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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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 centered at position -41.5 upstream of the transcript start, and this activation is modulated by upstream binding of the integration host factor (IHF) and Fis (factor for inversion stimulation) proteins. Thus, transcription initiation is repressed by the binding of IHF and Fis to sites centered 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 under anaerobic growth conditions.

Original languageEnglish
Pages (from-to)7258-7267
Number of pages10
JournalJournal of Bacteriology
Issue number21
Publication statusPublished - Nov 2008


  • Binding Sites/genetics
  • DNA Footprinting
  • DNA-Directed RNA Polymerases/metabolism
  • Escherichia coli/genetics
  • Escherichia coli Proteins/genetics
  • Factor For Inversion Stimulation Protein/genetics
  • Integration Host Factors/genetics
  • Iron-Sulfur Proteins/genetics
  • Models, Genetic
  • Operon/genetics
  • Promoter Regions, Genetic/genetics
  • Transcription, Genetic/genetics


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