DISCRIMINATIVE RECOGNITION OF MAJOR OR MINOR DNA GROOVES DRIVES IRON-RESPONSIVE FUR REGULATION IN THE HUMAN PATHOGEN HELICOBACTER PYLORI

Transcription factors (TFs) regulate gene expression by modulating their DNA binding affinity in response to a particular signal, or in the presence of a specific cofactor, much akin simple on-off switches. Whilst the vast majority of TFs recognize distinct elements through the readout of conserved nucleotide motifs in the major groove of DNA, a few are able to bind in the minor groove. Here we report the finding of a TF able to discriminatively exploit the binding to either the major or the minor DNA groove in order to mediate opposite read-out of the same regulatory signal. This mechanism accounts for the ability of the ferric uptake regulator Fur, a widespread prokaryotic transcriptional regulator involved in metal ion homeostasis and virulence in many bacteria, to repress the expression of both iron-induced and iron-repressed genes in the human pathogen Helicobacter pylori. In particular, we demonstrate that Fur exploits the two grooves of DNA to function like a molecular commutator switch. It binds with higher affinity to an iron-induced promoter in the apo-form, through the readout of a specific nucleotide motif in the major groove, contributing to its repression under iron-deplete conditions. Conversely, on iron-repressed promoters, the metal ion acts as co-repressor, inducing protein conformational changes that prompt the recognition of AT-rich stretches in the minor groove. This mechanism is mediated by an Arg residue in helix H1 of the Fur DNA-binding domain, and provides a novel regulatory paradigm that may be exploited also in other bacteria.