Discriminative Recognition of Major or Minor DNA Grooves Commutates Between Iron-inducible and Iron-repressible Fur Regulation in the Human Pathogen Helicobacter pylori

According to the grounding work of Jacob and Monod, 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 inducible or repressible 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 specifically 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-inducible and iron-repressible 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. In the apo-form, Fur binds with higher affinity to an iron-induced promoter as dimer, through the readout of thymine dimers in the major groove, contributing to its transcriptional repression under iron-deplete conditions. Conversely, on iron-repressed promoters, the metal ion acts as co-repressor, inducing protein conformational changes that prompt multimerization of the regulator and high affinity binding to the minor groove in occurrence of AT-rich inverted repeats. The latter mechanism appears to involve an Arg residue in helix H1 of the HTH-DNA-binding domain. In addition, molecular modelling and in silico docking indicate that binding to the minor groove involves conformation of the HTH-DNA binding domains of four Fur monomers into a tetrameric DNA clamp. These results provide evidence for a novel regulatory mechanism that may be exploited also in other bacteria