Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states

BMC Biol. 2014 Jan 24;12:4. doi: 10.1186/1741-7007-12-4.


Background: At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a σ-factor to recognize the genomic location at which the process initiates. Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function.

Results: Using multiple genome-scale measurements, we elucidated the network of σ-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 σ-factor-specific promoters corresponding to transcription units (TUs), representing an increase of more than 300% over what has been previously reported. The reconstructed network was used to investigate competition between alternative σ-factors (the σ70 and σ38 regulons), confirming the competition model of σ substitution and negative regulation by alternative σ-factors. Comparison with σ-factor binding in Klebsiella pneumoniae showed that transcriptional regulation of conserved genes in closely related species is unexpectedly divergent.

Conclusions: The reconstructed network reveals the regulatory complexity of the promoter architecture in prokaryotic genomes, and opens a path to the direct determination of the systems biology of their transcriptional regulatory networks.

Publication types

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

MeSH terms

  • DNA-Directed RNA Polymerases / metabolism
  • Databases, Genetic
  • Escherichia coli / genetics*
  • Gene Regulatory Networks*
  • Genome, Bacterial / genetics*
  • Holoenzymes / metabolism
  • Promoter Regions, Genetic
  • Protein Binding
  • Regulon / genetics
  • Sigma Factor / chemistry*
  • Sigma Factor / metabolism*
  • Transcription Initiation Site
  • Transcription, Genetic


  • Holoenzymes
  • Sigma Factor
  • DNA-Directed RNA Polymerases

Associated data

  • GEO/GSE46740