Minor Alterations in Core Promoter Element Positioning Reveal Functional Plasticity of a Bacterial Transcription Factor.

IscR is a global transcription factor that regulates Fe-S cluster homeostasis and other functions in Escherichia coli by either activating or repressing transcription. While the interaction of IscR with its DNA sites has been studied, less is known about the mechanism of IscR regulation of transcription. Here, we show that IscR recruits RNA polymerase to an activated promoter and that IscR binding compensates for the lack of an optimal RNA polymerase σ70 -35 promoter element. We also find that the position of the -35 promoter element within the IscR DNA site impacts whether IscR activates or represses transcription. RNA polymerase binding at a distally positioned -35 element within the IscR site results in IscR activation. Molecular modeling suggests that this position of the -35 element allows IscR and RNA polymerase to bind to the promoter from opposite faces of the helix. Shifting the -35 element 1 nucleotide upstream within the IscR binding site results in IscR repression and a steric clash of IscR and RNA polymerase binding in the models. We propose that the sequence similarity of the IscR binding site with the -35 element is an important feature in allowing plasticity in the mechanism of IscR regulation. IMPORTANCE Transcription regulation is a key process in all living organisms, involving a myriad of transcription factors. In E. coli, the regulator of the iron-sulfur cluster biogenesis pathway, IscR, acts as a global transcription factor, activating the transcription of some pathways and repressing others. The mechanism by which IscR is able to activate and repress from a similar sequence space within bacterial promoter elements was not known. In this work, we show that subtle changes in the position of the σ70 -35 promoter element within an IscR binding site can switch the role of IscR from an activator to a repressor. Our work provides insights as to how the IscR site might have evolved around the -35 promoter element to allow a single transcription factor to differentially regulate promoters.