RNA structures as processing signals and sensors
With an interdisciplinary approach using molecular biology tools together with algorithmics and information theory we want to identify the first "processosome" of an organism (the processosome is the sum of all processing sites in an organism). So far we already determined the processing sites of Haloferax volcanii which resulted in the identification of 117 processing clusters (each processing cluster contains processing sites which have the same processing motif).
With this extensive data set we will now determine the processosome and link the processing signals to specific ribonucleases. The established procedure can then be used to define processosomes in other organisms thereby unravelling a key layer of regulation and identifying signals for regulation.
In addition, we want to show that variation in RNA conformation depending on environmental signals is a general regulation principle in prokaryotes. Using different experimental and computer science methods we want to show that under different conditions different RNA structures exist and that a change in structure is used as signal for gene expression.