Activation by NarL at the Escherichia coli ogt promoter

Biochem J. 2020 Aug 14;477(15):2807-2820. doi: 10.1042/BCJ20200408.


The Escherichia coli NarX/NarL two-component response-regulator system regulates gene expression in response to nitrate ions and the NarL protein is a global transcription factor, which activates transcript initiation at many target promoters. One such target, the E. coli ogt promoter, which controls the expression of an O6-alkylguanine-DNA-alkyltransferase, is dependent on NarL binding to two DNA targets centred at positions -44.5 and -77.5 upstream from the transcript start. Here, we describe ogt promoter derivatives that can be activated solely by NarL binding either at position -44.5 or position -77.5. We show that NarL can also activate the ogt promoter when located at position -67.5. We present data to argue that NarL-dependent activation of transcript initiation at the ogt promoter results from a direct interaction between NarL and a determinant in the C-terminal domain of the RNA polymerase α subunit. Footprinting experiments show that, at the -44.5 promoter, NarL and the C-terminal domain of the RNA polymerase α subunit bind to opposite faces of promoter DNA, suggesting an unusual mechanism of transcription activation. Our work suggests new organisations for activator-dependent transcription at promoters and future applications for biotechnology.

Keywords: NarL; molecular interactions; promoters; transcription activation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA-Binding Proteins / genetics*
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli K12 / genetics*
  • Escherichia coli Proteins / genetics*
  • Gene Expression Regulation, Bacterial / drug effects
  • Methyltransferases / genetics*
  • Nitrates / pharmacology
  • Promoter Regions, Genetic*
  • Transcription Initiation, Genetic


  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Nitrates
  • NarL protein, E coli
  • Methyltransferases
  • Ogt protein, E coli
  • DNA-Directed RNA Polymerases
  • RNA polymerase alpha subunit