Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn2+ and pH

The Escherichiacoli yybP-ykoY riboswitch regulates mntP and alx gene expression on the translation level. It contains two tandem domains regulated by Mn2+ and pH. This study investigates the tertiary structure and conformational dynamics of the E. coli yybP-ykoY riboswitch using a combination of crystallography, small-angle X-ray scattering (SAXS), and chemical probing. Our crystal structure of the aptamer domain at 3.8 Å reveals that the yybP-ykoY riboswitch aptamer domain forms a coaxial superhelix containing three helices connected by a three-way junction (3WJ), with L1 and L3 creating a pocket-like structure that binds Mg2+ and Mn2+. SHAPE probing and SAXS show that the yybP-ykoY riboswitch maintains a consistent conformation across pH conditions without Mn2+ but exhibits significant conformational changes under alkaline conditions when Mn2+ is present. These findings align with our proposed model, where Mn2+ binding induces a transition from an "OFF" to an "ON" state in alkaline conditions, while the Mn2+ remains bound to the aptamer independent of pH. This regulatory mechanism allows for more sophisticated control of gene expression, providing a finely tuned adaptive response to environmental changes.