Intracellular detection of viral nucleic acids

Abstract

Successful clearance of a microbial infection depends on the concerted action of both the innate and adaptive arms of the immune system. Accurate recognition of an invading pathogen is the first and most crucial step in eliciting effective antimicrobial defense mechanisms. In recent years, remarkable progress has been made towards understanding the molecular details of how the innate immune system recognizes microbial signatures, commonly called pathogen-associated molecular patterns (PAMPs). For viral pathogens, nucleic acids-both viral genomes and viral replication products-represent a major class of PAMPs that trigger antiviral host responses via activation of germline-encoded innate immune receptors. Here we summarize recent advances in intracellular innate sensing mechanisms of viral RNA and DNA.

Figure 1

Detection of cytosolic vRNA by RLRs and other proteins. Viral 5′-triphosphate (5′-ppp)-containing or 5′-diphosphate (5′-pp)-containing short dsRNA as well as poly-U/UC motifs are recognized by RIG-I, whereas MDA5 binds to long dsRNA or non-2′-O-methylated vRNA. The RNA binding and/or signaling activities of RIG-I and MDA5 are negatively and positively regulated by LGP2, respectively. Signaling induced by RIG-I and MDA5 converges on MAVS, which serves as a scaffolding protein to activate the key transcription factors NF-κB, AP-1 and IRF3/7 via several kinases (IKKs, MAPK, TBK1). NF-κB, AP-1 and IRF3/7 then act in concert to induce the gene expression of type-I IFNs and other pro-inflammatory cytokines. PKR and OAS both recognize viral dsRNA. Upon activation, PKR leads to inhibition of cellular translation. Furthermore, PKR activates the inflammasome, resulting in IL-1β and IL-18 processing and release. Upon dsRNA binding, OAS produces 2′–5′ oligoA, which activates RNase L. RNA fragments generated by RNase L can serve as RIG-I ligands, amplifying RIG-I-mediated antiviral signaling. Viral RNA is also sensed (directly or indirectly) by DHX9, DDX3, DDX60, NLRX1 and NOD2, leading to activation of MAVS-dependent signaling. The DDX1–DDX21–DHX36 complex signals downstream via the adaptor protein TRIF (not depicted), leading to TBK1 and IRF activation. In response to RNA virus infection, NLRP3 and inflammasomes are activated, which leads to maturation of IL-1β and IL-18. Solid arrows indicate well-established signaling events. Dashed arrows indicate signaling events that are indirect or that have not yet been fully elucidated.

Figure 2

Proteins involved in the detection of intracellular vDNA. Cytoplasmic vDNA triggers activation of a number of different innate immune receptors. Following vDNA binding, cGAS produces the cyclic dinucleotide cGAMP, which serves as a second messenger leading to the activation of the adaptor protein STING. Activation of STING induces the gene expression of type-I IFNs and other pro-inflammatory cytokines via the TBK1-IRF3 axis. Proteins involved in DNA repair (MRE11 and DNA-PK), DDX/DHX proteins (DHX36, DDX41, DHX9), and DAI have also been reported to sense vDNA and to induce antiviral signaling via STING. AIM2 senses cytoplasmic vDNA and subsequently activates inflammasomes, leading to IL-1β and IL-18 maturation. IFI16 is another cytosolic vDNA sensor that triggers inflammasome activation. In addition, IFI16 induces IFN gene expression via STING. In many cell types, IFI16 also localizes to the nucleus, where it senses herpesviral DNA. RNA Pol III specifically detects poly(dA:dT) DNA and subsequently transcribes it into 5′-triphosphate (5′-ppp)-containing short dsRNA that serves as a PAMP for RIG-I. Solid arrows indicate well-established signaling events. Dashed arrows indicate signaling events that are indirect or that have not yet been fully elucidated.