Activation and inhibition of transcription by supercoiling

Stimulation of transcriptional activity in vitro is observed at low and moderate negative superhelical densities up to the level of the natural superhelical form of the plasmid pBR322. We have isolated and identified three specific transcription products: ampicillinR RNA, tetracyclineR RNA and "Rep" RNA. Their enhancement of transcription occurs at different levels of superhelicity, suggesting a sequence-dependent structural alteration of promoters upon changes of axial writhe, which may generate kink formation. The activation of transcription is drastically inhibited at higher specific linking differences exceeding that of the natural superhelical form of pBR322, which is correlated with a transition from the right-handed B to a left-handed DNA form of particular sequences induced by supercoiling. We have identified a new stop point in the beta-lactamase coding sequence composed of eight alternating purine-pyrimidine residues which, at higher torsional stress, causes transcription to stop, leading to the synthesis of a short RNA of about 55 nucleotides instead of AmpR RNA (about 580 nucleotides). In the "Rep" promoter, two alternating purine-pyrimidine segments are found, which conformational change at higher superhelical densities may be implicated in repression of "Rep" RNA synthesis. The enhancement and inhibition of transcription by supercoiling support the role of energetic and structural changes in topologically constrained DNA as elements of a control mechanism.