Transcription does not proceed at a uniform rate and pausing is an essential function in both pro- and eukaryotic cells. In bacteria, pausing is required for the efficient coupling of transcription and translation, formation of RNA secondary structures (e.g. in attenuation), transcription coupled DNA repair, and transcription termination. The essential transcription elongation factor NusA is required for full pause activity. How NusA functions has remained a mystery for more than 40 years.
We have determined the binding sites on NusA and RNA polymerase required for their interaction at the amino acid level allowing us to model the complex. This permitted functional analysis of NusA and the identification of two highly conserved, non redundant, basic amino acids required for NusA pause activity, allowing us to propose a novel mechanism by which NusA is able to stablise transcription pause complexes.
Identification of the NusA binding site also allowed us to screen chemical libraries for potential inhibitors of the interaction. We identified potential hits that overlap the RNA polymerase binding site on NusA, and showed they were capable of specifically targeting NusA activity. Therefore, we have identified the mechanism of transcription pausing and successfully targeted the protein-protein interaction required for this activity for the development of new antimicrobial compounds.