Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation

Abstract

RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo‐state, the AMPPNP plus single‐stranded RNA (ssRNA) bound pre‐hydrolysis state, and the ADP‐bound post‐hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double‐stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus–host interface. It would benefit in developing therapeutics to combat the influenza virus infection.

The RNA helicase DDX5 promotes viral infection via regulating N6-methyladenosine levels on the DHX58 and NFκB transcripts to dampen antiviral innate immunity

“…Our findings are also in line with those of a recent study, which reported that DDX5 suppresses IFN-I antiviral innate immune response by interacting with PP2A-Cβ to deactivate IRF3 [43]. However, because DDX is a large family of conserved RNA-binding proteins, nearly all DDX family members have been demonstrated to regulate cellular metabolism and maintain immune homeostasis through regulating nucleic acid binding and to modulate nucleic acid interactions and RNA-protein complex remodeling in host cells, such as DDX58, MDA5, DHX58, DDX3X, DDX21, DDX19, DDX39A, and DDX46 [2,13,14,15,16,[44][45][46][47][48][49][50][51]. In fact, DDX5 has been demonstrated to regulate transcription in order to play its roles in tumorigenesis, proliferation, differentiation, and metastasis pathways [30,46].…”

Long noncoding RNA and protein abundance in lncRNPs

“…SLERT is exclusively localized at FC/DFC units, where it binds to DDX21 (Xing et al, 2017), a DEAD-box RNA helicase that can adopt an open or closed conformation upon substrate binding (Chen et al, 2020). DDX21 is largely enriched outside of each FC/DFC, where it forms a discontinuous shell-like structure coating each FC/DFC by switching its intermolecular and intramolecular interactions mediated by unstructured N-and C-termini.…”

DEAD-Box RNA Helicases in Cell Cycle Control and Clinical Therapy

“…DDX21, as an important nucleolar protein, plays a critical role in ribosomal RNA biogenesis and transcriptional regulation [ 64 ]. DDX21 is a transcriptional activator of c-Jun via their direct interaction to regulate mRNA expression of the downstream target genes, including EGFR and cyclin D1 [ 65 ].…”