Processing and degradation of regulatory RNAs in Escherichia coli

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To understand the regulation by RNA it is necessary to know how these RNA molecules are generated and turned-over. While some small RNAs represent primary transcripts, others are generated from larger RNA transcripts by processing. Some small RNAs exert their function by influencing the stability of the target RNA. Even if the small RNA does not influence the decay of target RNAs, its own turn-over rate may strongly influence its regulatory impact. While some small RNAs are very stable (half-life 30 min or more), others are turned-over within few minutes. Initially we will concentrate our studies on three systems: i) the ibpBA mRNA which harbours two putative RNA thermometers that are analyzed in regard to function by Franz Narberhaus, ii) rpoS and the small RNAs influencing rpoS expression involved in stationary phase and stress regulation (studied by R. Hengge and J. Vogel) and iii) the GcvB and Omr RNAs (affect outer membrane composition) which exhibit remarkably different half-lives. The decay of the RNAs will be analyzed under different growth conditions and in RNase mutant strains in order to get first insights into the underlying mechanisms. This will be complemented by in vitro studies using in vitro transcripts in combination with target RNAs and/or the RNA chaperone Hfq and isolated RNases or degradosome complexes. Hypotheses on the decay mechanisms arising from these studies will then be challenged by generating modified RNAs, whose decay will again be analyzed in vivo and in vitro.