Structure and Dynamics of the Cytidine Repressor DNA Binding Domain

The Cytidine repressor (CytR) is a bacterial transcription factor involved in a complex regulation scheme in which several gene families are regulated differentially despite identical cellular conditions. A primary difference in the regulatory elements of these gene families is operator sequences which contain recognition sites for the CytR dimer with variable numbers of bases separating them. To better understand the mechanism of gene expression, I have characterized the structure of a monomer of the CytR DNA binding domain (DBD) in several states: bound to a single recognition site, bound to nonspecific DNA, and free in solution. Nuclear Magnetic Resonance (NMR) spectroscopy was employed for structure determination and characterization in addition to dynamics analysis. I find that the CytR DBD forms a single stable structure when bound to the recognition site. In contrast, in the free-state the DBD is highly flexible and exhibits multiple distinct conformations. The nonspecific DNA bound state retains the level of instability seen in the free-state, while structurally limited to a single conformation similar to the recognition site bound state. My studies show that the DNA sequence dictates the DBD structural conformations. These altered dynamics and structures of the DBD may be a part of the differential gene regulation of the full CytR protein.