Reconstitution of antiviral Dicer activity in vitro reveals distinct contributions of RDE-4 dsRNA-binding motifs

Abstract In C. elegans, antiviral RNA interference (RNAi) relies on the coordinated activity of Dicer (DCR-1), the helicase DRH-1, and the double-stranded RNA (dsRNA)-binding protein, RDE-4, yet the domain-specific contributions of RDE-4 remain unclear. Here, we reconstituted the antiviral complex from independently purified DCR-1•DRH-1 and RDE-4 to define how RDE-4 stabilizes and activates the complex. Addition of recombinant RDE-4 restored ATP hydrolysis and dsRNA cleavage to levels previously observed with the pre-assembled complex, and time-course assays revealed that RDE-4 is essential for maintaining DCR-1•DRH-1 activity. Mutational analysis of RDE-4 revealed that both dsRBM2 and dsRBM3, but not dsRBM1, are required for reconstituting ATP hydrolysis and cleavage. Disruption of the KKxAK motif in dsRBM2 drastically reduced dsRNA affinity and abolished catalytic rescue despite preserving robust binding to DCR-1•DRH-1. Mass photometry and pulldown assays revealed that RDE-4 primarily forms DCR-1 containing complexes, predominantly through interaction with dsRBM3, with no evidence for stable interaction with DRH-1 alone. Functionally, RDE-4 enhanced DRH-1-driven ATP hydrolysis on both 52 and 106 base-pair dsRNAs, but cleavage efficiency showed strong length dependence, implicating dsRNA substrate length as an effector in this system. Our findings establish RDE-4 as an important stabilizer of the antiviral complex and reveal distinct roles for dsRBM2 and dsRBM3 in ATP hydrolysis and dsRNA cleavage. Furthermore, our results suggest that substrate length modulates RDE-4 function, not just alone, but within the antiviral complex. These insights refine our understanding of antiviral RNAi in C. elegans and uncover regulatory mechanisms within the antiviral complex. Competing Interest Statement The authors have declared no competing interest.