Variation of half-site organization and DNA looping by AraC protein

The dimeric AraC protein of Escherichia coli binds specifically to DNA sequences upstream of promoters whose transcription is regulated by arabinose. Here we show with affinity measurements, DNase footprinting, dimethyl sulfate premethylation interference and dimethyl sulfate footprinting studies that AraC protein can recognize paired half-sites in direct repeat orientation or inverted repeat orientation. A similar high degree of flexibility was also seen in the ability of the protein in the absence of arabinose to bind tightly and specifically when the separation of its half-sites was increased by 10 or 21 bp. In the presence of arabinose the protein could specifically contact both half-sites of a +10 bp spacing construct but could not contact both in a +21 bp construct. Reduced extensibility of AraC protein in the presence of arabinose provides a simple mechanism for the protein's shift from a non-inducing, DNA looping state to an inducing, non-looping state that contacts two adjacent half-sites at the arapBAD promoter.