Interactions Between the 2.4 and 4.2 Regions of sigmaS, the Stress-Specific Sigma Factor of Escherichia Coli, and the -10 and -35 Promoter Elements

Nucleic Acids Res. 2004 Jan 2;32(1):45-53. doi: 10.1093/nar/gkh155. Print 2004.


The sigmas subunit of Escherichia coli RNA polymerase holoenzyme (EsigmaS) is a key factor of gene expression upon entry into stationary phase and in stressful conditions. The selectivity of promoter recognition by EsigmaS and the housekeeping Esigma70 is as yet not clearly understood. We used a genetic approach to investigate the interaction of sigmaS with its target promoters. Starting with down-promoter variants of a sigmaS promoter target, osmEp, altered in the -10 or -35 elements, we isolated mutant forms of sigmaS suppressing the promoter defects. The activity of these suppressors on variants of osmEp and ficp, another target of sigmaS, indicated that sigmaS is able to interact with the same key features within a promoter sequence as sigma70. Indeed, (i) sigmaS can recognize the -35 element of some but not all its target promoters, through interactions with its 4.2 region; and (ii) amino acids within the 2.4 region participate in the recognition of the -10 element. More specifically, residues Q152 and E155 contribute to the strong preference of sigmaS for a C in position -13 and residue R299 can interact with the -31 nucleotide in the -35 element of the target promoters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution / genetics
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial
  • Genes, Bacterial / genetics
  • Holoenzymes / chemistry
  • Holoenzymes / genetics
  • Holoenzymes / metabolism
  • Membrane Proteins / genetics
  • Molecular Sequence Data
  • Mutation / genetics
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • Response Elements / genetics*
  • Sigma Factor / chemistry*
  • Sigma Factor / genetics
  • Sigma Factor / metabolism*
  • Suppression, Genetic / genetics


  • Bacterial Proteins
  • Escherichia coli Proteins
  • Holoenzymes
  • Membrane Proteins
  • OsmE protein, E coli
  • Sigma Factor
  • sigma factor KatF protein, Bacteria

Associated data

  • PDB/1L9Z