TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence

XylS, an AraC family transcription factor, positively regulates transcription of Pseudomonas putida TOL plasmid meta operon from the Pm promoter. A tandem of 15 bp homologous direct repeats, separated by 6 bp and overlapping with the −35 hexamer of the promoter, is required for the activation of Pm by XylS in vivo. In this study we have characterized specific binding of XylS to the Pm operator Om . XylS was overexpressed with an epitope tag in its N-terminus Tagged XylS (N-XylS) was immunopurified and was shown to specifically bind to Om . We have used matrix-bound N-XylS in DNA footprinting and methylation interference experiments. Binding of N-XylS protects 44 bp in the Om region on both strands from DNase I digestion and generates hypersensitive sites (within the protected area) which lie on the same face of the DNA helix. Results of hydroxyl radical footprinting and methylation interference assays indicate that XylS binds along one side of the DNA and covers four helical turns. The protein has base-specific contacts in four adjacent major groove regions on the same helical face. Our data are in accord with the prediction of the presence of two separate DNA-binding units in an XylS molecule which are involved in base-specific contacts in two adjacent major-groove regions of a half-site. The direct repeat arrangement of the binding site and the mode of DNA binding of XylS are similar to the arrangement of recognition sites and the DNA contact pattern of AraC protein from Escherichia coli