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

Wamiah P Chowdhury,Patricia J Kiley,Kenneth A Satyshur,James L Keck,Susan Gottesman

doi:10.1128/mbio.02753-21

Wamiah P Chowdhury, Patricia J Kiley + Show 3 more

Open Access

https://doi.org/10.1128/mbio.02753-21

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Journal: mBio	Publication Date: Nov 2, 2021
Citations: 1	License type: CC BY 4.0

Affiliation: University of Wisconsin–Madison

Abstract

ABSTRACTIscR 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.

Highlights

iron-sulfur cluster regulator (IscR) is a global transcription factor that regulates Fe-S cluster homeostasis and other functions in Escherichia coli by either activating or repressing transcription
Since the 235 hexamer is suboptimal in this promoter, we predicted that IscR might activate transcription of PydiU by recruiting RNA polymerase
Our results show that IscR recruits s 70 RNA polymerase to PydiU, which contains a suboptimal 235 promoter element

Summary

Introduction

IscR is a global transcription factor that regulates Fe-S cluster homeostasis and other functions in Escherichia coli by either activating or repressing transcription. 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. In addition to the isc and suf operons, IscR regulates 40 other genes in E. coli [22] Promoters of these genes contain either a type I or a type II IscR binding site [22]. Type I sites are bound only by holo-IscR; promoters containing type I sites (e.g., the isc operon) are regulated by IscR primarily under anaerobic conditions [22]. E43 of the recognition helix plays an important role in discriminating between type I and II sites since the negative charge favors electrostatic interactions with the exocyclic amines of the CC dinucleotides in type II sites but would disrupt binding to type I sites, which contain TT at the corresponding positions in one half-site [24]

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