A Thermodynamic Perspective of sRNA-mRNA Interactions and the Role of Hfq

摘要

The RNA binding protein Hfq facilitates the hybridization of small regulatory RNAs (sRNA) to target mRNAs to regulate gene expression post-transcriptionally. The exact mechanism by which Hfq enhances RNA pairing is not well understood. In this work we examined the interaction of sRNAs and mRNAs and the effect of Hfq on sRNA thermal stability. We employed computational approaches to predict interaction sites of sRNA-mRNA pairs and the effects of single base changes on sRNA-mRNA binding, and compared the predictions to experimental data. The comparisons indicate that thermodynamic calculations predict functional characteristics of sRNA-mRNA binding with good accuracy. Experimental denaturation studies of segments of the sRNA DsrA in the absence and presence of Hfq show that Hfq is a melting protein. This observation and an analysis of DsrA-rpoS mRNA binding suggest that Hfq's ability to destabilize DsrA hairpin structures plays a role in enhancing its hybridization to rpoS mRNA.