Abstract
The Escherichiacoli yybP-ykoY riboswitch regulates mntP and alx gene expression on the translation level. It contains two tandem domains regulated by Mn(2+) 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 Mg(2+) and Mn(2+). SHAPE probing and SAXS show that the yybP-ykoY riboswitch maintains a consistent conformation across pH conditions without Mn(2+) but exhibits significant conformational changes under alkaline conditions when Mn(2+) is present. These findings align with our proposed model, where Mn(2+) binding induces a transition from an "OFF" to an "ON" state in alkaline conditions, while the Mn(2+) 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.