SMBP Group Meeting: Steve Bonilla (The Rockefeller University)

Tuesday Jun 18, 2024, 2:00 PM → 3:00 PM America/New_York

3rd Floor Classroom (162 5th Avenue)

Speaker: Steve Bonilla (The Rockefeller University)

Topic:  Visualizing RNA Dynamic Structural Landscapes in 3D

Abstract:  RNAs fold into complex three-dimensional (3D) structures and undergo conformational changes to recognize small molecules, catalyze chemical reactions, and assemble with proteins and/or other nucleic acids to form large macromolecular machines. Thus, a mechanistic understanding of many important cellular and viral processes requires a description of the dynamic conformational landscapes of RNA. Due to its ability to classify individual particles, cryo-EM can reveal multiple conformational states, allowing visualization of dynamic RNA 3D structures in a way not previously possible. We have used cryo-EM to study diverse functional RNAs and reveal conformational changes that are critical for their function.

I will discuss two examples. First, we used cryo-EM to visualize a virally encoded tRNA-like structure (TLS) that tricks the host tyrosyl-tRNA synthetase (TyrRS) into adding a tyrosine to the viral genome. Surprisingly, cryo-EM structures of the TLS RNA both in isolation and bound to TyrRS showed that the TLS undergoes large conformational rearrangements to bind TyrRS using a geometry that differs from genuine tRNA. More recently, we applied cryo-EM to the visualization of a long-lived misfolded state in the folding pathway of the Tetrahymena thermophila group I intron, a paradigmatic RNA structure-function model system. The structure revealed how this state forms native-like secondary structure and tertiary contacts but contains two incorrectly crossed strands that misposition a critical catalytic domain and cannot be resolved locally as extensive refolding is required.

In addition to answering specific biological questions about RNA structure-function relationships, our studies highlight the emerging power of cryo-EM for investigating dynamic mechanisms involving structured RNAs and RNA-protein complexes. The next challenge is to exploit the single-particle capabilities of cryo-EM to obtain quantitative information about the relative abundances of conformational states, potentially leading to a predictive understanding of RNA structural dynamics.