The effect of mutation in the stem of the MicroROSE thermometer on its thermosensing ability: insights from molecular dynamics simulation studies

Abstract

A large number of bacteria have been found to govern virulence and heat shock responses using temperature sensing RNAs known as RNA thermometers (RNATs). They repress translation initiation by base pairing to the Shine–Dalgarno (SD) sequence at low temperature. Increasing the temperature induces the RNA duplex to unfold and expose the SD sequence for translation. A prime example is the ROSE thermometer module known to regulate the production of the ROSE heat shock protein in Bradyrhizobium japonicum. The unfolding of a 29-nucleotide long MicroROSE RNA element which forms a critical component encompassing the SD sequence, and three mutants that differ from it by deletion of a guanine nucleotide or mutations near the SD and stem regions have been studied using high temperature molecular dynamics simulations. The simulations reveal the progressive manner in which a biologically functional RNA thermometer unfolds. Our simulations reveal that deletion of the highly conserved G10 residue, opposite to the SD region leads to the formation of a stable RNA helix that has lost its thermosensing ability. Mutations of bases A5 → U5 and U25 → A25 near the stem increase the thermosensing ability due to the allosteric effect which leads to a global destabilization effect on the structure. The temperature-dependant regulation of this thermometer has been investigated by estimation of differences in the unfolding paths by calculating individual residue fluctuation, stacking energy, the contact map plot and the lifetime dynamics plot of non-Watson–Crick hydrogen bonds at three different temperatures. Results reveal that partial unfolding at higher temperature starts from the hairpin tetra loop end and terminates at the stem region through the SD associated region. Two canonical hydrogen bonds between U9–A22 and four non-canonical hydrogen bonds between G10–G21 and U6–U24 around the internal loop play an important role in partial melting of the RNA helix. These results demonstrate how small alterations in RNA structure can regulate gene expression and illuminate the molecular basis of the function of an important bacterial regulatory motif.