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Nucleic Acids Research, 1990, Vol. 18, No. 5 1137-1143
© 1990

MOLECULAR BIOLOGY

Transcription in vivo directed by consensus sequences of E.coli promoters: their context heavily affects efficiencies and start sites

Marie-Ange Jacquet* and Claude Reiss

Institut Jacques Monod, CNRS-Université Paris VII tour 43, 2 Place Jussieu, 75251 Paris Cedex 05, France

*To whom correspondence should be addressed

Received December 14, 1989. Revised January 29, 1990. Accepted January 29, 1990.

We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer ilnking them is AT or GC rich, or is as short as 14 bp or as large as 26 bp (standard size 17 bp). However, we find that the context Influences transcription efficiency by as much as an order of magnitude, and is able to scatter transcription start sites over a region of as much as 30 bp, including start sites within a CH or even between the two sequences of the CH pair. The results demonstrate that, aithough the CH pair can be sufficient for directing transcription by E.coli RNAP, important determinants for promoter activity are at least in part contained in the context of the consensus sequences; they advocate a synergic interplay of signals borne by the CH pair and its context, extending over au parts of the promoter sequence. A two-step model is proposed, in which properly located consensus sequences provide RNAP with facilities required for stereospecific docking along the promoter sequence; the result would be a sharp change in the local environment of the double helix inducing local isothermal unwinding. The size of the loop (related to the AT constraint in the promoter) and the extend of the environmental change required for unwinding would determine the rate of transcriptionalty competent complex formation, positioning and grouping of start sites.


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