Molecular interactions between the transcription factor Crl and sigma s RNA polymerase holoenzyme in Escherichia coli

Bacteria must change their cellular composition in response to changing environmental conditions and stress. They implement these changes by altering gene expression and/or protein activity. Central to changes in gene expression during stress responses is regulation of transcription. In bacteria, transcription is directed by a suite of RNA polymerase (RNAP) holoenzymes, comprised of a core enzyme, possessing the catalytic activity for RNA synthesis, and one of a collection of transcription initiation factors, known as σ factors, which recognizes promoter DNA sequences upstream of genes. Increasing the formation of a particular type of RNAP holoenzyme by switching the σ factor will lead to expression of its cognate regulon. My thesis research focuses on deciphering the complex molecular interactions between the transcription factor Crl and the general stress response sigma factor, Sigma S, in order to understand Escherichia coli's response to stress at the molecular level. Crl is a small (133 amino acids in E. coli) protein that stimulates transcription mediated by Sigma S. At the outset of my research, little was known about how Crl interacts with the transcription machinery to stimulate Sigma S-mediated transcription. I used a combination of biochemical, genetic, and molecular biological techniques in vitro and in vivo to identify key interactions and gain insight into the mechanism of transcriptional regulation by Crl. I identify a key binding determinant (the DPE motif) in Sigma S conserved domain 2 underlying its specific recognition by Crl. I demonstrate directly that Crl requires this determinant for positive regulation of Sigma S-mediated transcription and to enhance Sigma S holoenzyme formation. I made the primary Sigma factor recognizable by Crl by substitution of the DPE motif along with deletion of a large non-conserved region (NCR). I also localized the area of Crl required for the interaction with Sigma S to Crl's conserved central cleft. Finally, I identified an interaction between the Beta prime subunit of core RNAP and Crl, which occurs only in the context of the holoenzyme, that has begun to clarify the mechanism by which Crl functions as a Sigma S-specific RNAP holoenzyme assembly factor.