Talk on Friday 04:00-04:15pm submitted by Beau Champ
A mechanistic and structural study of a yet uncharacterized RNA sensor: the ykkCD riboswitch
Beau Champ (Ball State University), Ambar Rana (Ball State University), Nicholas Frecker (Ball State University), Delores James (Ball State University), Timea Gerczei (Ball State University)
Riboswitches are RNA aptamers that are involved in cellular regulatory functions. They fold in a specific 3D shape and often undergo structural transition when bound to the target molecule. This allosteric structural transition typically allows or prevents the downstream translation of a protein. Here, we will present the ykkCD riboswitch, which recognizes the antibiotic tetracycline and regulates expression of a multidrug resistant efflux pump in Bacillus subtilis. We will show that ykkCD directly binds to tetracycline with high affinity and selectivity and upregulates expression of downstream genes by attenuating transcription. To map the conformational change that is triggered by tetracycline binding and leads to upregulation of gene expression we will show perform nucleic acid footprinting studies of the ykkCD aptamer-tetracycline complex.
Keywords: riboswitch, SHAPE, fluorescent binding assays