The <em>glmS</em> ribozyme is an antibacterial target

Abstract

Bacteria increasingly develop resistances to the known antibiotics, this threatens human health. Thus, novel antibiotics are urgently needed. The currently used antibiotics mainly target five bacterial processes and are therefore limited in the target structures they address. This problem calls for the development of antibiotics that address new targets.<br /> Riboswitches are RNA elements mostly found in the non-coding region of bacterial mRNA molecules. Several classes of riboswitches regulate the expression of essential bacterial genes by the recognition of their cognate metabolites. Compounds that exhibit at least part of their activity through the action as metabolite analogs of riboswitches corroborate the suitability of riboswitches as antibacterial targets. <br /> The glmS riboswitch constitutes a unique class of riboswitches that regulate the expression of the essential glmS gene by a self-cleavage mechanism, resulting in the degradation of the glmS mRNA. This mechanism is induced by the metabolite glucosamine 6-phosphate (GlcN6P) and magnesium ions, consequently, the glmS riboswitch is also a co-factor dependent ribozyme. The thesis at hand deals with the analysis of different aspects regarding glmS ribozymes from different bacteria. <br /> The investigation of potential modulators of glmS ribozyme activity is displayed in section 3.1 and revealed insights into the interaction of the glmS ribozyme RNA with putative metabolite analogs. This section analyses the activity of compounds that originate from an in silico prediction based on the 3D shape of the ribozyme’s natural metabolite, GlcN6P. Section 3.2 studies the potential of the glmS ribozyme as antibacterial target. The investigation of the intracellular mode of action of the metabolite analog carba-glucosamine (CGlcN) is displayed. It is demonstrated that the antibacterial activity of CGlcN is based on the in vivo activation of the glmS ribozyme, presumably by carba-glucosamine 6-phosphate (CGlcN6P). Apart from the analysis of potential glmS ribozyme activators, different glmS ribozyme variants and their properties were studied. The analysis and characterization of putative novel glmS ribozyme sequences and the differential recognition of already known glmS ribozyme activators by those validated glmS ribozymes is displayed in section 3.3. In a similar manner as described for the in silico predicted GlcN6P analogs (section 3.1) putative glmS ribozyme activators, originating from a focused library based on the scaffold of an already described activator, are analyzed regarding their potential activation of glmS ribozyme variants (section 3.3) in section 3.4. The mode of action of the in section 3.4 identfied novel glmS ribozyme activator was subsequently analyzed utilizing the same approach as described in section 3.2.<br /> This study underlines the potential of riboswitches as antibacterial targets and furthermore represents the first proven study on ribozymes as antibacterial targets.