Helicobacter pylori FlgR is an enhancer-independent activator of σ54-RNA polymerase holoenzyme

Helicobacter pylori FlgR activates transcription with sigma(54)-RNA polymerase holoenzyme (sigma(54)-holoenzyme) from at least five flagellar operons. Activators of sigma(54)-holoenzyme generally bind enhancer sequences located >70 bp upstream of the promoter and contact sigma(54)-holoenzyme bound at the promoter through DNA looping to activate transcription. H. pylori FlgR lacks the carboxy-terminal DNA-binding domain present in Most sigma(54)-dependent activators. As little as 42 bp of DNA upstream of the flaB promoter and 26 bp of DNA sequence downstream of the transcriptional start site were sufficient for efficient FlgR-mediated expression from a flaB'-xylE reporter gene in H. pylori, indicating that FlgR does not use an enhancer to activate transcription. Other examples of sigma(54)-dependent activators that lack a DNA-binding domain include Chlamydia trachomatis CtcC and activators from the other Chlamydia spp. whose genomes have been sequenced. FlgR from Helicobacter hepaticus and Campylobacter jejuni, which are closely related to H. pylori, appear to have carboxy-terminal DNA-binding domains, suggesting that the loss of the DNA-binding domain from H. pylori FlgR occurred after the divergence of these bacterial species. Removal of the amino-terminal regulatory domain of FlgR resulted in a constitutively active form of the protein that activated transcription from sigma(54)-dependent genes in Escherichia coli. The truncated FlgR protein also activated transcription with E. coli sigma(54)-holoenzyme in an in vitro transcription assay.