Studies on the structure and function of bacterial 6S RNA, a putative transcriptional regulator

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6S RNA is a widespread non-coding RNA (ncRNA) in bacteria, which affects transcription. Due to the structural similarity with open promoter DNA 6S RNA binds to RNA polymerase and thereby inhibits the interaction with many but not all promoters. Based on the results of genome-wide transcriptome analysis we plan to investigate the molecular details of the still unresolved differences of the 6S RNA specificity, causing a differential regulation of individual genes. Moreover, under condition of 6S RNA depletion the significance of the strikingly changed expression level of the components constituting the translational apparatus shall be determined. The exceptionally striking property of RNA polymerase bound 6S RNA to direct the transcription of small de novo RNA products, thereby releasing the 6S RNA-mediated inhibition of RNA polymerase, is of special interest for the future investigation. To analyze the details of this process and to discover possible intrinsic functions of the de novo RNAs in the cell we plan to construct 6S RNA mutations and characterize their expression and function. In addition, experiments to identify potential 6S RNA-interacting molecules in the cell shall be performed. Finally, a screen for possible further functions of the interesting riboregulator, which may have escaped our notion so far, shall be carried out.