Microbial sensing by Toll-like receptors and intracellular nucleic acid sensors

Abstract

Recognition of an invading pathogen is critical to elicit protective responses. Certain microbial structures and molecules, which are crucial for their survival and virulence, are recognized by different families of evolutionarily conserved pattern recognition receptors (PRRs). This recognition initiates a signaling cascade that leads to the transcription of inflammatory cytokines and chemokines to eliminate pathogens and attract immune cells, thereby perpetuating further adaptive immune responses. Considerable research on the molecular mechanisms underlying host-pathogen interactions has resulted in the discovery of multifarious PRRs. In this review, we discuss the recent developments in microbial recognition by Toll-like receptors (TLRs) and intracellular nucleic acid sensors and the signaling pathways initiated by them.

Figure 1.

Signaling pathway of cell surface TLRs. TLR4 recognizes LPS in complex with MD2 to start a signaling cascade by recruiting adaptors MyD88 and TIRAP and forming a complex of IRAK4, 1, and 2, and TRAF6. TRAF6 catalyzes formation of K-63 linked polyubiquitin chains on TRAF6 itself and generates an unconjugated polyubiquitin chain. TRAF6 activates TAK1 complex, which further activates IKK complex and MAP kinases. IKK complex phosphorylates IκB, which undergoes proteosomal degradation to release NF-κB for further translocation to nucleus and subsequent induction of proinflammatory cytokines. MAP kinases phosphorylate Jun kinases (JNK), p38 kinase, extracellular signal regulated kinase 1(ERK1), and ERK2. TLR4 also signals through TRIF-dependent pathways with the help of adaptor TRAM after translocation to endosome and activates IRF3 for type I IFN production. TLR1/2 and TLR6/2 heterodimers recognize triacylated and diacylated lipoproteins, respectively, whereas TLR5 recognizes flagellin and all of them initiate a MyD88-dependent signaling pathway that culminates in the induction of proinflammatory cytokines. TLR signaling is modulated by CD14, CD36, Nrdp1, CHIP, MHCII, Regnase-1, A20, SHP-1, TMED7, CD11b, NLRP4, NLRX1, and miRNAs (miR-146a, miR-29, miR-148/152).

Figure 2.

Signaling pathway of endosomal TLRs. Endosomal residents of TLR family are TLR3, TLR7, TLR8, TLR9, TLR11, TLR12, and TLR13. dsRNA recognition by TLR3 recruits TRIF to initiate signaling cascade that further activates TBK1 to induce IRF3-mediated type I IFN production. Concurrently, TRIF can also interact with TRAF6 to activate NF-κB for transcription of proinflammatory cytokines. TLR7 and TLR8 recognize viral ssRNA, whereas TLR9 recognizes CpG DNA from both bacteria and viruses. Ligand stimulation facilitates UNC93B1-dependent trafficking of TLR7 and TLR9 from ER to endosomes, where TLR9 undergoes proteolytic cleavage. Following this TLR7 and TLR9 recruit MyD88 to activate NF-κB and IRF7 to induce transcription of proinflammatory cytokines and type I IFN genes, respectively. TLR11, TLR12, and TLR13 recognize flagellin, profilin, and bacterial 23sRNA, respectively, and induce NF-κB signaling through MyD88 and TIRAP. Endosomal TLR signaling can be modulated by MARCH5 and viperin.

Figure 3.

RLR Signaling pathway. RLR family contains of RIG-I, MDA5, and LGP2. RIG-I and MDA5 recognize viruses differentially. RIG-I recognizes SeV, VSV, RSV, NDV, EBV, and JEV, whereas MDA5 recognizes viruses of picornavirus family members. After virus infection, long viral dsRNA or short dsRNA activates MDA5 or RIG-I, respectively, and they undergo conformational change to obtain an open confirmation and their CARD domain interacts with CARD domain of IPS-1 localized in mitochondria and peroxisomes to start signaling. Mitochondrial IPS-1 signaling leads to activation of NF-κB and RF3/IRF7 resulting in the production of type I interferons and proinflammatory cytokines, whereas peroxisomal IPS-1 activates IRF1- and IRF3-dependent signaling leading to interferon stimulatory genes (ISGs) expression. LGP2 is a positive regulator of RIG-I and MDA5. RIG-I signaling is also positively regulated by Trim25 and RIPLET, whereas it is negatively regulated by CYLD, USP4, and RNF125.

Figure 4.

Cytosolic DNA sensors and their signaling pathways. DNA present in the cytoplasm derived from either hosts or microbes are recognized by various kinds of DNA sensors. DDX41, DAI, DNA-PK, IFI16, MRE11, and cGAS recognize dsDNA and induce type I IFN production through STING via TBK1- and IRF3-dependent pathways. AT-rich dsDNA recognized by RNA polymerase III is transcribed to 5′-triphosphate RNA to be further sensed by RIG-I to induce IPS-1-dependent type I production; similarly, H2B also recognizes dsDNA and signals through IPS1. LRRFIP1 binds both dsDNA and dsRNA and activates β-catenin, which enhances a TBK1-independent and IRF3-dependent IFN-β transcription. DHX9 and DHX36 are MyD88-dependent DNA sensors. AIM2 and nuclear IFI16 can form inflammasomes together with ASC and caspase-1 on recognition of dsDNA to mediate a caspase-1-dependent cleavage of IL-1β and IL-18 from pro-IL-1β and pro-1L-18. Finally, Ku-70 recognizes dsDNA to induce IRF1/IRF7-dependent type III IFN.