Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide‐inducible promoters

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Abstract
SoxS is the direct transcriptional activator of the member genes of the Escherichia coli superoxide regulon. At class I SoxS‐dependent promoters, e.g. zwf and fpr, whose SoxS binding sites (‘soxbox’) lie upstream of the −35 region of the promoter, activation requires the C‐terminal domain of the RNA polymerase α‐subunit, while at class II SoxS‐dependent promoters, e.g. fumC and micF, whose binding sites overlap the −35 region, activation is independent of the α‐CTD. To determine whether SoxS activation of its class I promoters shows the same helical phase‐dependent spacing requirement as class I promoters activated by catabolite gene activator protein, we increased the 7 bp distance between the 20 bp zwf soxbox and the zwf−35 promoter hexamer by 5 bp and 11 bp, and we decreased the 15 bp distance between the 20 bp fpr soxbox and the fpr−35 promoter hexamer by the same amounts. In both cases, displacement of the binding site by a half or full turn of the DNA helix prevented transcriptional activation. With constructs containing the binding site of one gene fused to the promoter of the other, we demonstrated that the positional requirements are a function of the specific binding site, not the promoter. Supposing that opposite orientation of the SoxS binding site at the two promoters might account for the positional requirements, we placed the zwf and fpr soxboxes in the reverse orientation at the various positions upstream of the promoters and determined the effect of orientation on transcription activation. We found that reversing the orientation of the zwf binding site converts its positional requirement to that of the fpr binding site in its normal orientation, and vice versa. Analysis by molecular information theory of DNA sequences known to bind SoxS in vitro is consistent with the opposite orientation of the zwf and fpr soxboxes.