Extensive functional overlap between sigma factors in Escherichia coli

Nat Struct Mol Biol. 2006 Sep;13(9):806-14. doi: 10.1038/nsmb1130. Epub 2006 Aug 6.


Bacterial core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Escherichia coli encodes seven sigma factors, each believed to be specific for a largely distinct subset of promoters. Using microarrays representing the entire E. coli genome, we identify 87 in vivo targets of sigma32, the heat-shock sigma factor, and estimate that there are 120-150 sigma32 promoters in total. Unexpectedly, 25% of these sigma32 targets are located within coding regions, suggesting novel regulatory roles for sigma32. The majority of sigma32 promoter targets overlap with those of sigma70, the housekeeping sigma factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAPsigma70 and RNAPsigma32 initiating transcription in vitro with similar efficiency and from identical positions. SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli / enzymology*
  • Heat-Shock Proteins / metabolism*
  • Open Reading Frames / genetics
  • Promoter Regions, Genetic / genetics
  • Sigma Factor / metabolism*
  • Transcription, Genetic


  • Heat-Shock Proteins
  • Sigma Factor
  • heat-shock sigma factor 32
  • RNA polymerase sigma 70
  • DNA-Directed RNA Polymerases