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Biochem Biophys Res Commun. 2002 Apr 12;292(4):922-30.

Mechanism of specific recognition of the aidB promoter by sigma(S)-RNA polymerase.

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Swiss Federal Institute of Environmental Technology (EAWAG), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland.


Transcription of the Escherichia coli aidB gene is controlled by an Esigma(S)-dependent promoter (PaidB) and is poorly transcribed by the Esigma(70) form of RNA polymerase in the absence of additional factors. In this report, we investigate the interaction between PaidB and either the Esigma(70) or the Esigma(S) forms of RNA polymerase in vitro. We show that although Esigma(70) can bind the aidB promoter, its interaction with the promoter results in the formation of an open complex inefficient in transcription initiation and sensitive to heparin challenge. Deletion of the C residue at position -13 of PaidB (Delta-13C) slightly impaired transcription initiation by Esigma(S), consistent with the role of -13C as a specific feature of Esigma(S)-dependent promoters. However, Esigma(S) could still bind and initiate transcription from the Delta-13C mutant aidB promoter more efficiently than Esigma(70), suggesting that sequence elements other than the -13C play an important role in specific promoter recognition by Esigma(S).

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