Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization

Mol Microbiol. 2010 Mar;75(5):1098-111. doi: 10.1111/j.1365-2958.2009.06913.x. Epub 2009 Oct 15.


The Escherichia coli aer regulatory region contains a single promoter that is recognized by RNA polymerase containing the flagellar sigma factor, sigma(28). Expression from this promoter is dependent on direct activation by the cyclic AMP receptor protein, which binds to a target centred 49.5 base pairs upstream from the transcript start. Activator-dependent transcription from the aer promoter was reconstituted in vitro, and a tethered inorganic nuclease was used to find the position of the C-terminal domains of the RNA polymerase alpha subunits in transcriptionally competent open complexes. We report that the ternary activator--RNA polymerase--aer promoter open complex is organized differently from complexes at previously characterized promoters. Among other E. coli promoters recognized by RNA polymerase containing sigma(28), only the trg promoter is activated directly by the cyclic AMP receptor protein. The organization of the different promoter elements and the activator binding site at the trg promoter is the same as at the aer promoter, suggesting a common activation mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Carrier Proteins / biosynthesis*
  • Carrier Proteins / genetics*
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli / genetics*
  • Escherichia coli / physiology
  • Escherichia coli Proteins / biosynthesis*
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism*
  • Genes, Reporter
  • Intercellular Signaling Peptides and Proteins
  • Models, Biological
  • Molecular Sequence Data
  • Promoter Regions, Genetic*
  • Receptors, Cyclic AMP / metabolism*
  • Sigma Factor / metabolism*
  • Transcription, Genetic*
  • beta-Galactosidase / metabolism


  • Aer protein, E coli
  • Bacterial Proteins
  • Carrier Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • FliA protein, Bacteria
  • Intercellular Signaling Peptides and Proteins
  • Receptors, Cyclic AMP
  • Sigma Factor
  • cyclic AMP receptor protein, E coli
  • beta-Galactosidase