The role of small RNAs in the control of amino sugar metabolism in Escherichia coli

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In recent years, small non-coding frans-encoded RNAs emerged as a new class of gene regulators in all living organisms. In many bacteria, such as Escherichia coli, a plethora of such sRNAs has been identified but their physiological functions have been revealed in just a few cases. Where known, these sRNAs most often base-pair to and thereby affect translation and/or stability of their target mRNAs. We recently discovered that expression of the E. coli glucosamine-6-phosphate synthase (GlmS) is feedback-regulated by its product glucosamine-6-phosphate (GlcN-6-P) in a process that depends on the small RNA GlmZ (Kalamorz et al., 2007, Mol. Microbiol. 65, 1518-1533). GlmS initiates the hexosamine pathway leading to the formation of UDP-N-acetylglucosamine, the major intermediate in the biosynthesis of peptidoglycan of bacterial cell walls. The sRNA GlmZ is subject to processing and we found that a decrease in cellular GlcN-6-P concentrations leads to accumulation of its unprocessed form. This full-length GlmZ in turn stabilizes the glmS mRNA presumably by direct basepairing which results in higher GlmS synthesis levels. Furthermore, we identified the novel protein YhbJ as a regulator of GlmZ processing. In addition, we identified a second sRNA, GlmY, that is also affected by a yhbJ mutation and by GlcN-6-P concentrations and which when overexpressed also induces glmS expression. Our data suggest that GlmY affects processing of GlmZ and thereby indirectly regulates glmS expression. Here we propose to investigate this novel genetic control mechanism in detail. Our goals are to clarify the interference of the two sRNAs GlmZ and GlmY in the control of glmS expression and to identify the GlcN-6-P sensor. Furthermore, we would like to characterize the GlmZ/glmS basepairing using in vivo as well as in vitro techniques. Another important task is to find out the molecular mechanism by which YhbJ governs processing of these sRNAs. For this purpose, we will investigate the in vitro properties of YhbJ. Finally, using global proteome and transcriptome approaches we want to find out whether additional genes involved in amino sugar or nitrogen metabolism are controlled by YhbJ, GlmZ and/or GlmY i.e. whether these factors govern a regulon.