RNA Structures as Processing Signals

Gene expression is regulated on several levels, one of which is the level of RNA maturation. While we have some knowledge about RNA processing in Bacteria and Eukarya, little is known about this process in the third domain of life, Archaea. The aim of this project is to identify processing signals in the model archaeon, the halophilic archaeon Haloferax volcanii. To achieve that goal, two approaches will be taken: (i) an in silico approach and (ii) an experimental approach. Both approaches are dependent upon and complementary to each other. Processing sites identified in silico will be tested in the laboratory and results from the experimental approach will allow refinement of parameters for the in silico searches. In this interdisciplinary project the partner from computer science/information theory will help designing software tools (based on information theoretic methods) to identify putative positions in the Haloferax genome where tRNA like structures exist. In addition, the complete set of newly identified processing sites will be searched (and clustered) for common features. The proposed project will lead to the identification of maturation signals in Haloferax volcanii, unravelling the RNA processing pathways and thus this level of regulation of gene expression in Haloferax.