JB Accepts, published online ahead of print on 29 August 2008

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J. Bacteriol. doi:10.1128/JB.01015-08
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter

Douglas F. Browning^*, Jeffrey A. Cole, and Stephen J. W. Busby

School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK

^* To whom correspondence should be addressed. Email: D.F.Browning{at}bham.ac.uk.

The Escherichia coli K-12 nir operon promoter can be fully activated by binding of the regulator of fumarate and nitrate reduction (FNR) to a site centred at position -41.5 upstream of the transcript start, and this activation is modulated by upstream binding of integration host factor (IHF) and factor for inversion stimulation (Fis). Thus, transcription initiation is repressed by IHF and Fis binding to sites centred at position -88 (IHF I) and position -142 (Fis I), and activated by IHF binding to a site at position -115 (IHF II). Here, we have exploited mutational analysis and biochemistry to investigate the actions of IHF and Fis at these sites. We show that the effects of IHF and Fis are position dependent, and that IHF II functions independently of IHF I and Fis I. Using in vitro assays, we report that IHF and Fis repress transcription initiation by interfering with RNA polymerase binding. Differences in the upstream IHF and Fis binding sites at the nir promoter in related enteric bacteria fix the level of nir operon expression in anaerobic growth conditions.

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