Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding

Bacterial RNA polymerases must associate with a sigma factor to bind promoter DNA and initiate transcription. There are two families of s factor: the sigma(70) family and the sigma(54) family. Members of the sigma(54) family are distinct in their ability to bind promoter DNA sequences, in the context of RNA polymerase holoenzyme, in a transcriptionally inactive state. Here, we map the genome-wide association of Escherichia coli sigma(54), the archetypal member of the sigma(54) family. Thus, we vastly expand the list of known sigma(54) binding sites to 135. Moreover, we estimate that there are more than 250 sigma(54) sites in total. Strikingly, the majority of sigma(54) binding sites are located inside genes. The location and orientation of intragenic sigma(54) binding sites is non-random, and many intragenic sigma(54) binding sites are conserved. We conclude that many intragenic sigma(54) binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic sigma(54) promoters that drive transcription of mRNAs with unusually long 5' UTRs.