Control of Bacillus subtilis physiology by RNA-binding proteins and RNA degradation

Of all biological macromolecules, RNA is outstanding. Based on its biochemical properties, it can form complex structures that can interact with a wide variety of other macromolecules or even have enzymatic activity. We have studied the expression of several genes involved the transport of sugars by RNA-binding proteins. These proteins recognize specific elements in their RNA targets, and allow thus transcription beyond a terminator structure. In the absence of the respective sugar, the RNA-binding proteins are phosphorylated by the sugar permeases, and thus inactivated. This results in transcription termination as long as there is no need for the specific transporter (Fig. A). Moreover, the short lifespan of bacterial cells requires a rapid RNA turnover to allow adaptation to changing environments by expressing novel sets of proteins. Thus, RNA degradation and processing are of key importance for bacterial cells. We have analyzed RNA processing in B. subtilis, and discovered the central player in RNA degradation and processing in Gram-positive bacteria, RNase Y. This enzyme is responsible for the initial cut in the RNA molecules which consequently results in RNA degradation by a set of exoribonucleases (Fig. E). We have studied the functions of these enzymes, their localization in the cell as well as their interactions. Current work focusses on mechanisms that can bypass the need for a functional RNase Y enzyme.