Z-RNA biology: a central role in the innate immune response?

Abstract

Z-RNA is a higher-energy, left-handed conformation of RNA, whose function has remained elusive. A growing body of work alludes to regulatory roles for Z-RNA in the immune response. Here, we review how Z-RNA features present in cellular RNAs-especially containing retroelements-could be recognized by a family of winged helix proteins, with an impact on host defense. We also discuss how mutations to specific Z-contacting amino acids disrupt their ability to stabilize Z-RNA, resulting in functional losses. We end by highlighting knowledge gaps in the field, which, if addressed, would significantly advance this active area of research.

Keywords: E3L; Z-D/RNA-binding protein 1 (ZBP1); Z-RNA; Zα; adenosine deaminase acting on RNA (ADAR1); innate immune response; retroelement.

FIGURE 1.

Left-handed Z-conformations can be found within a variety of RNA functional sites. (A) Double-stranded Z-RNA (middle) is best described as being composed of dinucleotide building blocks, where the nucleobase alternates between the anti- and syn-conformations, along with alternating ribose sugar puckers (C2′-endo/C3′-endo conformations). The weak but characteristic lone pair–π contact is shown as a red triangle. The particular Z-geometry with sugar pointing in opposite directions is found in other structural contexts, such as, for example, the ligand binding site of the purine riboswitch (PDB: 4FE5, Batey et al. 2004), and the core of the pUG G-quadruplex (PDB: 7MKT, Roschdi et al. 2022). (B) Potential mechanisms for Z-RNA formation and stabilization in vivo. First, Zα binds nonspecifically to A-RNA near a Z-prone region. From here, Zα may allosterically push the Z-prone region into the Z-conformation or may have to stabilize transiently sampled Z-conformations. Each of these mechanisms may involve one or more intermediate steps.

FIGURE 2.

Z-RNA is a natural ligand of Zα domains. (A) Zα amino acids interacting with a r(CpG)₃ duplex (PDB ID: 2GXB). Underlined residues are mutated in cases of Aicardi Goutières syndrome (Herbert 2019). (B) Cartoon schematic of the key residues of Zα and their interactions with the r(CpG)₃ duplex in the Z-conformation. (C) Sequence alignment between Zα domains from different Zα-containing proteins and species. Only sequences from Zα domains with structures solved in complex with Z-DNA or Z-RNA were used for the alignment. The residue numbering is based off ADAR1 Zα. Consensus sequence: uppercase, 100% conserved; lowercase, one letter with high frequency; +, two letters with high-frequency; −, no consensus.

FIGURE 3.

Competition for Z-RNA by dsRNA sensors modulates the innate immune response. (A) General domain architecture of Zα-containing RBPs, all of which have one or more Zα domains on their amino terminus, followed by one or more dsRBDs, and finally by a functional domain (such as a deaminase or kinase domain). (B) Summary of our current understanding of the interactions between Zα-containing proteins and Z-RNA within a hypothetical folded molecule, and how these interactions modulate pathways that depend on dsRNA sensor activation. Direct shielding of dsRNA and Z-RNA by viral E3L as well as host ADAR1 proteins prevent recognition by ZBP1 and PKR, preventing activation of necroptosis and the stress response. In addition, editing of dsRNA by ADAR1 prevents MDA5 activation. Abbreviations are explained within the text, except for CARDs (caspase recruitment domains), which mediate interactions with downstream signaling proteins, and RHIM (receptor-interaction protein [RIP] homotypic interaction motifs).