| TraR of A. tumefaciens is a member of the LuxR family of transcriptional regulators, all of which respond to specific N-acylhomoserine lactones that accumulate at high population densities. TraR binds to N-3-oxooctanoyl-L-homoserine lactone (OOHL), which induces dimerization. These complexes can then bind to target binding sites (tra boxes) at TraR-dependent promoters on the Ti plasmid. Structural and biochemical studies indicate that TraR has an N-terminal OOHL binding domain connected by a flexible linker to a C-terminal DNA binding domain (CTD).; There are seven TraR-dependent promoters on the Ti plasmid. Five resemble class II type promoters, with a tra box overlapping the binding site of core RNA polymerase. At the other two promoters, the binding site is located farther upstream (class I promoters). I used saturating point mutagenesis of the surface of the TraR CTD to identify residues of the protein that might contact RNA polymerase. I identified six residues that are critical for transcription activation but not DNA binding. These six residues form a patch on the surface of the CTD. As this patch is critical for activation at both class I and class II promoters, I predict that it contacts the C-terminal domain of the RNA polymerase alpha-subunit.; The seven TraR-dependent promoters on the Ti plasmid are each activated from one of four different tra boxes. The tra boxes are 18 bp sequences with perfect or near-perfect dyad symmetry, and each half-site is contacted by the helix-turn-helix (HTH) DNA binding motif of each subunit of the TraR dimer. I performed an analysis of the DNA binding surface of TraR and the bases of the tra box to determine the contributions of each residue and base to affinity and specificity of binding. I confirm that the major determinants of specificity are the interactions between residues of the recognition helix of the HTH and bases in the major groove of each tra box half-site. The bases of the non-contacted central spacer of the box are also important for sequence recognition, due to their effect on DNA flexibility. |
