The ferric uptake regulation (Fur) repressor is a zinc metalloprotein

Iron uptake pathway of Escherichia coli as an entry route for peptide nucleic acids conjugated with a siderophore mimic

Bacteria secrete various iron-chelators (siderophores), which scavenge Fe3+ from the environment, bind it with high affinity, and retrieve it inside the cell. After the Fe3+ uptake, bacteria extract the soluble iron(II) from the siderophore. Ferric siderophores are transported inside the cell via the TonB-dependent receptor system. Importantly, siderophore uptake paths have been also used by sideromycins, natural antibiotics. Our goal is to hijack the transport system for hydroxamate-type siderophores to deliver peptide nucleic acid oligomers into Escherichia coli cells. As siderophore mimics we designed and synthesized linear and cyclic Nδ-acetyl-Nδ-hydroxy-l-ornithine based peptides. Using circular dichroism spectroscopy, we found that iron(III) is coordinated by the linear trimer with hydroxamate groups but not by the cyclic peptide. The internal flexibility of the linear siderophore oxygen atoms and their interactions with Fe3+ were confirmed by all-atom molecular dynamics simulations. Using flow cytometry we found that the designed hydroxamate trimer transports PNA oligomers inside the E. coli cells. Growth recovery assays on various E. coli mutants suggest the pathway of this transport through the FhuE outer-membrane receptor, which is responsible for the uptake of the natural iron chelator, ferric-coprogen. This pathway also involves the FhuD periplasmic binding protein. Docking of the siderophores to the FhuE and FhuD receptor structures showed that binding of the hydroxamate trimer is energetically favorable corroborating the experimentally suggested uptake path. Therefore, this siderophore mimic, as well as its conjugate with PNA, is most probably internalized through the hydroxamate pathway.

Zinc acquisition and its contribution to Klebsiella pneumoniae virulence

Klebsiella pneumoniae is a World Health Organization priority pathogen and a significant clinical concern for infections of the respiratory and urinary tracts due to widespread and increasing resistance to antimicrobials. In the absence of a vaccine, there is an urgent need to identify novel targets for therapeutic development. Bacterial pathogens, including K. pneumoniae, require the d-block metal ion zinc as an essential micronutrient, which serves as a cofactor for ~6% of the proteome. During infection, zinc acquisition necessitates the use of high affinity uptake systems to overcome niche-specific zinc limitation and host-mediated nutritional immunity. Here, we report the identification of ZnuCBA and ZniCBA, two ATP-binding cassette permeases that are highly conserved in Klebsiella species and contribute to K. pneumoniae AJ218 zinc homeostasis, and the high-resolution structure of the zinc-recruiting solute-binding protein ZniA. The Znu and Zni permeases appear functionally redundant with abrogation of both systems required to reduce K. pneumoniae zinc accumulation. Disruption of both systems also exerted pleiotropic effects on the homeostasis of other d-block elements. Zinc limitation perturbed K. pneumoniae cell morphology and compromised resistance to stressors, such as salt and oxidative stress. The mutant strain lacking both systems showed significantly impaired virulence in acute lung infection models, highlighting the necessity of zinc acquisition in the virulence and pathogenicity of K. pneumoniae.

Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs

The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.

RT-IVT method allows multiplex real-time quantification of in vitro transcriptional mRNA production

For the past 30 years, in vitro transcription (IVT) technology has been extensively used for RNA production or for basic transcriptional mechanism research. However, methods for mRNA quantification still need to be improved. In this study, we designed a RT-IVT method using binary fluorescence quencher (BFQ) probes and the PBCV-1 DNA ligase to quantify mRNA production in real-time by fluorescence resonance energy transfer (FRET) and RNA-splinted DNA ligation. Compared with existing methods, the RT-IVT method is inexpensive and non-radioactive, and can detect mRNA production in unpurified systems in real-time and shows high sensitivity and selectivity. The activity of T7 RNA polymerase and Escherichia coli RNA polymerase holoenzyme was then characterized with this method. We then multiplexed the real-time mRNA quantification for three T7 promoters on a RT-PCR thermocycler by using BFQ probes with different colored fluorophores that were specific for each target. Ultimately, we created an inexpensive multiplexed method to quantify mRNA production in real-time, and future research could use these methods to measure the affinity of transcriptional repressors to their target DNA sequence.

A single sensor controls large variations in zinc quotas in a marine cyanobacterium

Marine cyanobacteria are critical players in global nutrient cycles that crucially depend on trace metals in metalloenzymes, including zinc for CO₂ fixation and phosphorus acquisition. How strains proliferating in the vast oligotrophic ocean gyres thrive at ultra-low zinc concentrations is currently unknown. Using Synechococcus sp. WH8102 as a model we show that its zinc-sensor protein Zur differs from all other known bacterial Zur proteins in overall structure and the location of its sensory zinc site. Uniquely, Synechococcus Zur activates metallothionein gene expression, which supports cellular zinc quotas spanning two orders of magnitude. Thus, a single zinc sensor facilitates growth across pico- to micromolar zinc concentrations with the bonus of banking this precious resource. The resultant ability to grow well at both ultra-low and excess zinc, together with overall lower zinc requirements, likely contribute to the broad ecological distribution of Synechococcus across the global oceans.

The zinc-sensor protein Zur in a marine cyanobacterium is distinct from those in other bacteria in structure and location of its sensory zinc site, and facilitates growth across a range of zinc concentrations via activation of a metallothionein gene.

Ferric uptake regulators (Fur) from Vibrio cholerae and Helicobacter pylori bind a [2Fe-2S] cluster in response to elevation of intracellular free iron content

Intracellular iron homeostasis in bacteria is primarily regulated by ferric uptake regulator (Fur). Since its discovery, Fur has been assumed to bind ferrous iron and regulate expression of target genes. However, the iron-bound Fur has never been isolated from any bacteria. In previous studies, we have shown that Escherichia coli Fur and Haemophilus influenzae Fur bind a [2Fe-2S] cluster via the conserved Cys-93 and Cys-96 when expressed in the E. coli mutant cells in which intracellular free iron content is elevated. Here we report that Fur homologs from Vibrio cholerae and Helicobacter pylori which contain Cys-93 and Cys-96 can also bind a [2Fe-2S] cluster. On the other hand, Fur homolog from Magnetospirillum gryphiswaldense MSR-1 which has no cysteine residues fails to bind any [2Fe-2S] clusters. Interestingly, different Fur proteins with the conserved Cys-93 and Cys-96 have distinct binding activities for the [2Fe-2S] cluster, with H. influenzae Fur having the highest, followed by E. coli Fur, V. cholera Fur, and H. pylori Fur. Binding of the [2Fe-2S] cluster in the Fur proteins is significantly decreased when expressed in wild-type E. coli cells, indicating that binding of the [2Fe-2S] clusters in Fur proteins is regulated by the levels of intracellular free iron content. Finally, unlike the [2Fe-2S] clusters in E. coli ferredoxin, the [2Fe-2S] clusters in the Fur proteins are not stable and quickly release ferrous iron when the clusters are reduced, suggesting that Fur may undergo reversible binding of the [2Fe-2S] cluster in response to intracellular free iron content in bacteria.

Structural basis for zinc-induced activation of a zinc uptake transcriptional regulator

The zinc uptake regulator (Zur) is a member of the Fur (ferric uptake regulator) family transcriptional regulators that plays important roles in zinc homeostasis and virulence of bacteria. Upon zinc perception, Zur binds to the promoters of zinc responsive genes and controls their transcription. However, the mechanism underlying zinc-mediated Zur activation remains unclear. Here we report a 2.2-Å crystal structure of apo Zur from the phytopathogen Xanthomonas campestris pv. campestris (XcZur), which reveals the molecular mechanism that XcZur exists in a closed inactive state before regulatory zinc binding. Subsequently, we present a 1.9-Å crystal structure of holo XcZur, which, by contrast, adopts an open state that has enough capacity to bind DNA. Structural comparison and hydrogen deuterium exchange mass spectrometry (HDX-MS) analyses uncover that binding of a zinc atom in the regulatory site, formed by the hinge region, the dimerization domain and the DNA binding domain, drives a closed-to-open conformational change that is essential for XcZur activation. Moreover, key residues responsible for DNA recognition are identified by site-directed mutagenesis. This work provides important insights into zinc-induced XcZur activation and valuable discussions on the mechanism of DNA recognition.

YdiV regulates Escherichia coli ferric uptake by manipulating the DNA-binding ability of Fur in a SlyD-dependent manner

Iron is essential for all bacteria. In most bacteria, intracellular iron homeostasis is tightly regulated by the ferric uptake regulator Fur. However, how Fur activates the iron-uptake system during iron deficiency is not fully elucidated. In this study, we found that YdiV, the flagella gene inhibitor, is involved in iron homeostasis in Escherichia coli. Iron deficiency triggers overexpression of YdiV. High levels of YdiV then transforms Fur into a novel form which does not bind DNA in a peptidyl-prolyl cis-trans isomerase SlyD dependent manner. Thus, the cooperation of YdiV, SlyD and Fur activates the gene expression of iron-uptake systems under conditions of iron deficiency. Bacterial invasion assays also demonstrated that both ydiV and slyD are necessary for the survival and growth of uropathogenic E. coli in bladder epithelial cells. This reveals a mechanism where YdiV not only represses flagella expression to make E. coli invisible to the host immune system, but it also promotes iron acquisition to help E. coli overcome host nutritional immunity.

Ferric uptake regulator (Fur) reversibly binds a [2Fe-2S] cluster to sense intracellular iron homeostasis in Escherichia coli

The ferric uptake regulator (Fur) is a global transcription factor that regulates intracellular iron homeostasis in bacteria. The current hypothesis states that when the intracellular "free" iron concentration is elevated, Fur binds ferrous iron, and the iron-bound Fur represses the genes encoding for iron uptake systems and stimulates the genes encoding for iron storage proteins. However, the "iron-bound" Fur has never been isolated from any bacteria. Here we report that the Escherichia coli Fur has a bright red color when expressed in E. coli mutant cells containing an elevated intracellular free iron content because of deletion of the iron-sulfur cluster assembly proteins IscA and SufA. The acid-labile iron and sulfide content analyses in conjunction with the EPR and Mössbauer spectroscopy measurements and the site-directed mutagenesis studies show that the red Fur protein binds a [2Fe-2S] cluster via conserved cysteine residues. The occupancy of the [2Fe-2S] cluster in Fur protein is ∼31% in the E. coli iscA/sufA mutant cells and is decreased to ∼4% in WT E. coli cells. Depletion of the intracellular free iron content using the membrane-permeable iron chelator 2,2´-dipyridyl effectively removes the [2Fe-2S] cluster from Fur in E. coli cells, suggesting that Fur senses the intracellular free iron content via reversible binding of a [2Fe-2S] cluster. The binding of the [2Fe-2S] cluster in Fur appears to be highly conserved, because the Fur homolog from Hemophilus influenzae expressed in E. coli cells also reversibly binds a [2Fe-2S] cluster to sense intracellular iron homeostasis.

Genetic Regulation of Metal Ion Homeostasis in Staphylococcus aureus

The acquisition of metal ions and the proper maturation of holo-metalloproteins are essential processes for all organisms. However, metal ion homeostasis is a double-edged sword. A cytosolic accumulation of metal ions can lead to mismetallation of proteins and cell death. Therefore, maintenance of proper concentrations of intracellular metals is essential for cell fitness and pathogenesis. Staphylococcus aureus, like all bacterial pathogens, uses transcriptional metalloregulatory proteins to aid in the detection and the genetic response to changes in metal ion concentrations. Herein, we review the mechanisms by which S. aureus senses and responds to alterations in the levels of cellular zinc, iron, heme, and copper. The interplay between metal ion sensing and metal-dependent expression of virulence factors is also discussed.

Evaluation of the regulatory model for Ni2+ sensing by Nur from Streptomyces coelicolor

Streptomyces coelicolor is a soil-dwelling bacterium that is medically important due to its ability to produce several antibiotics, and nickel accumulation within this organism has been shown to prevent the production of the antibiotic undecylprodigiosin. The transcriptional repressor important in regulation of nickel uptake is the homodimeric Nur, a member of the Fur family. Nur contains two metal-binding sites per monomer: the M-site and the Ni-site. The work described here seeks to determine the roles of each of the metal-binding sites to establish a model of Nur activity through mutational studies, metal titrations, and fluorescence anisotropy. Through these studies, a model of Nur activity is proposed in which femtomolar metal binding to one M-site of Nur prompts DNA-binding, and metal binding to the second M-site fully activates the protein. Evidence is provided that shows cooperative metal binding to the Ni-site, but this process dampens affinity for promoter DNA.

Bacterial sensors define intracellular free energies for correct enzyme metalation

There is a challenge for metalloenzymes to acquire their correct metals because some inorganic elements form more stable complexes with proteins than do others. These preferences can be overcome provided some metals are more available than others. However, while the total amount of cellular metal can be readily measured, the available levels of each metal have been more difficult to define. Metal-sensing transcriptional regulators are tuned to the intracellular availabilities of their cognate ions. Here we have determined the standard free energy for metal complex formation to which each sensor, in a set of bacterial metal sensors, is attuned: The less competitive the metal, the less favorable the free energy and hence greater availability to which the cognate allosteric mechanism is tuned. Comparing these free energies with values derived from the metal affinities of a metalloprotein reveals the mechanism of correct metalation exemplified here by a cobalt-chelatase for vitamin B₁₂.

Redox Sensing by Fe2+ in Bacterial Fur Family Metalloregulators

SIGNIFICANCE

Iron is required for growth and is often redox active under cytosolic conditions. As a result of its facile redox chemistry, iron homeostasis is intricately involved with oxidative stress. Bacterial adaptation to iron limitation and oxidative stress often involves ferric uptake regulator (Fur) proteins: a diverse set of divalent cation-dependent, DNA-binding proteins that vary widely in both metal selectivity and sensitivity to metal-catalyzed oxidation. Recent Advances: Bacteria contain two Fur family metalloregulators that use ferrous iron (Fe²⁺) as their cofactor, Fur and PerR. Fur functions to regulate iron homeostasis in response to changes in intracellular levels of Fe²⁺. PerR also binds Fe²⁺, which enables metal-catalyzed protein oxidation as a mechanism for sensing hydrogen peroxide (H₂O₂).

CRITICAL ISSUES

To effectively regulate iron homeostasis, Fur has an Fe²⁺ affinity tuned to monitor the labile iron pool of the cell and may be under selective pressure to minimize iron oxidation, which would otherwise lead to an inappropriate increase in iron uptake under oxidative stress conditions. Conversely, Fe²⁺ is bound more tightly to PerR but exhibits high H₂O₂ reactivity, which enables a rapid induction of peroxide stress genes.

FUTURE DIRECTIONS

The features that determine the disparate reactivity of these proteins with oxidants are still poorly understood. A controlled, comparative analysis of the affinities of Fur/PerR proteins for their metal cofactors and their rate of reactivity with H₂O₂, combined with structure/function analyses, will be needed to define the molecular mechanisms that have facilitated this divergence of function between these two paralogous regulators.

PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

Background

Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activity of other pathways. Past efforts to identify relationships between biological processes have evaluated overlap in knowledge bases or evaluated changes that occur after specific treatments. Individual experiments can highlight condition-specific pathway-pathway relationships; however, constructing a complete network of such relationships across many conditions requires analyzing results from many studies.

Results

We developed PathCORE-T framework by implementing existing methods to identify pathway-pathway transcriptional relationships evident across a broad data compendium. PathCORE-T is applied to the output of feature construction algorithms; it identifies pairs of pathways observed in features more than expected by chance as functionally co-occurring. We demonstrate PathCORE-T by analyzing an existing eADAGE model of a microbial compendium and building and analyzing NMF features from the TCGA dataset of 33 cancer types. The PathCORE-T framework includes a demonstration web interface, with source code, that users can launch to (1) visualize the network and (2) review the expression levels of associated genes in the original data. PathCORE-T creates and displays the network of globally co-occurring pathways based on features observed in a machine learning analysis of gene expression data.

Conclusions

The PathCORE-T framework identifies transcriptionally co-occurring pathways from the results of unsupervised analysis of gene expression data and visualizes the relationships between pathways as a network. PathCORE-T recapitulated previously described pathway-pathway relationships and suggested experimentally testable additional hypotheses that remain to be explored.

Electronic supplementary material

The online version of this article (10.1186/s13040-018-0175-7) contains supplementary material, which is available to authorized users.

The Microbiology of Ruthenium Complexes

Ruthenium is seldom mentioned in microbiology texts, due to the fact that this metal has no known, essential roles in biological systems, nor is it generally considered toxic. Since the fortuitous discovery of cisplatin, first as an antimicrobial agent and then later employed widely as an anticancer agent, complexes of other platinum group metals, such as ruthenium, have attracted interest for their medicinal properties. Here, we review at length how ruthenium complexes have been investigated as potential antimicrobial, antiparasitic and chemotherapeutic agents, in addition to their long and well-established roles as biological stains and inhibitors of calcium channels. Ruthenium complexes are also employed in a surprising number of biotechnological roles. It is in the employment of ruthenium complexes as antimicrobial agents and alternatives or adjuvants to more traditional antibiotics, that we expect to see the most striking developments in the future. Such novel contributions from organometallic chemistry are undoubtedly sorely needed to address the antimicrobial resistance crisis and the slow appearance on the market of new antibiotics.

CO-Releasing Molecules Have Nonheme Targets in Bacteria: Transcriptomic, Mathematical Modeling and Biochemical Analyses of CORM-3 [Ru(CO)3Cl(glycinate)] Actions on a Heme-Deficient Mutant of Escherichia coli

AIMS

Carbon monoxide-releasing molecules (CORMs) are being developed with the ultimate goal of safely utilizing the therapeutic potential of CO clinically, including applications in antimicrobial therapy. Hemes are generally considered the prime targets of CO and CORMs, so we tested this hypothesis using heme-deficient bacteria, applying cellular, transcriptomic, and biochemical tools.

RESULTS

CORM-3 [Ru(CO)3Cl(glycinate)] readily penetrated Escherichia coli hemA bacteria and was inhibitory to these and Lactococcus lactis, even though they lack all detectable hemes. Transcriptomic analyses, coupled with mathematical modeling of transcription factor activities, revealed that the response to CORM-3 in hemA bacteria is multifaceted but characterized by markedly elevated expression of iron acquisition and utilization mechanisms, global stress responses, and zinc management processes. Cell membranes are disturbed by CORM-3.

INNOVATION

This work has demonstrated for the first time that CORM-3 (and to a lesser extent its inactivated counterpart) has multiple cellular targets other than hemes. A full understanding of the actions of CORMs is vital to understand their toxic effects.

CONCLUSION

This work has furthered our understanding of the key targets of CORM-3 in bacteria and raises the possibility that the widely reported antimicrobial effects cannot be attributed to classical biochemical targets of CO. This is a vital step in exploiting the potential, already demonstrated, for using optimized CORMs in antimicrobial therapy.

The Porphyromonas gingivalis ferric uptake regulator orthologue binds hemin and regulates hemin-responsive biofilm development

Porphyromonas gingivalis is a Gram-negative pathogen associated with the biofilm-mediated disease chronic periodontitis. P. gingivalis biofilm formation is dependent on environmental heme for which P. gingivalis has an obligate requirement as it is unable to synthesize protoporphyrin IX de novo, hence P. gingivalis transports iron and heme liberated from the human host. Homeostasis of a variety of transition metal ions is often mediated in Gram-negative bacteria at the transcriptional level by members of the Ferric Uptake Regulator (Fur) superfamily. P. gingivalis has a single predicted Fur superfamily orthologue which we have designated Har (heme associated regulator). Recombinant Har formed dimers in the presence of Zn²⁺ and bound one hemin molecule per monomer with high affinity (K_d of 0.23 µM). The binding of hemin resulted in conformational changes of Zn(II)Har and residue ⁹⁷Cys was involved in hemin binding as part of a predicted -⁹⁷C-⁹⁸P-⁹⁹L- hemin binding motif. The expression of 35 genes was down-regulated and 9 up-regulated in a Har mutant (ECR455) relative to wild-type. Twenty six of the down-regulated genes were previously found to be up-regulated in P. gingivalis grown as a biofilm and 11 were up-regulated under hemin limitation. A truncated Zn(II)Har bound the promoter region of dnaA (PGN_0001), one of the up-regulated genes in the ECR455 mutant. This binding decreased as hemin concentration increased which was consistent with gene expression being regulated by hemin availability. ECR455 formed significantly less biofilm than the wild-type and unlike wild-type biofilm formation was independent of hemin availability. P. gingivalis possesses a hemin-binding Fur orthologue that regulates hemin-dependent biofilm formation.

Structural and mechanistic basis of zinc regulation across the E. coli Zur regulon

Structural, thermodynamic, and gene expression studies provide a comprehensive picture of how the bacterial metalloregulatory transcriptional repressor Zur achieves its exquisite sensitivity to zinc concentrations.

Commensal microbes, whether they are beneficial or pathogenic, are sensitive to host processes that starve or swamp the prokaryote with large fluctuations in local zinc concentration. To understand how microorganisms coordinate a dynamic response to changes in zinc availability at the molecular level, we evaluated the molecular mechanism of the zinc-sensing zinc uptake regulator (Zur) protein at each of the known Zur-regulated genes in Escherichia coli. We solved the structure of zinc-loaded Zur bound to the P_znuABC promoter and show that this metalloregulatory protein represses gene expression by a highly cooperative binding of two adjacent dimers to essentially encircle the core element of each of the Zur-regulated promoters. Cooperativity in these protein-DNA interactions requires a pair of asymmetric salt bridges between Arg52 and Asp49′ that connect otherwise independent dimers. Analysis of the protein-DNA interface led to the discovery of a new member of the Zur-regulon: pliG. We demonstrate this gene is directly regulated by Zur in a zinc responsive manner. The pliG promoter forms stable complexes with either one or two Zur dimers with significantly less protein-DNA cooperativity than observed at other Zur regulon promoters. Comparison of the in vitro Zur-DNA binding affinity at each of four Zur-regulon promoters reveals ca. 10,000-fold variation Zur-DNA binding constants. The degree of Zur repression observed in vivo by comparison of transcript copy number in wild-type and Δzur strains parallels this trend spanning a 100-fold difference. We conclude that the number of ferric uptake regulator (Fur)-family dimers that bind within any given promoter varies significantly and that the thermodynamic profile of the Zur-DNA interactions directly correlates with the physiological response at different promoters.

Zinc is an essential nutrient for most organisms, with the Zn²⁺ ion performing numerous structural, regulatory, and catalytic roles in a range of proteins. However, this nutrient can neither be synthesized nor degraded and individual cells need to be able to maintain steady levels of zinc in the face of near-zero or excessively high environmental concentrations. Here we look at how the bacterium E. coli does this, by examining the structure and function of Zur, a transcriptional repressor that is exquisitely sensitive to Zn²⁺ concentration. Although the structures of related Zur proteins on their own are known, here we show how E. coli protein binds to DNA and explain its extreme sensitivity and specificity (it responds to Zn²⁺ concentrations in the femtomolar range). Our results reveal how the Zur protein switches on and off a bank of bacterial genes that control zinc physiology. Extensive analysis of protein-DNA interactions revealed both a surprising degree of cooperativity and an extremely large range of Zur-DNA binding affinities across the set of genes known as the Zur regulon. The results provide strong support for a controversial idea that the thermodynamics of an ensemble of protein-DNA interactions play a dominant role in the physiological control of gene regulation networks. In addition, we have used our structural and thermodynamic analysis to identify a novel gene target of Zur regulation.

The Yersinia pestis siderophore, yersiniabactin, and the ZnuABC system both contribute to zinc acquisition and the development of lethal septicaemic plague in mice

Bacterial pathogens must overcome host sequestration of zinc (Zn(2+) ), an essential micronutrient, during the infectious disease process. While the mechanisms to acquire chelated Zn(2+) by bacteria are largely undefined, many pathogens rely upon the ZnuABC family of ABC transporters. Here we show that in Yersinia pestis, irp2, a gene encoding the synthetase (HMWP2) for the siderophore yersiniabactin (Ybt) is required for growth under Zn(2+) -deficient conditions in a strain lacking ZnuABC. Moreover, growth stimulation with exogenous, purified apo-Ybt provides evidence that Ybt may serve as a zincophore for Zn(2+) acquisition. Studies with the Zn(2+) -dependent transcriptional reporter znuA::lacZ indicate that the ability to synthesize Ybt affects the levels of intracellular Zn(2+) . However, the outer membrane receptor Psn and TonB as well as the inner membrane (IM) ABC transporter YbtPQ, which are required for Fe(3+) acquisition by Ybt, are not needed for Ybt-dependent Zn(2+) uptake. In contrast, the predicted IM protein YbtX, a member of the Major Facilitator Superfamily, was essential for Ybt-dependent Zn(2+) uptake. Finally, we show that the ZnuABC system and the Ybt synthetase HMWP2, presumably by Ybt synthesis, both contribute to the development of a lethal infection in a septicaemic plague mouse model.

The FUR (ferric uptake regulator) superfamily: diversity and versatility of key transcriptional regulators

Control of metal homeostasis is essential for life in all kingdoms. In most prokaryotic organisms the FUR (ferric uptake regulator) family of transcriptional regulators is involved in the regulation of iron and zinc metabolism through control by Fur and Zur proteins. A third member of this family, the peroxide-stress response PerR, is present in most Gram-positives, establishing a tight functional interaction with the global regulator Fur. These proteins play a pivotal role for microbial survival under adverse conditions and in the expression of virulence in most pathogens. In this paper we present the current state of the art in the knowledge of the FUR family, including those members only present in more reduced numbers of bacteria, namely Mur, Nur and Irr. The huge amount of work done in the two last decades shows that FUR proteins present considerable diversity in their regulatory mechanisms and interesting structural differences. However, much work needs to be done to obtain a more complete picture of this family, especially in connection with the roles of some members as gas and redox sensors as well as to fully characterize their participation in bacterial adaptative responses.

A new approach to studying ion uptake by actinomycetes

A streptomycete that had the ability to avidly sequester iron via siderophores was previously isolated from environmental soil samples. The chelating agent expressed by this organism is confirmed by HPLC as desferrioxamine E. Although the traditional chromo azuerol sulphate (CAS) assay for detection of siderophores is based upon the chelation of iron we were interested to examine the relationship of these iron-capturing molecules with other ions. Consequently, a new approach was employed that enabled the assessment of the affinity of the siderophore moieties for other ions by adapting the CAS assay. The present study reveals that the isolate produced a siderophore that was capable of sequestering a range of ions including Mn, Co, Cd, Ni, Al, Li, Cu, Zn and Mg. On the basis of the assay described it would appear that the organism sequesters copper more readily than iron. This raises an age-old debate surrounding the replacement of copper as a fundamentally essential element with iron as a consequence of the evolution of the di-oxygen environment.

Control of iron metabolism in bacteria

Bacteria depend upon iron as a vital cofactor that enables a wide range of key metabolic activities. Bacteria must therefore ensure a balanced supply of this essential metal. To do so, they invest considerable resourse into its acquisition and employ elaborate control mechanisms to eleviate both iron-induced toxitiy as well as iron deficiency. This chapter describes the processes that bacteria engage in maintaining iron homeostasis. The focus is Escherichia coli, as this bacterium provides a well studied example. A summary of the current status of understanding of iron management at the 'omics' level is also presented.

Non-heme iron sensors of reactive oxygen and nitrogen species

SIGNIFICANCE

In bacteria, transcriptional responses to reactive oxygen and nitrogen species (ROS and RNS, respectively) are typically coordinated by regulatory proteins that employ metal centers or reactive thiols to detect the presence of those species. This review is focused on the structure, function and mechanism of three regulatory proteins (Fur, PerR, and NorR) that contain non-heme iron and regulate the transcription of target genes in response to ROS and/or RNS. The targets for regulation include genes encoding detoxification activities, and genes encoding proteins involved in the repair of the damage caused by ROS and RNS.

RECENT ADVANCES

Three-dimensional structures of several Fur proteins and of PerR are revealing important details of the metal binding sites of these proteins, showing a surprising degree of structural diversity in the Fur family.

CRITICAL ISSUES

Discussion of the interaction of Fur with ROS and RNS will illustrate the difficulty that sometimes exists in distinguishing between true physiological responses and adventitious reactions of a regulatory protein with a reactive ligand.

FUTURE DIRECTIONS

Consideration of these three sensor proteins illuminates some of the key questions that remain unanswered, for example, the nature of the biochemical determinants that dictate the sensitivity and specificity of the interaction of the sensor proteins with their cognate signals.

Origins of specificity and cross-talk in metal ion sensing by Bacillus subtilis Fur

Fur (ferric uptake regulator) is the master regulator of iron homeostasis in many bacteria, but how it responds specifically to Fe(II) in vivo is not clear. Biochemical analyses of Bacillus subtilis Fur (BsFur) reveal that in addition to Fe(II), both Zn(II) and Mn(II) allosterically activate BsFur-DNA binding. Dimeric BsFur co-purifies with site 1 structural Zn(II) (Fur(2) Zn(2) ) and can bind four additional Zn(II) or Mn(II) ions per dimer. Metal ion binding at previously described site 3 occurs with highest affinity, but the Fur(2) Zn(2) :Me(2) form has only a modest increase in DNA binding affinity (approximately sevenfold). Metallation of site 2 (Fur(2) Zn(2) :Me(4) ) leads to a ~ 150-fold further enhancement in DNA binding affinity. Fe(II) binding studies indicate that BsFur buffers the intracellular Fe(II) concentration at ~ 1 μM. Both Mn(II) and Zn(II) are normally buffered at levels insufficient for metallation of BsFur site 2, thereby accounting for the lack of cross-talk observed in vivo. However, in a perR mutant, where the BsFur concentration is elevated, BsFur may now use Mn(II) as a co-repressor and inappropriately repress iron uptake. Since PerR repression of fur is enhanced by Mn(II), and antagonized by Fe(II), PerR may co-regulate Fe(II) homeostasis by modulating BsFur levels in response to the Mn(II)/Fe(II) ratio.

The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: identification of new Fur targets

Background

The Ferric uptake regulator (Fur) is a transcriptional regulator that controls iron homeostasis in bacteria. Although the regulatory role of Fur in Escherichia coli is well characterized, most of the studies were conducted under routine culture conditions, i.e., in ambient oxygen concentration. To reveal potentially novel aspects of the Fur regulon in Salmonella enterica serovar Typhimurium under oxygen conditions similar to that encountered in the host, we compared the transcriptional profiles of the virulent wild-type strain (ATCC 14028s) and its isogenic Δfur strain under anaerobic conditions.

Results

Microarray analysis of anaerobically grown Δfur S. Typhimurium identified 298 differentially expressed genes. Expression of several genes controlled by Fnr and NsrR appeared to be also dependent on Fur. Furthermore, Fur was required for the activity of the cytoplasmic superoxide disumutases (MnSOD and FeSOD). The regulation of FeSOD gene, sodB, occurred via small RNAs (i.e., the ryhB homologs, rfrA and rfrB) with the aid of the RNA chaperone Hfq. The transcription of sodA was increased in Δfur; however, the enzyme was inactive due to the incorporation of iron instead of manganese in SodA. Additionally, in Δfur, the expression of the gene coding for the ferritin-like protein (ftnB) was down-regulated, while the transcription of the gene coding for the nitric oxide (NO^·) detoxifying flavohemoglobin (hmpA) was up-regulated. The promoters of ftnB and hmpA do not contain recognized Fur binding motifs, which indicated their probable indirect regulation by Fur. However, Fur activation of ftnB was independent of Fnr. In addition, the expression of the gene coding for the histone-like protein, H-NS (hns) was increased in Δfur. This may explain the observed down-regulation of the tdc operon, responsible for the anaerobic degradation of threonine, and ftnB in Δfur.

Conclusions

This study determined that Fur is a positive factor in ftnB regulation, while serving to repress the expression of hmpA. Furthermore, Fur is required for the proper expression and activation of the antioxidant enzymes, FeSOD and MnSOD. Finally, this work identified twenty-six new targets of Fur regulation, and demonstrates that H-NS repressed genes are down-regulated in Δfur.

An extracytoplasmic function sigma factor-mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores

The diversity of regulatory systems encoded by bacteria provides an indication of the variety of stresses and interactions that these organisms encounter in nature. We have been investigating how the plant pathogen Pseudomonas syringae pv. tomato DC3000 responds to iron limitation and have focused on the iron starvation (IS) sigma factors to identify regulon members and to explore the mechanistic details of genetic control for this class of regulators. In the study described in this report, we used chromatin immunoprecipitation paired with high-throughput sequencing (ChIP-Seq) to screen the genome for locations associated with binding of the P. syringae IS sigma factor PSPTO_1203. We used multiple methods to demonstrate differential regulation of two genes identified in the ChIP-Seq screen and characterize the promoter elements that facilitate PSPTO_1203-dependent regulation. The genes regulated by PSPTO_1203 encode a TonB-dependent transducer (PSPTO_1206) and a cytoplasmic membrane protein (PSPTO_2145), which is located in the P. syringae pyoverdine cluster. Additionally, we identified siderophores that induce the activity of PSPTO_1203 and used this information to investigate the functional components of the signal transduction cascade.

Sequential binding and sensing of Zn(II) by Bacillus subtilis Zur

Bacillus subtilis Zur (BsZur) represses high-affinity zinc-uptake systems and alternative ribosomal proteins in response to zinc replete conditions. Sequence alignments and structural studies of related Fur family proteins suggest that BsZur may contain three zinc-binding sites (sites 1–3). Mutational analyses confirm the essential structural role of site 1, while mutants affected in sites 2 and 3 retain partial repressor function. Purified BsZur binds a maximum of two Zn(II) per monomer at site 1 and site 2. Site 3 residues are important for dimerization, but do not directly bind Zn(II). Analyses of metal-binding affinities reveals negative cooperativity between the two site 2 binding events in each dimer. DNA-binding studies indicate that BsZur is sequentially activated from an inactive dimer (Zur₂:Zn₂) to a partially active asymmetric dimer (Zur₂:Zn₃), and finally to the fully zinc-loaded active form (Zur₂:Zn₄). BsZur with a C84S mutation in site 2 forms a Zur₂:Zn₃ form with normal metal- and DNA-binding affinities but is impaired in formation of the Zur₂:Zn₄ high affinity DNA-binding state. This mutant retains partial repressor activity in vivo, thereby supporting a model in which stepwise activation by zinc serves to broaden the physiological response to a wider range of metal concentrations.

BosR (BB0647) controls the RpoN-RpoS regulatory pathway and virulence expression in Borrelia burgdorferi by a novel DNA-binding mechanism

In Borrelia burgdorferi (Bb), the Lyme disease spirochete, the alternative σ factor σ⁵⁴ (RpoN) directly activates transcription of another alternative σ factor, σ^S (RpoS) which, in turn, controls the expression of virulence-associated membrane lipoproteins. As is customary in σ⁵⁴-dependent gene control, a putative NtrC-like enhancer-binding protein, Rrp2, is required to activate the RpoN-RpoS pathway. However, recently it was found that rpoS transcription in Bb also requires another regulator, BosR, which was previously designated as a Fur or PerR homolog. Given this unexpected requirement for a second activator to promote σ⁵⁴-dependent gene transcription, and the fact that regulatory mechanisms among similar species of pathogenic bacteria can be strain-specific, we sought to confirm the regulatory role of BosR in a second virulent strain (strain 297) of Bb. Indeed, BosR displayed the same influence over lipoprotein expression and mammalian infectivity for strain Bb 297 that were previously noted for Bb strain B31. We subsequently found that recombinant BosR (rBosR) bound to the rpoS gene at three distinct sites, and that binding occurred despite the absence of consensus Fur or Per boxes. This led to the identification of a novel direct repeat sequence (TAAATTAAAT) critical for rBosR binding in vitro. Mutations in the repeat sequence markedly inhibited or abolished rBosR binding. Taken together, our studies provide new mechanistic insights into how BosR likely acts directly on rpoS as a positive transcriptional activator. Additional novelty is engendered by the facts that, although BosR is a Fur or PerR homolog and it contains zinc (like Fur and PerR), it has other unique features that clearly set it apart from these other regulators. Our findings also have broader implications regarding a previously unappreciated layer of control that can be involved in σ⁵⁴–dependent gene regulation in bacteria.

Lyme disease, caused by the bacterium Borrelia burgdorferi (Bb), remains the most common arthropod-borne illness in the United States. A critical strategy for Bb to maintain its presence in nature is adaptation to its diverse tick and mammalian (mouse) hosts. To accomplish this, Bb encodes a potential gene regulator, BB0647 (BosR). Herein, we confirmed that BosR is essential for Bb to establish mammalian infection. We then found that purified recombinant BosR bound to the promoter DNA (regulatory region) of rpoS, suggesting that BosR directly controls the expression of the rpoS gene. This study has revealed a new mechanism of bacterial gene control. The discovery that BosR governs Bb's virulence may lead to new strategies to interrupt the bacterium's complex life cycle.

The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites

Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S-C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur-like proteins, the crystal structure of HpFur reveals a unique structured N-terminal extension and an unusual C-terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS₄ site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site-directed mutagenesis and spectroscopy analyses of purified wild-type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site.

Mutagenesis of conserved amino acids of Helicobacter pylori fur reveals residues important for function

The ferric uptake regulator (Fur) of the medically important pathogen Helicobacter pylori is unique in that it has been shown to function as a repressor both in the presence of an Fe2+ cofactor and in its apo (non-Fe2+-bound) form. However, virtually nothing is known concerning the amino acid residues that are important for Fur functioning. Therefore, mutations in six conserved amino acid residues of H. pylori Fur were constructed and analyzed for their impact on both iron-bound and apo repression. In addition, accumulation of the mutant proteins, protein secondary structure, DNA binding ability, iron binding capacity, and the ability to form higher-order structures were also examined for each mutant protein. While none of the mutated residues completely abrogated the function of Fur, we were able to identify residues that were critical for both iron-bound and apo-Fur repression. One mutation, V64A, did not alter regulation of any target genes. However, each of the five remaining mutations showed an effect on either iron-bound or apo regulation. Of these, H96A, E110A, and E117A mutations altered iron-bound Fur regulation and were all shown to influence iron binding to different extents. Additionally, the H96A mutation was shown to alter Fur oligomerization, and the E110A mutation was shown to impact oligomerization and DNA binding. Conversely, the H134A mutant exhibited changes in apo-Fur regulation that were the result of alterations in DNA binding. Although the E90A mutant exhibited alterations in apo-Fur regulation, this mutation did not affect any of the assessed protein functions. This study is the first for H. pylori to analyze the roles of specific amino acid residues of Fur in function and continues to highlight the complexity of Fur regulation in this organism.

Deletion of a fur-like gene affects iron homeostasis and magnetosome formation in Magnetospirillum gryphiswaldense

Magnetotactic bacteria synthesize specific organelles, the magnetosomes, which are membrane-enveloped crystals of the magnetic mineral magnetite (Fe(3)O(4)). The biomineralization of magnetite involves the uptake and intracellular accumulation of large amounts of iron. However, it is not clear how iron uptake and biomineralization are regulated and balanced with the biochemical iron requirement and intracellular homeostasis. In this study, we identified and analyzed a homologue of the ferric uptake regulator Fur in Magnetospirillum gryphiswaldense, which was able to complement a fur mutant of Escherichia coli. A fur deletion mutant of M. gryphiswaldense biomineralized fewer and slightly smaller magnetite crystals than did the wild type. Although the total cellular iron accumulation of the mutant was decreased due to reduced magnetite biomineralization, it exhibited an increased level of free intracellular iron, which was bound mostly to a ferritin-like metabolite that was found significantly increased in Mössbauer spectra of the mutant. Compared to that of the wild type, growth of the fur mutant was impaired in the presence of paraquat and under aerobic conditions. Using a Fur titration assay and proteomic analysis, we identified constituents of the Fur regulon. Whereas the expression of most known magnetosome genes was unaffected in the fur mutant, we identified 14 proteins whose expression was altered between the mutant and the wild type, including five proteins whose genes constitute putative iron uptake systems. Our data demonstrate that Fur is a regulator involved in global iron homeostasis, which also affects magnetite biomineralization, probably by balancing the competing demands for biochemical iron supply and magnetite biomineralization.

Chemistry and biology of siderophores

Siderophores are compounds produced by bacteria, fungi and graminaceous plants for scavenging iron from the environment. They are low-molecular-weight compounds (500-1500 daltons) possessing a high affinity for iron(III) (Kf > 1030), the biosynthesis of which is regulated by iron levels and the function of which is to supply iron to the cell. This article briefly describes the classification and chemical properties of siderophores, before outlining research on siderophore biosynthesis and transport. Clinically important siderophores and the therapeutic potential of siderophore design are described. Appendix 1 provides a comprehensive list of siderophore structures.

TonB-dependent transporters: regulation, structure, and function

TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that bind and transport ferric chelates, called siderophores, as well as vitamin B(12), nickel complexes, and carbohydrates. The transport process requires energy in the form of proton motive force and a complex of three inner membrane proteins, TonB-ExbB-ExbD, to transduce this energy to the outer membrane. The siderophore substrates range in complexity from simple small molecules such as citrate to large proteins such as serum transferrin and hemoglobin. Because iron uptake is vital for almost all bacteria, expression of TBDTs is regulated in a number of ways that include metal-dependent regulators, σ/anti-σ factor systems, small RNAs, and even a riboswitch. In recent years, many new structures of TBDTs have been solved in various states, resulting in a more complete understanding of siderophore selectivity and binding, signal transduction across the outer membrane, and interaction with the TonB-ExbB-ExbD complex. However, the transport mechanism is still unclear. In this review, we summarize recent progress in understanding regulation, structure, and function in TBDTs and questions remaining to be answered.

Domain analysis of the Edwardsiella tarda ferric uptake regulator

Recent studies have shown that the ferric uptake regulator (Fur) of Edwardsiella tarda (Fur(Et)) shares high sequence identity with the Escherichia coli Fur (Fur(Ec)) at the N-terminal DNA-binding region. In the present study, the functional importance of the C-terminal region of Fur(Et) was investigated. It was found that Fur(Et) bearing deletion of the C-terminal 12 residues still possesses most of the repressor activity, whereas Fur(Et) bearing deletions of the C-terminal 16 and more than 16 residues are severely affected in activity. Domain swapping analyses indicated that the chimeric Fur proteins (Et75Ec73 and Et75Vh74) consisting of the N-terminal 1-75 region of Fur(Et) fused to the C-terminal 76-148 region of Fur(Ec) and the C-terminal 76-149 region of the Vibrio harveyi Fur (Fur(Vh)), respectively, are fully active. C92 of Fur(Ec) and C137 of Fur(Vh), which are functionally essential in Fur(Ec) and Fur(Vh), respectively, are also essential in Et75Ec73 and Et75Vh74, respectively. Further study identified an artificial Fur protein, EtMF54, which is composed of the N-terminal 49 residues of Fur(Et) and five artificial residues. Compared to Fur(Et), EtMF54 possesses partial Fur activity that is iron-dependent. These results (i) indicate that there exist certain functional/structural compatibilities among Fur(Et), Fur(Ec), and Fur(Vh) at the C-terminal region; (ii) provide insights to the potential location of the regulatory ion-binding site of Fur(Et).

Iron-based redox switches in biology

By virtue of its unique electrochemical properties, iron makes an ideal redox active cofactor for many biologic processes. In addition to its important role in respiration, central metabolism, nitrogen fixation, and photosynthesis, iron also is used as a sensor of cellular redox status. Iron-based sensors incorporate Fe-S clusters, heme, and mononuclear iron sites to act as switches to control protein activity in response to changes in cellular redox balance. Here we provide an overview of iron-based redox sensor proteins, in both prokaryotes and eukaryotes, that have been characterized at the biochemical level. Although this review emphasizes redox sensors containing Fe-S clusters, proteins that use heme or novel iron sites also are discussed.

Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co-ordination

The ferric uptake regulator (Fur) is a metal-dependent DNA-binding protein that acts as both a repressor and an activator of numerous genes involved in maintaining iron homeostasis in bacteria. It has also been demonstrated in Vibrio cholerae that Fur plays an additional role in pathogenesis, opening up the potential of Fur as a drug target for cholera. Here we present the crystal structure of V. cholerae Fur that reveals a very different orientation of the DNA-binding domains compared with that observed in Pseudomonas aeruginosa Fur. Each monomer of the dimeric Fur protein contains two metal binding sites occupied by zinc in the crystal structure. In the P. aeruginosa study these were designated as the regulatory site (Zn1) and structural site (Zn2). This V. cholerae Fur study, together with studies on Fur homologues and paralogues, suggests that in fact the Zn2 site is the regulatory iron binding site and the Zn1 site plays an auxiliary role. There is no evidence of metal binding to the cysteines that are conserved in many Fur homologues, including Escherichia coli Fur. An analysis of the metal binding properties shows that V. cholerae Fur can be activated by a range of divalent metals.

Roles of the extraintestinal pathogenic Escherichia coli ZnuACB and ZupT zinc transporters during urinary tract infection

Roles of the ZnuACB and ZupT transporters were assessed in Escherichia coli K-12 and uropathogenic E. coli (UPEC) CFT073. K-12 and CFT073 Deltaznu DeltazupT mutants demonstrated decreased (65)Zn(2+) uptake and growth in minimal medium. CFT073Deltaznu demonstrated an intermediate decrease of (65)Zn(2+) uptake and growth in minimal medium, whereas the CFT073DeltazupT mutant grew as well as CFT073 and exhibited a less marked decrease in (65)Zn(2+) uptake. CFT073 mutants grew as well as the wild type in human urine. In competitive infections in CBA/J mice, the DeltazupT mutant demonstrated no disadvantage during urinary tract infection. In contrast, the UPEC Deltaznu and Deltaznu DeltazupT strains demonstrated significantly reduced numbers in the bladders (mean 4.4- and 30-fold reductions, respectively) and kidneys (mean 41- and 48-fold reductions, respectively). In addition, in single-strain infection experiments, the Deltaznu and Deltaznu DeltazupT mutants were reduced in the kidneys (P = 0.0012 and P < 0.0001, respectively). Complementation of the CFT073 Deltaznu DeltazupT mutant with the znuACB genes restored growth in Zn-deficient medium and bacterial numbers in the bladder and kidneys. The loss of the zinc transport systems decreased both motility and resistance to hydrogen peroxide, which could be restored by supplementation with zinc. Overall, the results indicate that Znu and ZupT are required for growth in zinc limited-conditions, that Znu is the predominant zinc transporter, and that the loss of Znu and ZupT has a cumulative effect on fitness during UTI, which may in part be due to reduced resistance to oxidative stress and motility.

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro

BACKGROUND

Pseudomonas syringae pv tomato DC3000 (DC3000) is a Gram-negative model plant pathogen that is found in a wide variety of environments. To survive in these diverse conditions it must sense and respond to various environmental cues. One micronutrient required for most forms of life is iron. Bioavailable iron has been shown to be an important global regulator for many bacteria where it not only regulates a wide variety of genes involved in general cell physiology but also virulence determinants. In this study we used microarrays to study differential gene regulation in DC3000 in response to changes in levels of cell-associated iron.

RESULTS

DC3000 cultures were grown under highly controlled conditions and analyzed after the addition of iron citrate or sodium citrate to the media. In the cultures supplemented with iron, we found that cell-associated iron increased rapidly while culture densities were not significantly different over 4 hours when compared to cultures with sodium citrate added. Microarray analysis of samples taken from before and after the addition of either sodium citrate or iron citrate identified 386 differentially regulated genes with high statistical confidence. Differentially regulated genes were clustered based on expression patterns observed between comparison of samples taken at different time points and with different supplements. This analysis grouped genes associated with the same regulatory motifs and/or had similar putative or known function.

CONCLUSION

This study shows iron is rapidly taken up from the medium by iron-depleted DC3000 cultures and that bioavailable iron is a global cue for the expression of iron transport, storage, and known virulence factors in DC3000. Furthermore approximately 34% of the differentially regulated genes are associated with one of four regulatory motifs for Fur, PvdS, HrpL, or RpoD.

Retracted: A catechol type siderophore, bacillibactin: biosynthesis, regulation and transport in Bacillus subtilis

Retraction: The following article from the Journal of Basic Microbiology, "A catechol type siderophore, bacillibactin: biosynthesis, regulation and transport in Bacillus subtilis" by Waseem Raza, Hongsheng Wu, Muhammad Ali Abdullah Shah and Qirong Shen, published online on 11 September 2008 in Wiley InterScience (www.interscience.wiley.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Erika Kothe, and the publisher Wiley-VCH. The retraction has been agreed due to substantial overlap of the content of this article with previously published articles in other journals.The Journal of Basic Microbiology apologises to our readership.

The Metal-Dependent Regulators FurA and FurB from Mycobacterium Tuberculosis

The ferric uptake regulators (Fur) form a large family of bacterial metal-activated DNA-binding proteins that control a diverse set of genes at the transcriptional level. Mycobacterium tuberculosis, the causative agent of tuberculosis, expresses two members of the Fur family, designated FurA and FurB. Although both belong to the same family, they share only approximately 25% sequence identity and as a consequence, they differ significantly in some of their key biological functions. FurA appears to be a specialized iron-dependent regulator that controls the katG gene, which encodes for a catalase-peroxidase involved in the response of M. tuberculosis to oxidative stress. KatG is also the key mycobacterial enzyme responsible for the activation of the first-line tuberculosis drug Isoniazid. FurB in contrast requires Zn(2+) rather than Fe(2+), to bind to its target sequence in regulated genes, which include those involved in Zn(2+)-homeostasis. Recent biochemical, crystallographic and spectroscopic data have now shed light on the activation and metal discrimination mechanisms in this protein family.

Molecular analysis of the fur (ferric uptake regulator) gene of a pathogenic Edwardsiella tarda strain

The gene encoding the Edwardsiella tarda ferric uptake regulator (Fur(Et)) was cloned from a pathogenic E. tarda strain isolated from diseased fish. Fur(Et) shares 90% overall sequence identity with the Escherichia coli Fur (Fur(Ec)) and was able to complement the mutant phenotype of a fur (Ec)-defective E. coli strain. Mutational analysis indicated that C92S and C95S mutations inactivated Fur(Et) whereas E112K mutation resulted in a superactive Fur(Et) variant. Fur(Et) negatively regulated its own expression; interruption of this regulation impaired bacterial growth, altered the production of certain outer membrane proteins, and attenuated bacterial virulence.

The Bradyrhizobium japonicum Irr protein is a transcriptional repressor with high-affinity DNA-binding activity

The Irr protein is a global regulator of iron homeostasis in Bradyrhizobium japonicum, and a subset of genes within the Irr regulon are negatively controlled under iron limitation. However, repressor function, high-affinity DNA binding in vitro, or promoter occupancy in vivo of Irr for a negatively regulated gene has not been demonstrated. Here, we show that the blr7895 and bll6680 genes are negatively regulated by Irr as determined by derepression of transcript levels in iron-limited cells of an irr mutant strain. Electrophoretic gel mobility shift analysis showed that a component in extracts of wild-type cells grown under iron limitation bound the iron control elements (ICE) within the promoters of blr7895 and bll6680 identified previously (G. Rudolph, G. Semini, F. Hauser, A. Lindemann, M. Friberg, H. Hennecke, and H. M. Fischer, J. Bacteriol. 188:733-744, 2006). Binding was not observed with extracts of cells from the parent strain grown under high iron conditions or with those from an irr mutant. Furthermore, gel mobility supershift experiments identified Irr as a component of the binding complex. Purified recombinant Irr bound to ICE DNA with high affinity in the presence of divalent metal, with K(d) values of 7 to 19 nM, consistent with a physiological role for Irr as a transcriptional regulator. In addition, in vitro transcription initiated from the blr7895 promoter was inhibited by Irr. Whole-cell cross-linking and immunoprecipitation experiments showed that Irr occupies the promoters of blr7895 and bll6680 in vivo in an iron-dependent manner. The findings demonstrate that Irr is a transcriptional repressor that binds DNA with high affinity.

Redox control in actinobacteria

As most actinobacteria are obligate aerobes, they have to cope with endogenously generated reactive oxygen species, and actinobacterial pathogens have to resist oxidative attack by phagocytes. Actinobacteria also have to survive long periods under low oxygen tension; for example, Mycobacterium tuberculosis can persist in the host for years under apparently hypoxic conditions in a latent, non-replicative state. Here we focus on the regulatory switches that control actinobacterial responses to peroxide stress, disulfide stress and low oxygen tension. Other unique aspects of their redox biology will be highlighted, including the use of the pseudodisaccharide mycothiol as their major low-molecular-weight thiol buffer, and the [4Fe-4S]-containing WhiB-like proteins, which play diverse, important roles in actinobacterial biology, but whose biochemical role is still controversial.