Cryo-EM of a viral RNA and RNA-protein complex reveals how structural dynamics and novel tRNA mimicry combine to hijack host machinery

Abstract

Structured RNA elements are essential for biology and are ubiquitously used by viruses to control diverse infection-critical processes. Single-stranded RNA viruses often encode multiple processes into a single RNA element to maximize the functional capacity of their compact genomes. These important and elegant ‘multifunctional’ RNAs are hypothesized to use programmed structural changes to coordinate several, sometimes opposing, functions. However, detailed molecular mechanisms of such elements are largely mysterious because of the difficulty of solving dynamic RNA structures. We exploited recent advances in cryo-EM to directly visualize the architecture and infer conformational dynamics of the brome mosaic virus tRNA-like structure (BMV TLS), a multifunctional tRNA mimic that participates in replication, translation, and encapsidation of viral RNAs and that has eluded structure determination for decades. We found that although BMV TLS is aminoacylated by cellular tyrosyl-synthetase (TyrRS), its primary conformation is incompatible with TyrRS binding. Rather, the RNA is preorganized for replication, positioning the replicase promoter and the initiation site in close proximity to each other. An alternative ‘tyrosylation-ready’ conformation requires repositioning of a conformationally dynamic structural domain, and this change must induce additional rearrangements that disrupt the ‘replication-ready’ configuration. These results demonstrate how programmed RNA dynamics can evolve to coordinate interactions with diverse cellular and viral proteins and thus organize multiple functions on a single RNA platform. Our results support the paradigm that RNA structures are inherently dynamic conformational ensembles, which enables multifunctionality. This work also highlights the emerging power of cryo-EM to dissect the dynamic conformational landscape of small discrete functional RNAs. Furthermore, we anticipate our method of rapidly mapping RNA domains within cryo-EM maps to be broadly useful.