Structure and regulon of Campylobacter jejuni ferric uptake regulator Fur define apo-Fur regulation

Abstract

The full regulatory potential of the ferric uptake regulator (Fur) family of proteins remains undefined despite over 20 years of study. We report herein an integrated approach that combines both genome-wide technologies and structural studies to define the role of Fur in Campylobacter jejuni (Cj). CjFur ChIP-chip assays identified 95 genomic loci bound by CjFur associated with functions as diverse as iron acquisition, flagellar biogenesis, and non-iron ion transport. Comparative analysis with transcriptomic data revealed that CjFur regulation extends beyond solely repression and also includes both gene activation and iron-independent regulation. Computational analysis revealed the presence of an elongated holo-Fur repression motif along with a divergent holo-Fur activation motif. This diversity of CjFur DNA-binding elements is supported by the crystal structure of CjFur, which revealed a unique conformation of its DNA-binding domain and the absence of metal in the regulatory site. Strikingly, our results indicate that the apoCjFur structure retains the canonical V-shaped dimer reminiscent of previously characterized holo-Fur proteins enabling DNA interaction. This conformation stems from a structurally unique hinge domain that is poised to further contribute to CjFur's regulatory functions by modulating the orientation of the DNA-binding domain upon binding of iron. The unique features of the CjFur crystal structure rationalize the binding sequence diversity that was uncovered during ChIP-chip analysis and defines apo-Fur regulation.gene regulation | metal regulation | transcription factor | DNA-protein interactions | structural characterization

Inactivation of the LysR regulator Cj1000 of Campylobacter jejuni affects host colonization and respiration

“…Nevertheless, the expression of most genes involved in respiratory functions is modulated by iron (Butcher et al, , 2012, whereas only three of them, napA, napG and cj0415, are direct targets of Fur (Butcher et al, 2012). Cj1000 may be a key regulator of regulatory functions in C. jejuni.…”

“…In C. jejuni, peroxide-sensing and iron-uptake mechanisms are mainly controlled by two regulators, PerR and Fur, which share a partially overlapping regulon. Their respective regulons have been partially defined but remain still not completely understood, suggesting the presence of unknown elements (Butcher et al, , 2012.…”

“…Under microaerobic conditions, oxygen is reduced by either a low-O 2 -affinity CioAB oxidase or by a cytochrome cb9 oxidase (Jackson et al, 2007). This diversity is likely essential for the C. jejuni ability to colonize and survive in various ecological niches (Butcher et al, 2012;Weingarten et al, 2008).…”

The Fur homologue BosR requires Arg39 to activate rpoS transcription in Borrelia burgdorferi and thereby direct spirochaete infection in mice

“…Pfam alignments of FUR proteins (PF01475) show that BosR's Arg39 aligns with a highly conserved arginine present in virtually all FUR proteins. X-ray crystallography studies show that FUR proteins consist of two domains: an N-terminal DNA-binding domain and a C-terminal dimerization domain Butcher et al, 2012;Dian et al, 2011;Gilston et al, 2014;Jacquamet et al, 2009;Lin et al, 2014;Lucarelli et al, 2007;Makthal et al, 2013;Pohl et al, 2003;Sheikh & Taylor, 2009;Shin et al, 2011;Traoré et al, 2006Traoré et al, , 2009. The DNA-binding domain contains a winged helix-turn-helix (wHTH) motif that provides the protein with the means to bind DNA (Pohl et al, 2003).…”

α-fur, an antisense RNA gene to fur in the extreme acidophile Acidithiobacillus ferrooxidans

“…Genes regulated in this manner include those involved in the biosynthesis of siderophores and iron uptake (Friedman & O'Brian, 2003; Quatrini et al, 2007;Gao et al, 2008;Butcher et al, 2012), genes encoding small RNAs such as fsrA and ryhB (Smaldone et al, 2012;Massé & Gottesman, 2002;Salvail & Massé, 2012), and many other genes involved in iron homeostasis (reviewed by Salvail & Massé, 2012). Under iron-limiting conditions, Fur no longer binds Fe 2+ , reducing its affinity for Fur boxes and thus allowing transcription to proceed (Baichoo et al, 2002;Ochsner et al, 2002;Butcher et al, 2012). In the case of the siderophore and iron-uptake genes, this results in increased uptake of iron into the cell.…”