Transcription by the multi-subunit RNA polymerases is a complex process consisting of multiple steps at which regulation can occur. To understand the relevant molecular interactions and regulatory mechanisms, we are taking advantage of the relative simplicity of the prokaryotic transcription machinery and the power of bacterial genetics. The RNA polymerase (RNAP) core enzyme is evolutionarily conserved from bacteria to man, as has been strikingly confirmed by recent crystallographic studies. Accordingly, insights into the function of the bacterial enzyme are likely to be relevant to the function of all multi-subunit RNAPs. We are using a variety of genetic tools developed in our laboratory, including a transcription-based bacterial two-hybrid assay, to functionally dissect the transcription apparatus. By identifying informative mutants, analyzing their phenotypes in vivo, performing mechanistic analyses in vitro and drawing on relevant structural information, we are probing the events that occur during transcription initiation, elongation and termination, as well as the ways in which regulators modulate these events.

Our study of the protein-protein interactions that underlie transcription and its regulation has led to a more general interest in protein-protein interactions. A newer project in the lab is focused on the potentially pathogenic protein-protein interactions that mediate the formation of prion-like protein aggregates. We are using E. coli cells to develop assays that would allow us to study prion proteins from other organisms and potentially to identify prion-like proteins of bacterial origin.