Extensive functional overlap between σ factors in Escherichia coli

Bacterial core RNA polymerase (RNAP) must associate with a σ factor to recognize promoter sequences. Escherichia coli encodes seven σ 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 σ 32 , the heat-shock σ factor, and estimate that there are 120–150 σ 32 promoters in total. Unexpectedly, 25% of these σ 32 targets are located within coding regions, suggesting novel regulatory roles for σ 32 . The majority of σ 32 promoter targets overlap with those of σ 70 , the housekeeping σ factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAPσ 70 and RNAPσ 32 initiating transcription in vitro with similar efficiency and from identical positions. σ E -regulated promoters also overlap extensively with those for σ 70 . These results suggest that extensive functional overlap between σ factors is an important phenomenon.