Regulation of Transcription
The activities of bacterial transcription initiation complexes are regulated in response to environmental, cell-type, and developmental signals. In most cases, regulation is mediated by factors that bind to specific DNA sites in or near a promoter and inhibit (repressors) or stimulate (activators) one or more of the steps on the transcription initiation pathway.
To provide the first complete structural and mechanistic descriptions of activation, we study two of the simplest examples of activation in bacteria: (1) activation of the lac promoter by catabolite activator protein (CAP) and (2) activation of the gal promoter by CAP. These model systems each involve only a single activator molecule and a single activator DNA site and, as such, are more tractable than typical examples of activation in bacteria and substantially more tractable than typical examples of activation in eukaryotes (which can involve tens of activator molecules and activator DNA sites).
We have established that activation at lac involves an interaction between CAP and the RNA polymerase (RNAP) alpha-subunit C-terminal domain that facilitates closed-complex formation. Activation at gal involves this same interaction and also interactions between CAP and the RNAP alpha-subunit N-terminal domain, and between CAP and sigma, that facilitate isomerization of closed complex to open complex.
Together with collaborators, we are using electron microscopy, x-ray crystallography, and NMR to determine the structures of the interfaces between CAP and its targets on RNAP. In addition, we are using FRET, photocrosslinking, and single-molecule FRET and single-molecule DNA nanomanipulation methods to define when each CAP-RNAP interaction is made as RNAP enters the promoter and when each interaction is broken as RNAP leaves the promoter.