High Angle and Ligand-induced Low Angle DNA Bends Incited by OccR Lie in the Same Plane with OccR Bound to the Interior Angle

Abstract The OccR protein of Agrobacterium tumefaciens activates transcription of the occQ operon in response to octopine. Octopine shortens the DNase I footprint of OccR and relaxes an OccR-incited DNA bend. In this study we used hydroxyl radical footprinting to show that OccR contacts only one face of the operator. This contact spans 50 nucleotide pairs in the absence of octopine, and 39 nucleotide pairs in the presence of octopine. Octopine enhanced protection of the central region of the footprint. OccR blocked intercalation by methidiumpropyl EDTA along most of the operator, but did not block intercalation at the bend center. OccR protected DNA against both reagents far more completely at the promoter-distal half of the operator than at the promoter-promixal half. Experiments to alter the phasing between the operator bend and an adjacent sequence-directed bend indicated that the high angle DNA bend in the absence of octopine, and the low angle bend in the presence of octopine, lie in the same plane. Operator DNA was bent toward the helical face that OccR protected from hydroxyl radicals, indicating that OccR occupies the interior angle of this bend.