Discriminating self from non-self in nucleic acid sensing

Abstract

Innate immunity against pathogens relies on an array of immune receptors to detect molecular patterns that are characteristic of the pathogens, including receptors that are specialized in the detection of foreign nucleic acids. In vertebrates, nucleic acid sensing is the dominant antiviral defence pathway. Stimulation of nucleic acid receptors results in antiviral immune responses with the production of type I interferon (IFN), as well as the expression of IFN-stimulated genes, which encode molecules such as cell-autonomous antiviral effector proteins. This Review summarizes the tremendous progress that has been made in understanding how this sophisticated immune sensory system discriminates self from non-self nucleic acids in order to reliably detect pathogenic viruses.

Figure 1. Principles of self versus non-self recognition of nucleic acids.

The detection of foreign nucleic acids is based on their availability, localization and structure. Nucleases rapidly degrade most self nucleic acids before they can be sensed by nucleic acid receptors, and the localization of nucleic acids determines if the potentially immunoactive nucleic acids are accessible for their detectors. The nucleic acid receptors can be divided into two main categories: immune sensing receptors, which include Toll-like receptor 3 (TLR3), TLR7, TLR8, TLR9, retinoic acid inducible gene I (RIG-I), melanoma differentiation associated gene 5 (MDA5), absent in melanoma 2 (AIM2) and cyclic GMP–AMP synthetase (cGAS); and nucleic acid receptors with direct antiviral activity, including double-stranded RNA (dsRNA)-activated protein kinase R (PKR), IFN-induced protein with tetratricopeptide repeats 1 (IFIT1), 2′-5′-oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNase L), and adenosine deaminase acting on RNA 1 (ADAR1). Immune sensing receptors can detect structural features such as dsRNA or 5′-triphosphate RNA, which indicate non-self, and indirectly or directly induce transcription factors that upregulate the expression of antiviral effector proteins, chemokines and cytokines, including type I interferon (IFN), to promote an antiviral immune response. In addition, these immune sensing receptors induce the expression of nucleic acid receptors with direct antiviral activity through the induction of IFN-stimulated genes. Those effector proteins primarily do not induce transcription factors but act directly on the target RNA. Of note, in addition to its primary role as a sensor, RIG-I has direct antiviral activity. ssRNA, single-stranded RNA. PowerPoint slide

Figure 2. RNA-sensing receptors.

Double-stranded RNA (dsRNA) in the endosome is detected by Toll-like receptor 3 (TLR3) and TLR7, whereas single-stranded RNA (ssRNA) is sensed by TLR7 and TLR8. These receptors signal via myeloid differentiation primary response protein 88 (MYD88) and TIR domain-containing adaptor protein inducing IFNβ (TRIF) to induce interferon (IFN)-regulatory factor 3 (IRF3)–IRF7 and type I IFN production and via nuclear factor-κB (NF-κB) to induce pro-interleukin-1β (pro-IL-1β) and the inflammasome component NLRP3. The helicases retinoic acid inducible gene I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) detect dsRNA in the cytosol and signal through mitochondrial antiviral signalling protein (MAVS) to induce type I IFN production and pro-apoptotic signalling via IRF3–IRF7, and to activate the NOD-, LRR- and pyrin domain-containing 3 (NLRP3) inflammasome resulting in IL-1β production. The RNA receptor 2′-5′-oligoadenylate synthetase 1 (OAS1) has direct antiviral activity and degrades RNA via the generation of 2′-5′-oligoadenylates that activate ribonuclease L (RNase L). RNase L generates 5′ OH- and 3′ phosphate-containing RNA fragments that can stimulate RIG-I. The crucial RIG-I-stimulating structure has not been determined to date. The RNA receptors IFN-induced protein with tetratricopeptide repeats 1 (IFIT1) and double- stranded RNA (dsRNA)-activated protein kinase R (PKR) inhibit cap-dependent translation. BAX, BCL-2-associated X protein; BCL-2, B cell lymphoma 2; BIRC3, baculoviral IAP repeat-containing protein 3; IFNAR, interferon-α/β receptor; PRKCE, protein kinase Cε; PUMA, p53-upregulated modulator of apoptosis; TRAIL, TNF-related apoptosis-inducing ligand. PowerPoint slide

Figure 3. Immune sensing of double-stranded RNA.

Double-stranded RNA (dsRNA), which is the prototypic non-self nucleic acid stimulus, is detected by three signalling receptors: Toll-like receptor 3 (TLR3), which is located on the cell membrane and in the endosomal membrane, and retinoic acid inducible gene I (RIG-I) and melanoma differentiation associated gene 5 (MDA5), which are located in the cytosol. Long forms of dsRNA are recognized independently of the structure at the ends (TLR3 recognizes dsRNA >35 bp, and MDA5 recognises dsRNA >300 bp). A short stretch of dsRNA (>19 bp) is sufficient for recognition by RIG-I if a triphosphate or a diphosphate is present at the 5′ end, and if the end is blunt with no overhangs. A 2′-O-methyl group at the first nucleotide (N1) of the 5′ end is part of the cap 1 structure of self RNA that labels it as self, and thus prevents recognition by RIG-I. PowerPoint slide

Figure 4. Immune sensing receptors of DNA.

Toll-like receptor 9 (TLR9) in the endolysosomal compartment detects CpG motif-containing DNA and RNA–DNA hybrids that have not been degraded by nucleases such as DNase I and DNase II. TLR9 signals via myeloid differentiation primary response protein 88 (MYD88), interferon (IFN)-regulatory factor 7 (IRF7) and nuclear factor-κB (NF-κB) to induce type I IFN and the inflammasome-related factors pro-interleukin-1β (pro-IL-1β) and NOD-, LRR- and pyrin domain-containing 3 (NLRP3). In the cytosol, cyclic GMP–AMP synthetase (cGAS), IFNγ-inducible protein 16 (IFI16) and absent in melanoma 2 (AIM2) detect DNA that has not been degraded by nucleases such as 3′ repair exonuclease 1 (TREX1). Knockout models reveal that cGAS signals via stimulator of IFN genes (STING) to stimulate type I IFN production. IFI16, DEAD box protein 41 (DDX41) and cGAS also induce apoptosis via STING, IRF3 and BCL-2-associated X protein (BAX) in response to double-stranded DNA (dsDNA). Polyglutamine binding protein 1 (PQBP1) is a co-receptor of cGAS that recognizes HIV reverse transcripts. AIM2 activation results in the formation of the AIM2 inflammasome, which induces IL-1β maturation and pyroptosis via ASC and caspase 1 (not shown). Recognition of dsDNA in the nucleus by RAD50 activates caspase recruitment domain 9 (CARD9)–BCL-10 to induce NF-κB, which upregulates pro-IL-1β transcription. DNA-sensing receptors implicated in the DNA damage response and nuclear recognition of viral nuclear DNA includes breast cancer type 1 susceptibility protein (BRCA1), IFI16, DNA-dependent serine/threonine protein kinase (DNA-PK) and MRE11, and these molecules also signal via STING. Ribonuclease H (RNase H) degrades DNA–RNA hybrids. ssDNA, single-stranded DNA. PowerPoint slide

Figure 5. Immune sensing of cytoplasmic double-stranded DNA as non-self nucleic acid.

The cytosolic immune receptor cyclic GMP–AMP synthetase (cGAS) detects long double-stranded DNA (dsDNA) or short dsDNA with unpaired open ends containing guanosines, which is present in highly structured single-stranded DNA (ssDNA) of certain viruses, such as retroviruses. Cytosolic DNA is efficiently degraded by 3′ repair exonuclease 1 (TREX1) located in the cytosol. Oxidation of DNA, which occurs in situations of oxidative stress caused by UV radiation or cell stress, leads to oxidation of DNA, the most common of which is 8-hydroxyguanosine (8-OHG). This stabilizes DNA against degradation by TREX1, resulting in an accumulation of DNA in the cytosol. Oxidated DNA is recognized by cGAS, resulting in the formation of the cyclic dinucleotide cGAMP, which activates STING to induce type I interferon (IFN) production. PowerPoint slide