Common sequence determinants of the response of a prokaryotic promoter to DNA bending and supercoiling

Abstract

Inhibiting the activity of DNA gyrase by mutation or by drugs in S. typhimurium causes the loss of transcription attenuation in the histidine operon. We show that gyrase activity is needed to maintain high-level expression of the tRNA(His) gene (hisR), a prerequisite for proper functioning of the attenuation mechanism. A point mutation in the promoter of the tRNA gene cluster which includes the hisR gene, specifically relieves the promoter response to negative supercoiling thereby restoring full hisR transcription (and, in turn, his attenuation) in the presence of a defective gyrase. The very same mutation, a single base-pair substitution between the -10 box and the transcription start site (-7), was found independently among suppressors of the transcriptional deficiency caused by disruption of DNA curvature upstream from the hisR promoter. We show that the -7 change does not lead to a generalized increase of promoter strength; the effects of the mutation are seen only when gyrase is inhibited or the upstream curvature is altered. This suggests that the upstream curvature intervenes in the same initiation step which is sensitive to superhelical tension. Three additional promoter mutations correcting (or alleviating) the effects of the upstream alteration (including a change at -8) are described and discussed.