BPS2026 – Dynamic remodeling of long-range flavivirus RNA interactions in translation initiation

Long-range tertiary interactions are a widespread structural feature in viral RNAs (vRNAs) and mRNAs. In the flaviviruses, conserved complementary sequences in the 5ʹ and 3ʹ terminal regions have an essential role in viral replication. Long-range pairing of these conserved sequences is proposed to facilitate a switch between two alternative vRNA conformations, but the detailed nature of these interactions, their relative populations, and their exchange are required to formulate a mechanistic model of their role in regulation of the viral life cycle. We have previously developed a single-molecule FRET assay to differentiate between these alternative conformations of vRNAs. Here, we demonstrate how interactions with host and viral RNA-binding proteins (RBPs) modulate the conformation of the vRNA to regulate its function across different stages of infection. Our data show that both long-range interactions and binding of viral nucleocapsid protein to the vRNA are inhibitory to protein synthesis. We also find that human translation initiation factors dynamically remodel inhibitory long-range interactions in a process driven by ATP hydrolysis to facilitate ribosome loading. Understanding the interplay between vRNA conformation and RBP binding during viral translation, replication, and packaging will help to elucidate mechanistic roles for these highly conserved flaviviral sequences.