FeON-FeOFF: the Helicobacter pylori Fur regulator commutates iron-responsive transcription by discriminative readout of opposed DNA grooves

Agriesti, Francesca; Roncarati, Davide; Musiani, Francesco; Campo, Cristian Del; Iurlaro, Mario; Sparla, Francesca; Danielli, Alberto; Scarlato, Vincenzo

doi:10.1093/nar/gkt1258

Cited by 37 publications

(64 citation statements)

References 68 publications

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“…2A,B). This result was unexpected because previous reports indicated that apo-Fur is mainly a dimer while holo-Fur is prevalently represented by tetramers or higher order oligomers12. Because the high surface charge of mica can readily disrupt the protein quaternary structure, we used glutaraldehyde crosslinking to fix the Fur oligomeric states.…”

Section: Resultsmentioning

confidence: 86%

Metal-responsive promoter DNA compaction by the ferric uptake regulator

et al. 2016

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Short-range DNA looping has been proposed to affect promoter activity in many bacterial species and operator configurations, but only few examples have been experimentally investigated in molecular detail. Here we present evidence for a metal-responsive DNA condensation mechanism controlled by the Helicobacter pylori ferric uptake regulator (Fur), an orthologue of the widespread Fur family of prokaryotic metal-dependent regulators. H. pylori Fur represses the transcription of the essential arsRS acid acclimation operon through iron-responsive oligomerization and DNA compaction, encasing the arsR transcriptional start site in a repressive macromolecular complex. A second metal-dependent regulator NikR functions as nickel-dependent anti-repressor at this promoter, antagonizing the binding of Fur to the operator elements responsible for the DNA condensation. The results allow unifying H. pylori metal ion homeostasis and acid acclimation in a mechanistically coherent model, and demonstrate, for the first time, the existence of a selective metal-responsive DNA compaction mechanism controlling bacterial transcriptional regulation.

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Section: Resultsmentioning

confidence: 86%

Metal-responsive promoter DNA compaction by the ferric uptake regulator

et al. 2016

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“…The holo-HpNikR model structure in the cis conformation was docked onto OP ureA using the data-driven docking program HADDOCK 2.1 [42,43] and a previously described protocol [44] that involves a two-stage protein-DNA docking approach [45]. In the first docking round, a rigid body energy minimization was carried out, 1000 structures were calculated and the 200 best solutions based on the intermolecular energy were used for a semiflexible, simulated annealing step followed by an explicit water refinement.…”

Section: Protein-dna Dockingmentioning

confidence: 99%

On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies

et al. 2015

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Helicobacter pylori (Hp) is a carcinogen that relies on Ni(II) to survive in the extreme pH conditions of the human guts. The regulation of genes coding for Ni(II) enzymes and proteins is effected by the nickel-responsive transcription factor NikR, composed of a DNA-binding domain (DBD) and a metal-binding domain (MBD). The scope of this study is to obtain the molecular details of the HpNikR interaction with the urease operator OP ureA , in solution. The size of the full-length protein prevents the characterization of the HpNikR-OP ureA interaction using NMR. We thus investigated the two separate domains of HpNikR. The conservation of their oligomeric state was established by multiple-angle light scattering. Isothermal calorimetric titrations indicated that the thermodynamics of Ni(II) binding to the isolated MBD is independent of the presence of the adjacent DBDs. The NMR spectra of the isolated DBD support considerable conservation of its structural properties. The spectral perturbations induced on the DBD by OP ureA provided information useful to calculate a structural model of the HpNikR-OP ureA complex using a docking computational protocol. The NMR assignment of the residues involved in the protein-DNA interaction represents a starting point for the development of drugs potentially able to eradicate H. pylori infections. All evidences so far collected, in this and previous studies, consistently indicate that binding of Ni(II) to the MBD increases the HpNikR-DNA affinity by modulating the dynamic, and not the structural, properties of the protein, suggesting that the formation of a stable complex relies upon an induced fit mechanism.

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“…Nucleotide sequence analyses (Tables 2 and 3) revealed the presence of a nonsynonymous fur mutation in all of the HSO strains, and previous studies have shown that Fur regulates the expression of frpB1, fecA1, and pdxA (39,43,(45)(46)(47)(48). Therefore, we hypothesized that the variations in Fur observed among the output strains (i.e., the WT [Fur-R88], Fur-R88H, or Fur-P45T) might account for the differences in frpB1, fecA1, and FIG 3 HSO strains demonstrate increased catalase enzymatic activity and elevated frpB1, pdxA, and fecA1 transcript levels.…”

Section: Figmentioning

confidence: 69%

“…Like Fur in other bacterial species, H. pylori Fur can, in the presence of ferrous iron, repress transcription by binding fur box sequences upstream of target genes. frpB1, fecA1, and pdxA are examples of H. pylori genes repressed by iron-bound Fur (39,43,(45)(46)(47)(48). The Fur R88H and P45T mutations are each located close to Fur amino acid residues important for iron coordination of Fur (E90 and H42, respectively) (55), and therefore, we speculate that these mutations might affect the ability of Fur to regulate its target genes.…”

Section: Figmentioning

confidence: 99%

Helicobacter pylori Adaptation In Vivo in Response to a High-Salt Diet

et al. 2015

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e Helicobacter pylori exhibits a high level of intraspecies genetic diversity. In this study, we investigated whether the diversification of H. pylori is influenced by the composition of the diet. Specifically, we investigated the effect of a high-salt diet (a known risk factor for gastric adenocarcinoma) on H. pylori diversification within a host. We analyzed H. pylori strains isolated from Mongolian gerbils fed either a high-salt diet or a regular diet for 4 months by proteomic and whole-genome sequencing methods. Compared to the input strain and output strains from animals fed a regular diet, the output strains from animals fed a highsalt diet produced higher levels of proteins involved in iron acquisition and oxidative-stress resistance. Several of these changes were attributable to a nonsynonymous mutation in fur (fur-R88H). Further experiments indicated that this mutation conferred increased resistance to high-salt conditions and oxidative stress. We propose a model in which a high-salt diet leads to high levels of gastric inflammation and associated oxidative stress in H. pylori-infected animals and that these conditions, along with the high intraluminal concentrations of sodium chloride, lead to selection of H. pylori strains that are most fit for growth in this environment. Helicobacter pylori is a Gram-negative bacterium that persistently colonizes the human stomach in half of the world's population (1, 2). H. pylori exhibits a high level of intraspecies genetic diversity, characterized by marked variation among strains in gene content, as well as a high level of variation in the nucleotide sequences of individual genes (3, 4). A high rate of allelic diversity is attributable to both a high mutation rate and intraspecies recombination (5, 6).Most H. pylori-infected persons remain asymptomatic, but the presence of this bacterium increases the risk of peptic ulcer disease and gastric cancer (1, 2, 7, 8). The clinical outcome of H. pylori infection is determined by a combination of bacterial, host, and environmental factors. For example, H. pylori strains containing the cag pathogenicity island (PAI) are associated with a higher risk of symptomatic disease than are strains that lack the cag PAI (9). One of the proteins encoded by the cag PAI, CagA, enters host cells and causes numerous cellular alterations linked to malignant transformation (10). The cag PAI also encodes multiple protein components of a type IV secretion system required for entry of CagA into host cells (11). H. pylori strains that secrete specific types of the VacA toxin are also linked to adverse disease outcome, in comparison to strains that secrete relatively nontoxic forms of the VacA protein (12, 13).One of the environmental factors associated with increased gastric cancer risk is a high-salt diet (14). Epidemiologic studies have demonstrated a link between high dietary salt consumption and increased gastric cancer risk in many parts of the world (15-17), and a high-salt diet also increases the gastric cancer risk in animal models (...

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FeON-FeOFF: the Helicobacter pylori Fur regulator commutates iron-responsive transcription by discriminative readout of opposed DNA grooves

Cited by 37 publications

References 68 publications

Metal-responsive promoter DNA compaction by the ferric uptake regulator

Metal-responsive promoter DNA compaction by the ferric uptake regulator

On the interaction of Helicobacter pylori NikR, a Ni(II)-responsive transcription factor, with the urease operator: in solution and in silico studies

Helicobacter pylori Adaptation In Vivo in Response to a High-Salt Diet

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