DEAD-Box Protein Assisted RNA Structure Conversion towards and against Thermodynamic Equilibrium Values

摘要

RNAs in biological processes often interconvert between defined structures. These RNA structure conversions are assisted by proteins and frequently coupled to ATP hydrolysis. It is not well understood how proteins coordinate RNA structure conversions and which role ATP hydrolysis plays in these processes. Here, we have investigated in vitro how the DEAD-box ATPase Ded1 facilitates RNA structure conversions on a simple model system. We find that Ded1 assists RNA structure conversions via two distinct pathways. One pathway requires ATP hydrolysis and involves the complete disassembly of the RNA structures. This pathway represents a kinetically controlled steady-state between the RNA structures, which allows formation of less stable RNA structures from more stable ones and thus RNA structure conversion against thermodynamic equilibrium values. The other pathway is ATP independent and proceeds via multipartite intermediates that are stabilized by Ded1. Our results provide a basic mechanistic framework for protein-assisted RNA conversions that illuminates the role of ATP hydrolysis and reveals an unexpected diversity of pathways.