New mechanisms of transcription regulation in prokaryotes

Regulation of gene expression is essential in every organism, as it allows cells to respond to environmental triggers. Intrinsically disordered proteins are frequently involved in this regulation in eukaryotes, but seem less ubiquitous in prokaryotes. In bacterial toxin-antitoxin (TA) systems, however, intrinsic disorder and structural flexibility play a key role in the transcriptional regulation. TA systems are genetic elements generally coding for two proteins: a toxin, which is able to kill the cell, and an antitoxin, which can form a complex with the toxin to neutralize it. In the proposed project, I will try to unravel the autoregulation of the paaR-paaA-parE system, an unconventional three-component TA system, where besides the toxin and the antitoxin themselves an additional third protein plays a role in the regulation. I will use X-ray crystallography and Small Angle X-ray Scattering (SAXS) to visualize the binding of the proteins on the DNA. Furthermore, I will study the interaction between the different components of the system using Electrophoretic Mobility Shift Assays (EMSA) and Surface Plasmon Resonance (SPR). The transcription and expression of the TA system will be monitored during different in vitro and in vivo assays. Using the results of these experiments, a mathematical model will be constructed describing the response of the paaR-paaA-parE system to changing external conditions.