rRNA Promoter Regulation by Nonoptimal Binding of Sigma Region 1.2: An Additional Recognition Element for RNA Polymerase

Cell. 2006 Jun 16;125(6):1069-82. doi: 10.1016/j.cell.2006.04.034.


Regulation of transcription initiation is generally attributable to activator/repressor proteins that bind to specific DNA sequences. However, regulators can also achieve specificity by binding directly to RNA polymerase (RNAP) and exploiting the kinetic variation intrinsic to different RNAP-promoter complexes. We report here a previously unknown interaction with Escherichia coli RNAP that defines an additional recognition element in bacterial promoters. The strength of this sequence-specific interaction varies at different promoters and affects the lifetime of the complex with RNAP. Selection of rRNA promoter mutants forming long-lived complexes, kinetic analyses of duplex and bubble templates, dimethylsulfate footprinting, and zero-Angstrom crosslinking demonstrated that sigma subunit region 1.2 directly contacts the nontemplate strand base two positions downstream of the -10 element (within the "discriminator" region). By making a nonoptimal sigma1.2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Footprinting
  • DNA-Directed RNA Polymerases / genetics
  • DNA-Directed RNA Polymerases / physiology*
  • Escherichia coli / enzymology
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / physiology
  • Indicators and Reagents
  • Models, Molecular
  • Mutation
  • Promoter Regions, Genetic*
  • Protein Binding
  • Sigma Factor / genetics
  • Sigma Factor / metabolism*
  • Sulfuric Acid Esters
  • Templates, Genetic
  • Transcription, Genetic*
  • rRNA Operon


  • Escherichia coli Proteins
  • Indicators and Reagents
  • Sigma Factor
  • Sulfuric Acid Esters
  • dksA protein, E coli
  • DNA-Directed RNA Polymerases
  • dimethyl sulfate