Genome-Scale Mapping of Escherichia coli σ54Reveals Widespread, Conserved Intragenic Binding

Abstract

Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription. There are two families of σ factor: the σ70family and the σ54family. Members of the σ54family 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 σ54, the archetypal member of the σ54family. Thus, we vastly expand the list of known σ54binding sites to 135. Moreover, we estimate that there are more than 250 σ54sites in total. Strikingly, the majority of σ54binding sites are located inside genes. The location and orientation of intragenic σ54binding sites is non-random, and many intragenic σ54binding sites are conserved. We conclude that many intragenic σ54binding sites are likely to be functional. Consistent with this assertion, we identify three conserved, intragenic σ54promoters that drive transcription of mRNAs with unusually long 5ʹ UTRs.