DNA Sensing in the Innate Immune Response

Abstract

The innate immune system recognizes conserved pathogen-associated molecular patterns and produces inflammatory cytokines that direct downstream immune responses. The inappropriate localization of DNA within the cell cytosol or endosomal compartments indicates that a cell may either be infected by a DNA virus or bacterium, or has problems with its own nuclear integrity. This DNA is sensed by certain receptors that mediate cytokine production and, in some cases, initiate an inflammatory and lytic form of cell death called pyroptosis. Dysregulation of these DNA-sensing pathways is thought to contribute to autoimmune diseases and the development of cancer. In this review, we will discuss the DNA sensors Toll-like receptor 9 (TLR9), cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING), absent in melanoma 2 (AIM2), and interferon gamma-inducible 16 (IFI16), their ligands, and their physiological significance. We will also examine the less-well-understood DEAH- and DEAD-box helicases DHX9, DHX36, DDX41, and RNA polymerase III, each of which may play an important role in DNA-mediated innate immunity.

Keywords: DNA sensing; autophagy; cGAS; cell death; infection; inflammasome; innate immunity; interferon.

FIGURE 1.

Toll-like receptor 9, a founding dsDNA sensor mediating type I IFN signaling The Toll-like receptor 9 (TLR9) receptor is cleaved inside the endolysosome, where the LRR domain composed of NH₂- (N-term) and COOH-terminal (C-term) ectodomains is required for CpG-DNA binding, receptor oligomerization, and signal transduction. The TIR domain of dimerized TLR9 recruits the MyD88 adaptor protein. This recruitment induces IRAK4/IRAK1/TRAF3/IKKα complex formation, and the LC3-TLR9 interaction serves as an anchor to activate IRF7 and type I IFN expression. A second pathway downstream of TLR9 leads to a MyD88-IRF1 interaction that facilitates the nuclear translocation of IRF1 and expression of IFN-inducible genes. Finally, TLR9 activation with CpG-DNA activates the NF-κB pathway and proinflammatory cytokine release.

FIGURE 2.

cGAS/STING pathway, a major cytosolic dsDNA sensing pathway mediating type I IFN signaling cGAS is localized close to the plasma membrane. The recognition of dsDNA forms a complex with cGAS dimers binding to two dsDNA strands. cGAS-dsDNA binding induces a conformational phase transition for the catalytic synthesis of cGAMP from ATP and GTP. The human cGAS (hcGAS) has K187 and L195 mutations, which necessitate longer dsDNA for activation and cause low levels of cGAMP production in response to dsDNA. cGAMP binds to STING and recruits IKKα and TBK1 to activate IRF3 for type I IFN production. Additionally, after cGAMP binding, STING interacts with LC3 and promotes non-canonical autophagy through an ATG5-dependent mechanism after TBK1 degradation to control viral replication.

FIGURE 3.

AIM2 and IFI16 (or IFI204 in mice), dsDNA sensors mediating inflammasome complex and type I IFN signaling Electrostatic interactions between the AIM2 HIN domain and the dsDNA sugar backbone are essential for keeping AIM2 in a quiescent state. IRF1-dependent GBPs and IRGB10 facilitate the release of bacterial DNA into the cytosol. AIM2 inflammasome sensing of DNA triggers recruitment of the inflammasome adaptor ASC and caspase-1. Caspase-1 directly cleaves pro-IL-1β, pro-IL-18, and gasdermin D. The NH₂-terminal gasdermin D fragment forms pores in the plasma membrane and initiates pyroptosis. IL-1β and IL-18 are released through the gasdermin D pore. HSV-1 and HCMV produce the viral proteins VP22 and pUL83, respectively, which interact with the HIN domain to block AIM2 oligomerization. IFI16 is localized in the nucleus and senses viral dsDNA directly from there. DNA recognition induces IFI16 oligomerization inside the nucleus, and then the oligomer migrates to the cytoplasm to finalize inflammasome complex formation. IFI16 activation in response to viral dsDNA or ionizing radiation mediates type I IFN production after a direct interaction with STING/TBK1/IKKα and IRF3 activation.

FIGURE 4.

RNA helicases, the proteins sensing dsDNA and the cross talk between dsDNA and dsRNA sensing DHX9 binds to CpG-B DNA through its DUF1605 domain and leads to NF-κB pathway activation and proinflammatory cytokine release. DHX36 binds to CpG-A DNA through its DEAH domain, resulting in IRF7 activation and IFN-α release. DDX41 recognizes dsDNA through its DEAD domain and interacts with STING/TBK1 to mediate IRF3 activation and type I IFN expression. DDX41 interacts directly with bacterial c-di-GMP and cGAMP from cGAS to mediate type I IFN signaling after interaction with STING. POL III binds to AT-rich dsDNA or VZV DNA to convert this DNA to 5′-triphosphate dsRNA (5′-ppp-dsRNA). 5′-ppp-dsRNA is recognized by RIG-I and interacts with MAVS to mediate type I IFN production.