A Kissing-Loop is Important for BtuB Riboswitch Ligand Sensing and Regulatory Control [Gene Regulation]

September 14th, 2015 by Lussier, A., Bastet, L., Chauvier, A., Lafontaine, D. A.

RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing-loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing-loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing-loop and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing-loop interaction is not essential for ligand binding. However, we showed that kissing-loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.