Extensive functional overlap between σ factors in Escherichia coli

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