Abstract

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.