Genome-Scale Mapping of Escherichia coli σ(54) Reveals Widespread, Conserved Intragenic Binding

Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ(70) family and the σ(54) family. Members of the σ(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 σ(54), the archetypal member of the σ(54) family. Thus, we vastly expand the list of known σ(54) binding sites to 135. Moreover, we estimate that there are more than 250 σ(54) sites in total. Strikingly, the majority of σ(54) binding sites are located inside genes. The location and orientation of intragenic σ(54) binding sites is non-random, and many intragenic σ(54) binding sites are conserved. We conclude that many intragenic σ(54) binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ(54) promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs.