Architecture of fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters

The transcription factor Fis activates the Escherichia coli rRNA promoters rrnB P1 and rrnE P1 by binding to sites centered at −71 and −72, respectively, and interacting with the C-terminal domain of the α subunit of RNA polymerase (RNAP αCTD). To understand the mechanism of activation by Fis at these promoters, we used oriented α-heterodimeric RNAPs and heterodimers of Fis to determine whether one or both subunits of α and Fis participate in the αCTD-Fis interaction. Our results imply that only one αCTD in the α dimer and only one activation-proficient subunit in the Fis dimer are required for activation by Fis. A library of alanine substitutions in α was used to identify the αCTD determinants required for Fis-dependent transcription at rrnB P1 and rrnE P1. We propose that the transcriptional activation region of the promoter-proximal subunit of the Fis dimer interacts with a determinant that includes E273 of one αCTD to activate transcription. We further suggest that the Fis contact to αCTD results in αCTD interactions with DNA that differ somewhat from those that occur at UP elements in the absence of Fis. The accompanying paper shows that the 273 determinant on αCTD is also targeted by Fis at the proP P2 promoter where the activator binds overlapping the −35 hexamer. Thus, similar Fis-αCTD interactions are used for activation of transcription when the activator is bound at very different positions on the DNA.