The Shape of Control: How Going in Circles Keeps RNA Catalytically Switched On

Abstract

RNase P was one of the first enzymes discovered to have an RNA-based catalytic component. Since its identification, it has been extensively studied, particularly in E. coli, due to the ability of its M1 RNA to exhibit in vitro catalytic activity even in the absence of associated protein. In this study, we report G-quadruplex formation as a potential regulatory mechanism that modulates the catalytic activity of this RNA. We observed a significantly higher propensity for G-quadruplex formation in the linear isoform (linM1) compared to its circular counterpart (circM1). G-quadruplex formation was confirmed through circular dichroism spectroscopy and a fluorescence-based assay using a G-quadruplex-binding small molecule. We compared the catalytic activity of linM1 and circM1 in lithium and potassium environments and found that G-quadruplex formation specifically reduced linM1 activity. Furthermore, we observed distinct condensate properties of linM1 in the presence or absence of G-quadruplex structures. Overall, our findings suggest that G-quadruplex formation serves as a regulatory switch for RNA activity in linM1, whereas circM1 resists G-quadruplex formation and remains catalytically active even under conditions that favor G-quadruplex assembly.