Ribozymes and riboswitches: modulation of RNA function by small molecules

Abstract

Riboswitches are mRNA domains that directly bind small‐molecule metabolites and control expression of the mRNA they are part of in a ligand‐dependent manner. The glmS riboswitch is thus far unique in that it is also a catalytic RNA, or ribozyme. The self‐cleaving activity of this RNA from Gram‐positive bacteria requires binding of glucosamine‐6‐phosphate (GlcN6P), an essential precursor to the bacterial cell wall. The ribozyme is part of the mRNA for the enzyme GlcN6P synthetase. Self‐cleavage leads to mRNA destruction, and therefore, negative‐feedback regulation. Crystallographic analysis of the glmS riboswitch reveals a remarkably rigid RNA and binding of GlcN6P in contact with the scissile phosphate. This and the inactivity of the ribozyme in the absence of GlcN6P indicate that the metabolite functions as a true coenzyme. However, the RNA is not simply an inert structural scaffold. Mutational, kinetic and structural analyses reveal that an active‐site guanosine and GlcN6P mutually modulate the ability of each other to function as general acid‐base catalysts. Supported by the Damon Runyon Cancer Research Foundation, the Howard Hughes Medical Institute, the NIH and the W.M. Keck Foundation.