The Role of the Z-DNA Binding Domain in Innate Immunity and Stress Granules

Abstract

Both DNA and RNA can maintain left-handed double helical Z-conformation under physiological condition, but only when stabilized by Z-DNA binding domain (ZDBD). After initial discovery in RNA editing enzyme ADAR1, ZDBD has also been described in pathogen-sensing proteins ZBP1 and PKZ in host, as well as virulence proteins E3L and ORF112 in viruses. The host-virus antagonism immediately highlights the importance of ZDBD in antiviral innate immunity. Furthermore, Z-RNA binding has been shown to be responsible for the localization of these ZDBD-containing proteins to cytoplasmic stress granules that play central role in coordinating cellular response to stresses. This review sought to consolidate current understanding of Z-RNA sensing in innate immunity and implore possible roles of Z-RNA binding within cytoplasmic stress granules.

Keywords: ADAR1; E3L; PKZ; Z-DNA binding domain; Z-RNA; ZBP1; innate immunity; stress granules.

Figure 1

Domain organization of ZDBD-containing proteins: ADAR1, ZBP1, E3L, PKZ, ORF112, and RBP7910. Zα domain (blue) denotes ZDBD that can bind Z-DNA/Z-RNA, while Zß domain (red) denotes ZDBD that cannot bind Z-DNA/Z-RNA. ADAR1_p150 harbors an extra Zα domain compared to ADAR1_p110, while sharing identical dsRNA binding domains (dsRBDs) and catalytic deaminase domain. Two natural isoforms were also described for ZBP1, where ZBP1ZΔ does not contain the first Zα domain present in full length ZBP1. Vaccinia virus E3L vital for its pathogenicity contains a single Zα domain and a dsRBD. Fish PKZ contains two N-terminal Zα domains as the RNA recognition motifs, in addition to a C-terminal kinase domain. On the other hand, the ORF112 protein identified from fish herpesvirus only has a single Zα domain at its amino-end. Most recently, trypanosome RBP7910 protein has been reported to contain two Zα-like domains, although further characterization of their function may be necessary.

Figure 2

Crosstalk between ZDBD-containing proteins, stress granules, and innate immunity signaling pathway following RNA virus infection. 1) Innate immune sensors like MDA5 and PKR are activated upon recognition of virus RNA in the cytoplasm, which in turn activates the NF-κB pathway culminating in expression of type I IFN. 2) At the same time, activated PKR also phosphorylates eIF2α, causing stalled mRNA translation that induce the formation of stress granules. Stress granules are instrumental in promoting cell survival under cellular stresses like virus infection. 3) Most ZDBD-containing proteins have been shown to localize to stress granules, mediated via respective Zα domains. Therefore, it is possible that RNA can adopt Z-conformation more readily within stress granules. 4) ADAR1_p150 is a negative regulator of immune response protecting against autoimmunity and chronic inflammation, as edited RNA transcripts lose immunogenicity. On the other hand, ZBP1 activation triggers IFN response and cell death mechanism. The vaccinia virus E3L is an inhibitory protein towards the antiviral response of its mammalian host, which is dependent of its Zα domain. In fish, PKZ is a paralog that complements PKR-mediated pathways, as PKZ can be activated by Z-RNA binding. The cyprinid herpesvirus ORF112 protein antagonizes the activation of PKZ as the virus immune evasion strategy. Incidentally, PKR and MDA5 had also been reported to localize to stress granules. It is therefore plausible that the close proximity through localization to stress granules facilitate the crosstalk between ZDBD-containing proteins and immune recognition and signaling pathways.