIG-I by other E3 Ub ligases, such as c-Cbl/RNF55, RNF122, RNF125, CHIP and TRIM40, negatively regulates anti-viral innate responses. (b) Phosphorylation-based regulatory mechanisms. DAPK1 interacts with RIG-I and directly phosphorylates its threonine (T) 667 to impair its RNA ligand binding and abolishes anti-viral signaling. DAPK1 and PKC-α/β phosphorylate the N-terminal serine(S) at position 8 of RIG-I to suppress TRIM25-mediated RIG-I ubiquitination. CK2 is responsible for this regulation, and constitutively phosphorylates T770 and S854 to S855 residues in the RIG-I CTD, which keeps a closed, inactivated conformation. (c) Other RIG-I-interacting factors and lncRNA-mediated regulatory mechanisms. OASL interacts with RIG-I and mimics polyubiquitin through the UBL domains to enhance RIG-I-mediated anti-viral signaling. ISG15-mediated ISGylation of RIG-I reduces the cellular level of active RIG-I and suppresses its downstream anti-viral innate responses. ZAPS, which is a shorter form of PARP-13, functions as a potent stimulator of RIG-I-mediated anti-viral signaling through its interaction with RIG-I to facilitate RIG-I oligomerization and its ATPase activity for the activation of both IRF-3 and NF-κB. PACT directly interacts with the CTD of RIG-I to potentiate the activation of RIG-I. DDX6 interacts with RIG-I and augments type I interferon gene induction.

Fig. 3.

Proposed model of dietary tryptophan-mediated regulation of anti-viral innate responses and immune homeostasis. An endogenous AHR ligand, kynurenine, is synthesized via oxidation of tryptophan, which is catalyzed by TDO and IDO1/2 in human liver and other organs. Constitutive AHR signaling activated by endogenous ligand(s), such as kynurenine, negatively modulates the type I interferon anti-viral response to prevent excessive responses. On the other hand, in the gut, some tryptophan metabolites such as kynurenine, IAld and I3S are generated by the bacterial catabolism of tryptophan, and act as AHR ligands to induce regulatory responses for the maintenance and function of ILC3 cells and the control of Treg and T_h17 differentiation.

Fig. 4.

Viral evasion from RIG-I activation and its signaling. IAV NS1 interacts with TRIM25, and leads to inhibition of TRIM25 multimerization and RIG-I CARD ubiquitination, thereby suppressing RIG-I signal transduction. NS1 also targets Riplet. Viral proteins that have a deubiquitinase activity, including a PLP from SARS-CoV, FMDV Lb^pro (a shorter form of the leader proteinase of FMDV) and a KSHV-derived tegument protein ORF64, directly remove the K63-linked ubiquitination of RIG-I and suppress its activity. HCV-derived NS3/4A protease cleaves MAVS/IPS-1, resulting in a blockade of RLR-signaling. HSV-1 ICP0 inhibits the nuclear accumulation of IRF-3 and enhances the degradation of activated IRF-3. HIV-1 also targets IRF-3 for protein depletion, in which HIV accessory proteins Vif and Vpr mediate the ubiquitination and proteasome-dependent degradation of IRF-3. In addition, HIV-1 PR targets RIG-I through the degradation of RIG-I.