Double-Stranded RNA Sensors and Modulators in Innate Immunity

Abstract

Detection of double-stranded RNAs (dsRNAs) is a central mechanism of innate immune defense in many organisms. We here discuss several families of dsRNA-binding proteins involved in mammalian antiviral innate immunity. These include RIG-I-like receptors, protein kinase R, oligoadenylate synthases, adenosine deaminases acting on RNA, RNA interference systems, and other proteins containing dsRNA-binding domains and helicase domains. Studies suggest that their functions are highly interdependent and that their interdependence could offer keys to understanding the complex regulatory mechanisms for cellular dsRNA homeostasis and antiviral immunity. This review aims to highlight their interconnectivity, as well as their commonalities and differences in their dsRNA recognition mechanisms.

Keywords: RIG-I-like receptor; RNA interference; dsRNA; dsRNA-dependent adenosine deaminase; oligoadenylate synthase; protein kinase R.

Figure 1

dsRNA-binding proteins in innate immunity. (a) Network of dsRNA sensors and modulators in innate immunity. The diagram below shows their interdependence. Blue arrows and red inhibition lines indicate reported stimulatory and inhibitory relationships, respectively. (b) Structures of dsRNA and dsDNA, which display A-form and B-form double helixes, respectively. (c) Watson-Crick base pair interactions, with edges facing major versus minor grooves indicated. Note that relative locations of hydrogen bond donors and acceptors differ for all four nucleotides in the major groove but are degenerate in the minor groove. Abbreviations: ADAR, adenosine deaminase acting on RNA; PKR, protein kinase R; RLR, RIG-I-like receptor.

Figure 2

RLR and PKR. (a) Domain architectures and structures of human RIG-I and MDA5 in complex with dsRNA (PDB: 3TMI and 4GL2). RIG-I binds the dsRNA end as a monomer (as shown in the crystal structure), but on long dsRNA, it assembles into filamentous oligomers. Filament formation of RIG-I on dsRNA promotes 2CARD tetramerization through a proximity-induced mechanism. The K63-linked polyubiquitin chain also promotes 2CARD tetramerization. In contrast to RIG-I, MDA5 only binds the dsRNA interior, not the end, and its filament formation is obligatory. As with RIG-I, 2CARD tetramerization (with or without the K63-linked polyubiquitin chain) is required for antiviral signal activation. (b) Domain architecture and structures of PKR. The structure of PKR dsRBDs in complex with dsRNA is not available, but studies suggest that PKR dsRBDs bind dsRNA in a manner similar to other canonical dsRBDs. The RNA-free structure of PKR dsRBD1 (blue) (PDB: 1QU6) is overlaid on the structure of Aquifex aeolicus RNase III in complex with dsRNA (green) (PDB: 2EZ6). On the right is the structure of the PKR kinase domain (dark blue) in the active dimeric state and in complex with eIF2α (gray) (PDB: 2A19). Analogous to RLRs, PKR utilizes dsRNA binding and the proximity-induced mechanism to dimerize and activate the kinase domain. Abbreviations: CTD, C-terminal domain; dsRBD, dsRNA-binding domain; PKR, protein kinase R; RLR, RIG-I-like receptor; Ub, ubiquitin.

Figure 3

OASes and ADARs. (a) Domain architectures and structures of human OAS1–3 and OASL. The structure of OAS1 in complex with dsRNA (PDB: 4IG8). The OAS1 structure is also superposed onto cGAS in complex with dsDNA (PDB: 6CT9) and OAS3 (first pseudo-NTase domain) in complex with dsRNA (PDB: 4S3N). The second UbL domain of OASL (green, PDB: 1WH3) is superposed onto the structure of Ub (dark blue) on the right. (b) Schematic of adenosine-to-inosine modification and domain architectures of human ADAR1–3. The structure of dsRBD1–2 of ADAR2 in complex with dsRNA (PDB: 2L3J). Structures of ADAR1 ZBD1 in complex with dsRNA in the Z-form (PDB: 2GXB) and the deaminase domain of ADAR2 (PDB: 5HP2) are also shown on the right. Abbreviations: ADAR, adenosine deaminase acting on RNA 1; dsRBD, dsRNA-binding domain; NTase, nucleotidyl transferase; OAS, oligoadenylate synthase; PDB, Protein Data Bank; Ub, ubiquitin; ZBD, Z-DNA-binding domain.

Figure 4

Drosha/Dicer/Ago2 and PACT/TRBP. (a) Domain architectures and structures of human Drosha, Dicer, and Ago2. The structures of human Dicer (PDB: 5ZAL and 4NHA) in complex with dsRNA showed two distinct conformations representing the preslicing mode (where dsRNA is far from the slicing center) and the slicing mode (where dsRNA contacts the slicing center). dsRNA in the slicing mode was modeled based on the structure of Dicer platform-PAZ in complex with dsRNA (PDB:4NHA). Note that in the preslicing conformation, the helicase domain (green) interacts with dsRNA in a manner distinct from the RLR helicase domains. By contrast, the structure of Drosophila Dicer-2 (PDB: 6BU9, right) shows that the Dicer helicase domain partially encircles dsRNA, similarly to the RLR helicase domains. (b) Domain architectures and structures of PACT and TRBP. The structures of canonical dsRBD1–2 of TRBP in complex with dsRNA (PDB: 5N8M) and noncanonical dsRBD3 in complex with Dicer Hel2i (PDB: 4WYQ). The overlay of the two structures on the right shows that noncanonical dsRBD3 is structurally similar to canonical dsRBDs. Abbreviations: dsRBD, dsRNA-binding domain; RLR, RIG-I-like receptor.