Nickel utilization by microorganisms

Exploring the conformational space of the mobile flap in Sporosarcina pasteurii urease by cryo-electron microscopy

To fully understand enzymatic dynamics, it is essential to explore the complete conformational space of a biological catalyst. The catalytic mechanism of the nickel-dependent urease, the most efficient enzyme known, holds significant relevance for medical, pharmaceutical, and agro-environmental applications. A critical aspect of urease function is the conformational change of a helix-turn-helix motif that covers the active site cavity, known as the mobile flap. This motif has been observed in either an open or a closed conformation through X-ray crystallography studies and has been proposed to stabilize the coordination of a urea molecule to the essential dinuclear Ni(II) cluster in the active site, a requisite for subsequent substrate hydrolysis. This study employs cryo-electron microscopy (cryo-EM) to investigate the transient states within the conformational space of the mobile flap, devoid of the possible constraints of crystallization conditions and solid-state effects. By comparing two cryo-EM structures of Sporosarcina pasteurii urease, one in its native form and the other inhibited by N-(n-butyl) phosphoric triamide (NBPTO), we have unprecedently identified an intermediate state between the open and the catalytically efficient closed conformation of the helix-turn-helix motif, suggesting a role of its tip region in this transition between the two states.

Is bismuth(III) able to inhibit the activity of urease? Puzzling results in the quest for soluble urease complexes for agrochemical and medicinal applications

Bismuth(III) complexes have been reported to act as inhibitors of the enzyme urease, ubiquitously present in soils and implicated in the pathogenesis of several microorganisms. The general insolubility of Bi(III) complexes in water at neutral pH, however, is an obstacle to their utilization. In our quest to improve the solubility of Bi(III) complexes, we selected a compound reported to inhibit urease, namely [Bi(HEDTA)]·2H2O, and co-crystallized it with (i) racemic DL-histidine to obtain the conglomerate [Bi2(HEDTA)2(μ-D-His)2]·6H2O + [Bi2(HEDTA)2(μ-L-His)2]·6H2O, (ii) enantiopure L-histidine to yield [Bi2(HEDTA)2(μ-L-His)2]·6H2O, and (iii) cytosine to obtain [Bi(HEDTA)]·Cyt·2H2O. All compounds, synthesised by mechanochemical methods and by slurry, were characterized in the solid state by calorimetric (DSC and TGA) and spectroscopic (IR) methods, and their structures were determined using powder X-ray diffraction (PXRD) data. All compounds show an appreciable solubility in water, with values ranging from 6.8 mg mL-1 for the starting compound [Bi(HEDTA)]·2H2O to 36 mg mL-1 for [Bi2(HEDTA)2(μ-L-His)2]·6H2O. The three synthesized compounds as well as [Bi(HEDTA)]·2H2O were then tested for inhibition activity against urease. Surprisingly, no enzymatic inhibition was observed during in vitro assays using Canavalia ensiformis urease and in vivo assays using cultures of Helicobacter pylori, raising questions on the efficacy of Bi(III) compounds to counteract the negative effects of urease activity in the agro-environment and in human health.

Sublethal nickel toxicity shuts off manganese oxidation and pellicle biofilm formation in Pseudomonas putida GB-1

In sediments, the bioavailability and toxicity of Ni are strongly influenced by its sorption to manganese (Mn) oxides, which largely originate from the redox metabolism of microbes. However, microbes are concurrently susceptible to the toxic effects of Ni, which establishes complex interactions between toxicity and redox processes. This study measured the effect of Ni on growth, pellicle biofilm formation and oxidation of the Mn-oxidizing bacteria Pseudomonas putida GB-1. In liquid media, Ni exposure decreased the intrinsic growth rate but allowed growth to the stationary phase in all intermediate treatments. Manganese oxidation was 67% less than control for bacteria exposed to 5 μM Ni and completely ceased in all treatments above 50 μM. Pellicle biofilm development decreased exponentially with Ni concentration (maximum 92% reduction) and was replaced by planktonic growth in higher Ni treatments. In solid media assays, growth was unaffected by Ni exposure, but Mn oxidation completely ceased in treatments above 10 μM of Ni. Our results show that sublethal Ni concentrations substantially alter Mn oxidation rates and pellicle biofilm development in P. putida GB-1, which has implications for toxic metal bioavailability to the entire benthic community and the environmental consequences of metal contamination.

Crystal engineering: from promise to delivery

Twenty years ago, I wrote a Chem. Commun. feature article entitled "Crystal Engineering: where from? Where to?": an update is in order. In this Highlight I argue that molecular crystal engineering, one of the areas of fast development of the field, has definitely reached the stage of "delivering the goods": new functional materials assembled via non-covalent interactions and/or improved properties of existing materials. As a proof of concept, the crystal engineering approach to tackle two contemporary emergencies, namely, urea fertilizer degradation and development of antimicrobial resistance by pathogens, is discussed and application-driven examples are provided.

TorC1 and nitrogen catabolite repression control of integrated GABA shunt and retrograde pathway gene expression

Despite our detailed understanding of how the lower GABA shunt and retrograde genes are regulated, there is a paucity of validated information concerning control of GAD1, the glutamate decarboxylase gene which catalyzes the first reaction of the GABA shunt. Further, integration of glutamate degradation via the GABA shunt has not been investigated. Here, we show that while GAD1 shares a response to rapamycin-inhibition of the TorC1 kinase, it does so independently of the Gln3 and Gat1 NCR-sensitive transcriptional activators that mediate transcription of the lower GABA shunt genes. We also show that GABA shunt gene expression increases dramatically in response to nickel ions. The α-ketoglutarate needed for the GABA shunt to cycle, thereby producing reduced pyridine nucleotides, derives from the retrograde pathway as shown by a similar high increase in the retrograde reporter, CIT2 when nickel is present in the medium. These observations demonstrate high integration of the GABA shunt, retrograde, peroxisomal glyoxylate cycle, and β-oxidation pathways.

Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study

Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a NiII -containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.

Developing a fluorometric urease activity microplate assay suitable for automated microbioreactor experiments

Quantifying urease activity is an important task for Microbial Induced Calcite Precipitation research. A new urease activity microplate assay using a fluorescent pH indicator is presented. The method is also suitable for automated measurements during microbioreactor experiments. The assay reagent consists of the green fluorescent pH-indicator fluorescein, urea and a phosphate buffer. After sample addition, the microbial urease hydrolyses urea, which results in a pH and hence fluorescence increase. The fluorescence signal can be measured with a microplate reader or with the microbioreactor system BioLector, allowing for automated urease activity measurements during cultivation experiments. In both measurement systems, the fluorescence signal slope highly correlates with the urease activity measured offline with standard methods. Automated measurement is possible, as no sample preparation such as centrifugation or adjusting of the optical density is required. The assay was developed so that the culture samples turbidity, salinity or buffer concentration does not have a negative impact on the fluorescence signal. The assay allows for straightforward, non-hazardous, parallelized, cheap and reliable measurements, making research on ureolytic bacteria for Microbial Induced Calcite Precipitation more efficient. The assay could be adapted to other enzymes, which have a strong impact on the pH value.

(NH4)2[Co(H2O)6]2V10O28·4H2O Vs. (NH4)2[Ni(H2O)6]2V10O28·4H2O: Structural, Spectral and Thermal Analyses and Evaluation of Their Antibacterial Activities

This paper presents the synthesis of two cluster compounds {(NH4)2[Co(H2O)6]2V10O28·4H2O (C1) and (NH4)2[Ni(H2O)6]2V10O28·4H2O (C2)} which were obtained as single crystals suitable for XRD analysis that revealed their crystallization in the monoclinic (C2/c) and triclinic (P-1) space groups, respectively. Additionally, C1 and C2 were characterized using CHN analysis and FT-IR spectroscopy and their thermal decomposition mechanisms were investigated. The antibacterial activities of both compounds were determined against three human pathogenic bacterial strains {Bacillus cereus ATCC 33,018, Escherichia coli O157:H7 and Pseudomonas aeruginosa ATCC 9027} and one phytopathogenic bacterial strain {Ralstonia solanacearum}, while drug standards {chloramphenicol and streptomycin} were used as control. The inhibitory activity and the minimum inhibitory concentration (MIC) values of the tested compounds clearly indicated higher antibacterial activities of the nickel compound against B. cereus ATCC 33,018, E. coli O157 and R. solanacearum with MIC values of 3.150, 3.150 and 6.300 mg/ml, respectively. On the other hand, (NH4)2[Co(H2O)6]2V10O28·4H2O exhibited higher antibacterial activity against P. aeruginosa ATCC 9027 (MIC value of 6.300 mg/ml) in comparison to the nickel analog. In general, the measured activities are lower than that obtained for the standards except for the higher activity given by C2 in comparison to streptomycin against the R. solanacearum strain.

Steps towards a nature inspired inorganic crystal engineering

This Perspective outlines the results obtained at the University of Bologna by applying crystal engineering strategies to develop nature inspired organic-inorganic materials to tackle challenges in the health and environment sectors. It is shown by means of a number of examples that co-crystallization of inorganic salts, such as alkali and transition metal halides, with organic compounds, such as amino acids, urea, thiourea and quaternary ammonium salts, can be successfully used for (i) chiral resolution and conglomerate formation from racemic compounds, (ii) inhibition of soil enzyme activity in order to reduce urea decomposition and environmental pollution, and (iii) preparation of novel agents to tackle antimicrobial resistance. All materials described in this Perspective have been obtained by mechanochemical solvent-free or slurry methods and characterized by solid state techniques. The fundamental idea is that a crystal engineering approach based on the choice of intermolecular interactions (coordination and hydrogen bonds) between organic and inorganic compounds allows obtaining materials with collective properties that are different, and often very much superior to those of the separate components. It is also demonstrated that the success of this strategy depends crucially on cross-disciplinary synergistic exchange with expert scientists in the areas of bioinorganics, microbiology, and chirality application-oriented developments of these novel materials.

A paean to the ineffable Marjory Stephenson

It is now 75 years since Marjory Stephenson became the second President of the Society for General Microbiology (SGM). Around the time of her death at the end of 1948 many articles appeared extolling Marjory Stephenson’s contribution to the fields of Biochemistry and Microbiology. Not that much has been written about her since that time, which is unfortunate. Therefore, this brief review is intended as a form of redress and aims to highlight the role of this remarkable scientist in establishing the Society and in promoting Microbiology as a discipline. Notwithstanding the significance of these achievements, however, it is her overall impact on the field of ‘Chemical Microbiology’ and what she achieved through her research that are extraordinary, even by today’s standards. Marjory Stephenson recognized that in order to understand a biological system, the ‘whole’ organism must be considered and this can only be achieved by adopting an interdisciplinary approach: inorganic and organic chemistry, biochemistry, genetics, metabolism and ultimately physiology. Her scientific ethos serves today as a beacon for how scientific research should be conducted, and what we as scientists can learn about how to inspire and mentor the next generation. It is impossible to overstate Marjory Stephenson’s scientific legacy, or her overall contribution to Microbiology.

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Urease catalyzes the hydrolysis of urea to form ammonia and carbamate, inducing an overall pH increase that affects both human health and agriculture. Inhibition, mutagenesis, and kinetic studies have provided insights into its enzymatic role, but there have been debates on the substrate binding mode as well as the reaction mechanism. In the present study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) calculations on urease that mainly investigate the binding mode of urea and the mechanism of the urease-catalyzed hydrolysis reaction. Comparison between the experimental data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that urea hydrolysis via a complex with bidentate-bound urea is much more favorable than via that with monodentate-bound urea for both nucleophilic attack and the subsequent proton transfer steps. We also indicate that the bidentate coordination of urea fits the active site with a closed conformation of the mobile flap and can facilitate the stabilization of transition states and intermediates by forming multiple hydrogen bonds with certain active site residues.

Microbial processes during deposition and diagenesis of Banded Iron Formations

Banded Iron Formations (BIFs) are marine chemical sediments consisting of alternating iron (Fe)-rich and silica (Si)-rich bands which were deposited throughout much of the Precambrian era. BIFs represent important proxies for the geochemical composition of Precambrian seawater and provide evidence for early microbial life. Iron present in BIFs was likely precipitated in the form of Fe3+ (Fe(III)) minerals, such as ferrihydrite (Fe(OH)3), either through the metabolic activity of anoxygenic photoautotrophic Fe2+ (Fe(II))-oxidizing bacteria (photoferrotrophs), by microaerophilic bacteria, or by the oxidation of dissolved Fe(II) by O2 produced by early cyanobacteria. However, in addition to oxidized Fe-bearing minerals such as hematite (FeIII 2O3), (partially) reduced minerals such as magnetite (FeIIFeIII 2O4) and siderite (FeIICO3) are found in BIFs as well. The presence of reduced Fe in BIFs has been suggested to reflect the reduction of primary Fe(III) minerals by dissimilatory Fe(III)-reducing bacteria, or by metamorphic (high pressure and temperature) reactions occurring in presence of buried organic matter. Here, we present the current understanding of the role of Fe-metabolizing bacteria in the deposition of BIFs, as well as competing hypotheses that favor an abiotic model for BIF deposition. We also discuss the potential abiotic and microbial reduction of Fe(III) in BIFs after deposition. Further, we review the availability of essential nutrients (e.g. P and Ni) and their implications on early Earth biogeochemistry. Overall, the combined results of various ancient seawater analogue experiments aimed at assessing microbial iron cycling pathways, coupled with the analysis of the BIF rock record, point towards a strong biotic influence during BIF genesis.

Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition

A few gold compounds were recently found to show antimicrobial properties in vitro, holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt₃)Cl, Au(PEt₃)Br, Au(PEt₃)I and [Au(PEt₃)₂]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC₅₀ values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC₅₀ value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt₃)I and [Au(PEt₃)₂]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.

Nickel induced cell impairments are negatively regulated by the Tor1 kinase in Schizosaccharomyces pombe

In our study we investigated the effect of different nickel (NiSO₄·6H₂O) (Ni) concentrations on cell division, cellular morphology and ionome homeostasis of the eukaryotic model organism Schizosaccharomyces pombe. Target of rapamycin (TOR) protein kinase is one of the key regulators of cell growth under different environmental stresses. We analyzed the effect of Ni on cell strains lacking the Tor1 signaling pathway utilizing light-absorbance spectroscopy, visualization, microscopy and inductively coupled plasma optical emission spectroscopy. Interestingly, our findings revealed that Ni mediated cell growth alterations are noticeably lower in Tor1 deficient cells. Greater size of Tor1 depleted cells reached similar quantitative parameters to wild type cells upon incubation with 400 μM Ni. Differences of ion levels among the two tested yeast strains were detected even before Ni addition. Addition of high concentration (1 mM) of the heavy metal, representing acute contamination, caused considerable changes in the ionome of both strains. Strikingly, Tor1 deficient cells displayed largely reduced Ni content after treatment compared to wild type controls (644.1 ± 49 vs. 2096.8 ± 75 μg/g), suggesting its significant role in Ni trafficking. Together our results predict yet undefined role for the Tor1 signaling in metal uptake and/or metabolism.

Synthesis, in vitro antiurease, in vivo antinematodal activity of quinoline analogs and their in-silico study

Synthesis of quinoline analogs and their urease inhibitory activities with reference to the standard drug, thiourea (IC₅₀ = 21.86 ± 0.40 µM) are presented in this study. The inhibitory activity range is (IC₅₀ = 0.60 ± 0.01 to 24.10 ± 0.70 µM) which displayed that it is most potent class of urease inhibitor. Analog 1-9, and 11-13 emerged with many times greater antiurease potential than thiourea, in which analog 1, 2, 3, 4, 8, 9, and 11 (IC₅₀ = 3.50 ± 0.10, 7.20 ± 0.20, 1.30 ± 0.10, 2.30 ± 0.10, 0.60 ± 0.01, 1.05 ± 0.10 and 2.60 ± 0.10 µM respectively) were appeared the most potent ones among the series. In this context, most potent analogs such as 1, 3, 4, 8, and 9 were further subjected for their in vitro antinematodal study against C. elegans to examine its cytotoxicity under positive control of standard drug, Levamisole. Consequently, the cytotoxicity profile displayed that analogs 3, 8, and 9 were found with minimum cytotoxic outline at higher concentration (500 µg/mL). All analogs were characterized through ¹H NMR, ¹³C NMR and HR-EIMS. The protein-ligand binding interaction for most potent analogs was confirmed via molecular docking study.

Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes

Soft metal ions can inactivate urease, a Ni(II)-dependent enzyme whose hydrolytic activity has significant implications in agro-environmental science and human health. Kinetic and structural studies of the reaction of Canavalia ensiformis urease (JBU) and Sporosarcina pasteurii urease (SPU) with Ag(I) compounds of general formula [Ag(PEt₃)X]₄ (X = Cl, Br, I), and with the ionic species [Ag(PEt₃)₂]NO₃, revealed the role of the Ag(I) ion and its ligands in modulating the metal-enzyme interaction. The activity of JBU is obliterated by the [Ag(PEt₃)X]₄ complexes, with IC₅₀ values in the nanomolar range; the efficiency of the inhibition increases in the Cl^- < Br^- < I^- order. The activity of JBU upon [Ag(PEt₃)₂]NO₃ addition decreases to a plateau corresponding to ca. 60% of the original activity and decreases with time at a reduced rate. Synchrotron X-ray crystallography on single crystals obtained after the incubation of SPU with the Ag(I) complexes yielded high-resolution (1.63-1.97 Å) structures. The metal-protein adducts entail a dinuclear Ag(I) cluster bound to the conserved residues αCys322, αHis323, and αMet367, with a bridging cysteine thiolate atom, a weak Ag^…Ag bond, and a quasi-linear Ag(I) coordination geometry. These observations suggest a mechanism that involves the initial substitution of the phosphine ligand, followed by a structural rearrangement to yield the dinuclear Ag(I) cluster. These findings indicate that urease, in addition to the active site dinuclear Ni(II) cluster, possesses a secondary metal binding site, located on the mobile flap domain, capable of recognizing pairs of soft metal ions and controlling catalysis.

The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate

This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.

Biodegradation of hydrocarbons by microbial strains in the presence of Ni and Pb

Microbial strains capable of degrading petroleum hydrocarbons were isolated from the Yellow River Delta and screened for bio-surfactant production. The bio-surfactant-producing characteristics of the isolates were evaluated, and all the isolates which could produce bio-surfactant were identified by 16S rRNA gene sequencing. The results showed that the isolates belong to Bacillus sp. (72%), Ochrobactrum sp. (0.16%), Brevundimonas sp. (0.06%) and Brevibacterium sp. (0.06%). The biodegradability of crude oil, gasoline, diesel oil and other hydrocarbons by microbial strains were studied, among which the biodegrading ability of strain P1 and strain P19 is higher than other strains. Both strains P1 and P19 can degrade n-hexane and n-hexadecane effectively and have wide substrate extensiveness. In addition, Ni promoted the biodegradability of toluene by both strain P1 and strain P19, while Pb inhibited the growth of strain P19 and decreased its ability to biodegrade toluene. The studies revealed that microbes including strain P1 and strain P19 can be utilized in bioremediation of co-contaminated water with petroleum and heavy metals including Ni and Pb.

czcD gene from Bacillus megaterium and Microbacterium liquefaciens as a potential nickel-vanadium soil pollution biomarker

Metals are among the most prevalent pollutants released into the environment. For these reasons, the use of biomarkers for environmental monitoring of individuals and populations exposed to metal pollution has gained considerable attention, offering fast and sensitive detection of chemical stress in organisms. There are different metal resistance genes in bacteria that can be used as biomarkers, including cation diffusion facilitators carrying metal ions; the prototype is the cobalt-zinc-cadmium transporter (czcD). The present study reports the expression changes in the czcD gene in Bacillus megaterium and Microbacterium liquefaciens under nickel and vanadium exposure by real-time polymerase chain reaction. The nickel-vanadium-resistant strains of B. megaterium and M. liquefaciens used in this study were isolated from mine tailings in Guanajuato, Mexico. The czcD gene showed high expression under exposure to 200 ppm of Ni and 200 ppm of V during the logarithmic growth phase of M. liquefaciens in PHGII liquid media. In contrast, no changes were observed in B. megaterium during logarithmic and stationary growth, perhaps due to the gene having differential expression during the growth phases. The expression profiles obtained for czcD show the possibility of using this gene from M. liquefaciens as a biomarker of nickel and vanadium pollution in microorganisms.

Inhibition Mechanism of Urease by Au(III) Compounds Unveiled by X-ray Diffraction Analysis

The nickel-dependent enzyme urease is a virulence factor for a large number of critical human pathogens, making this enzyme a potential target of therapeutics for the treatment of resistant bacterial infections. In the search for novel urease inhibitors, five selected coordination and organometallic Au(III) compounds containing N^∧N or C^∧N and C^∧N^∧N ligands were tested for their inhibitory effects against Canavalia ensiformis (jack bean) urease. The results showed potent inhibition effects with IC₅₀ values in the nanomolar range. The 2.14 Å resolution crystal structure of Sporosarcina pasteurii urease inhibited by the most effective Au(III) compound [Au(PbImMe)Cl₂]PF₆ (PbImMe = 1-methyl-2-(pyridin-2-yl)-benzimidazole) reveals the presence of two Au ions bound to the conserved triad αCys322/αHis323/αMet367. The binding of the Au ions to these residues blocks the movement of a flap, located at the edge of the active site channel and essential for enzyme catalysis, completely obliterating the catalytic activity of urease. Overall, the obtained results constitute the basis for the design of new gold complexes as selective urease inhibitors with future antibacterial applications.

Engineering the Dark Food Chain

Meeting global food needs in the face of climate change and resource limitation requires innovative approaches to food production. Here, we explore incorporation of new dark food chains into human food systems, drawing inspiration from natural ecosystems, the history of single cell protein, and opportunities for new food production through wastewater treatment, microbial protein production, and aquaculture. The envisioned dark food chains rely upon chemoautotrophy in lieu of photosynthesis, with primary production based upon assimilation of CH₄ and CO₂ by methane- and hydrogen-oxidizing bacteria. The stoichiometry, kinetics, and thermodynamics of these bacteria are evaluated, and opportunities for recycling of carbon, nitrogen, and water are explored. Because these processes do not require light delivery, high volumetric productivities are possible; because they are exothermic, heat is available for downstream protein processing; because the feedstock gases are cheap, existing pipeline infrastructure could facilitate low-cost energy-efficient delivery in urban environments. Potential life-cycle benefits include: a protein alternative to fishmeal; partial decoupling of animal feed from human food; climate change mitigation due to decreased land use for agriculture; efficient local cycling of carbon and nutrients that offsets the need for energy-intensive fertilizers; and production of high value products, such as the prebiotic polyhydroxybutyrate.

Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach

The nickel-dependent enzyme urease represents a negative element for the efficiency of soil nitrogen fertilization as well as a virulence factor for a large number of pathogenic and antibiotic-resistant bacteria. The development of ever more efficient urease inhibitors demands knowledge of their modes of action at the molecular level. N-( n-Butyl)-phosphoric triamide (NBPTO) is the oxo-derivative of N-( n-butyl)-thiophosphoric triamide (NBPT), which is extensively employed in agriculture to increase the efficiency of urea-based fertilizers. The 1.45 Å resolution structure of the enzyme-inhibitor complex obtained upon incubation of Sporosarcina pasteurii urease (SPU) with NBPTO shows the presence of diamido phosphoric acid (DAP), generated upon enzymatic hydrolysis of NBPTO with the release of n-butyl amine. DAP is bound in a tridentate binding mode to the two Ni(II) ions in the active site of urease via two O atoms and an amide NH₂ group, whereas the second amide group of DAP points away from the metal center into the active-site channel. The mobile flap modulating the size of the active-site cavity is found in a disordered closed-open conformation. A kinetic characterization of the NBPTO-based inhibition of both bacterial (SPU) and plant ( Canavalia ensiformis or jack bean, JBU) ureases, carried out by calorimetric measurements, indicates the occurrence of a reversible slow-inhibition mode of action. The latter is characterized by a very small value of the equilibrium dissociation constant of the urease-DAP complex caused, in turn, by the large rate constant for the formation of the enzyme-inhibitor complex. The much greater capability of NBPTO to inhibit urease, as compared with that of NBPT, is thus not caused by the presence of a P═O moiety versus a P═S moiety, as previously suggested, but rather by the readiness of NBPTO to react with urease without the need to convert one of the P-NH₂ amide moieties to its P-OH acid derivative, as in the case of NBPT. The latter process is indeed characterized by a very small equilibrium constant that reduces drastically the concentration of the active form of the inhibitor in the case of NBPT. This indicates that high-efficiency phosphoramide-based urease inhibitors must have at least one O atom bound to the central P atom in order for the molecule to efficiently and rapidly bind to the dinickel center of the enzyme.

Extra precision glide docking, free energy calculation and molecular dynamics studies of 1,2-diarylethane derivatives as potent urease inhibitors

For the latter half of the twentieth century, most medical professionals considered bacterial infection to be a primary cause of gastrointestinal ulcers in human beings. In 1994, the World Health Organization (WHO) recognized Helicobacter pylori, the bacterium most closely linked to ulcer development, as a type I carcinogen. Biological research has shown that there is a positive correlation between the number of species in the Helicobacter genus and the number of medical conditions associated with Helicobacter infection, both of which are increasing rapidly. N-Benzylaniline derivatives, frequently used in industrial manufacturing, are being considered as a strong candidate for ongoing drug modeling in search of novel therapies. The basic goal behind this study was to determine the potency of experimentally proved data, and to determine favorable substituents to enhance potency, and thereafter to support this finding through theoretical modification of the existing base skeleton by addition of suitable substituents. Ligands were investigated thoroughly by paying attention to the urease-inhibitory properties present in the selected series. Initially, docking was performed on ligands with protein to produce efficient docking poses. Molecular dynamics (MD) simulations were also performed to precisely understand the interactions between ligands and proteins. Thereafter, MM-GBSA was used in order to validate the methods and results. Good interaction was observed with amino acids Arg338, Ala169, Asp223, His322, and Asn168. This study also revealed that the electron rich hydroxyl group (-OH) substituent plays an important role during bond formation. In addition, various hydrogen bonds, ionic bonds, and pi-pi stacking bonds make significant contributions towards urease inhibition. Therefore, further research utilizing electron-rich moieties may lead to novel and efficacious urease inhibitors.

Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation

This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.

Inhibition of Urease by Disulfiram, an FDA-Approved Thiol Reagent Used in Humans

Urease is a nickel-dependent amidohydrolase that catalyses the decomposition of urea into carbamate and ammonia, a reaction that constitutes an important source of nitrogen for bacteria, fungi and plants. It is recognized as a potential antimicrobial target with an impact on medicine, agriculture, and the environment. The list of possible urease inhibitors is continuously increasing, with a special interest in those that interact with and block the flexible active site flap. We show that disulfiram inhibits urease in Citrullus vulgaris (CVU), following a non-competitive mechanism, and may be one of this kind of inhibitors. Disulfiram is a well-known thiol reagent that has been approved by the FDA for treatment of chronic alcoholism. We also found that other thiol reactive compounds (l-captopril and Bithionol) and quercetin inhibits CVU. These inhibitors protect the enzyme against its full inactivation by the thiol-specific reagent Aldrithiol (2,2'-dipyridyl disulphide, DPS), suggesting that the three drugs bind to the same subsite. Enzyme kinetics, competing inhibition experiments, auto-fluorescence binding experiments, and docking suggest that the disulfiram reactive site is Cys592, which has been proposed as a "hinge" located in the flexible active site flap. This study presents the basis for the use of disulfiram as one potential inhibitor to control urease activity.

Expression Analysis of Ni- and V-Associated Resistance Genes in a Bacillus megaterium Strain Isolated from a Mining Site

Bacillus megaterium strain MNSH1-9K-1 was isolated from a mining site in Guanajuato, Mexico. This B. megaterium strain presented the ability to remove Ni and V from a spent catalyst. Also, its associated metal resistance genes nccA, hant, VAN2, and smtAB were previously identified by a PCR approach. The present study reports for the first time, in B. megaterium, the changes in the expression of the genes nccA (Ni-Co-Cd resistance); hant (high-affinity nickel transporter); smtAB, a metal-binding protein gene; and VAN2 (V resistance) after exposure to 200 ppm of Ni and 200 ppm of V during the stationary phase of the microorganism in PHGII liquid media. The data presented here may contribute to the knowledge of the genes involved in the Ni and V resistances of B. megaterium, and the possible pathways implicated in the Ni-V removal processes, which may be potentiated for the biological treatment of high metal content residues.

Selective enrichment and production of highly urease active bacteria by non-sterile (open) chemostat culture

In general, bioprocesses can be subdivided into naturally occurring processes, not requiring sterility (e.g., beer brewing, wine making, lactic acid fermentation, or biogas digestion) and other processes (e.g., the production of enzymes and antibiotics) that typically require a high level of sterility to avoid contaminant microbes overgrowing the production strain. The current paper describes the sustainable, non-sterile production of an industrial enzyme using activated sludge as inoculum. By using selective conditions (high pH, high ammonia concentration, and presence of urea) for the target bacterium, highly active ureolytic bacteria, physiologically resembling Sporosarcina pasteurii were reproducibly enriched and then continuously produced via chemostat operation of the bioreactor. When using a pH of 10 and about 0.2 M urea in a yeast extract-based medium, ureolytic bacteria developed under aerobic chemostat operation at hydraulic retention times of about 10 h with urease levels of about 60 μmol min−1 ml−1 culture. For cost minimization at an industrial scale the costly protein-rich yeast extract medium could be replaced by commercial milk powder or by lysed activated sludge. Glutamate, molasses, or glucose-based media did not result in the enrichment of ureolytic bacteria by the chemostat. The concentration of intracellular urease was sufficiently high such that the produced raw effluent from the reactor could be used directly for biocementation in the field.

Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome

Background

Several links have been established between the human gut microbiome and conditions such as obesity and inflammatory bowel syndrome. This highlights the importance of understanding what properties of the gut microbiome can affect the health of the human host. Studies have been undertaken to determine the species composition of this microbiome and infer functional profiles associated with such host properties. However, lateral gene transfer (LGT) between community members may result in misleading taxonomic attributions for the recipient organisms, thus making species-function links difficult to establish.

Results

We identified a peptides/nickel transport complex whose components differed in abundance based upon levels of host obesity, and assigned the encoded proteins to members of the microbial community. Each protein was assigned to several distinct taxonomic groups, with moderate levels of agreement observed among different proteins in the complex. Phylogenetic trees of these proteins produced clusters that differed greatly from taxonomic attributions and indicated that habitat-directed LGT of this complex is likely to have occurred, though not always between the same partners.

Conclusions

These findings demonstrate that certain membrane transport systems may be an important factor within an obese-associated gut microbiome and that such complexes may be acquired several times by different strains of the same species. Additionally, an example of individual proteins from different organisms being transferred into one operon was observed, potentially demonstrating a functional complex despite the donors of the subunits being taxonomically disparate. Our results also highlight the potential impact of habitat-directed LGT on the resident microbiota.

Metabolic deficiences revealed in the biotechnologically important model bacterium Escherichia coli BL21(DE3)

The Escherichia coli B strain BL21(DE3) has had a profound impact on biotechnology through its use in the production of recombinant proteins. Little is understood, however, regarding the physiology of this important E. coli strain. We show here that BL21(DE3) totally lacks activity of the four [NiFe]-hydrogenases, the three molybdenum- and selenium-containing formate dehydrogenases and molybdenum-dependent nitrate reductase. Nevertheless, all of the structural genes necessary for the synthesis of the respective anaerobic metalloenzymes are present in the genome. However, the genes encoding the high-affinity molybdate transport system and the molybdenum-responsive transcriptional regulator ModE are absent from the genome. Moreover, BL21(DE3) has a nonsense mutation in the gene encoding the global oxygen-responsive transcriptional regulator FNR. The activities of the two hydrogen-oxidizing hydrogenases, therefore, could be restored to BL21(DE3) by supplementing the growth medium with high concentrations of Ni²⁺ (Ni²⁺-transport is FNR-dependent) or by introducing a wild-type copy of the fnr gene. Only combined addition of plasmid-encoded fnr and high concentrations of MoO₄²⁻ ions could restore hydrogen production to BL21(DE3); however, to only 25-30% of a K-12 wildtype. We could show that limited hydrogen production from the enzyme complex responsible for formate-dependent hydrogen evolution was due solely to reduced activity of the formate dehydrogenase (FDH-H), not the hydrogenase component. The activity of the FNR-dependent formate dehydrogenase, FDH-N, could not be restored, even when the fnr gene and MoO₄²⁻ were supplied; however, nitrate reductase activity could be recovered by combined addition of MoO₄²⁻ and the fnr gene. This suggested that a further component specific for biosynthesis or activity of formate dehydrogenases H and N was missing. Re-introduction of the gene encoding ModE could only partially restore the activities of both enzymes. Taken together these results demonstrate that BL21(DE3) has major defects in anaerobic metabolism, metal ion transport and metalloprotein biosynthesis.

Structural and functional role of nickel ions in urease by molecular dynamics simulation

Nickel ions play several roles in the biological processes of microorganisms and plants. Urease has a nickel-containing active site and catalyzes the hydrolysis of urea to yield ammonia and carbamate. In the present study, the role of nickel ions is examined using molecular dynamics simulations of the holo and apo forms. Nonbonded models used for the nickel ions provide good reproduction of the active-site structure as indicated in the crystallized structure. The results confirm that urease has a rigid active site in either its holo or its apo form. A new conformation of the flap is observed in apo urease. The connection between the metal center and His(α323) is proposed to be responsible for maintaining the flap conformation. The binding free energy of acetohydroxamic acid and urease is estimated using the molecular mechanics-generalized Born/surface area method. The binding free energy is primarily driven by electrostatic interactions in the presence of nickel ions. Normal mode analysis is employed to characterize the movements of the flap in apo urease.

Hydrogen enhances nickel tolerance in the purple sulfur bacterium Thiocapsa roseopersicina

A common microbial strategy for detoxifying metals involves redox transformation which often results in metal precipitation and/or immobilization. In the present study, the influence of ionic nickel [Ni(II)] on growth of the purple sulfur bacterium Thiocapsa roseopersicina was investigated. The results suggest that Ni(II) in the bulk medium at micromolar concentrations results in growth inhibition, specifically an increase in the lag phase of growth, a decrease in the specific growth rate, and a decrease in total protein concentration when compared to growth controls containing no added Ni(II). The inhibitory effects of Ni(II) on the growth of T. roseopersicina could be partially overcome by the addition of hydrogen (H(2)) gas. However, the inhibitory effects of Ni(II) on the growth of T. roseopersicina were not alleviated by H(2) in a strain containing deletions in all hydrogenase-encoding genes. Transmission electron micrographs of wild-type T. roseopersicina grown in the presence of Ni(II) and H(2) revealed a significantly greater number of dense nanoparticulates associated with the cells when compared to wild-type cells grown in the absence of H(2) and hydrogenase mutant strains grown in the presence of H(2). X-ray diffraction and vibrating sample magnetometry of the dense nanoparticles indicated the presence of zerovalent Ni, suggesting Ni(II) reduction. Purified T. roseopersicina hyn-encoded hydrogenase catalyzed the formation of zerovalent Ni particles in vitro, suggesting a role for this hydrogenase in Ni(II) reduction in vivo. Collectively, these results suggest a link among H(2) metabolism, Ni(II) tolerance, and Ni(II) reduction in T. roseopersicina .

Binding of Ni2+ to a histidine- and glutamine-rich protein, Hpn-like

Hpn-like (Hpnl) protein, encoded by the hpnl gene in Helicobacter pylori and featuring a histidine-rich and two glutamine-rich motifs, can render nickel tolerance to H. pylori when the external nickel level reaches toxic limits. We found that the recombinant Hpnl exists as an oligomer in the native state and binds to two molar equivalents of nickel ions per monomer with a dissociation constant of 3.8 microM. Nickel could be released from Hpnl either at acidic pH (pH(1/2) 4.6) or in the presence of chelate ligands, such as EDTA (t(1/2) = 220, 355, and 716 min at pH 6.0, 7.0, and 7.5, respectively). Our combined spectroscopic data show that nickel ion coordinates to a nitrogen of a histidine residue possibly with a coordination number of four (square-planar geometry) or five. The growth of Escherichia coli cells with or without the hpnl gene implied a protective role of Hpnl under higher concentrations of external nickel ions. Hpnl may serve a role in binding/storage or detoxification of excess nickel ions.

Role of nickel in high rate methanol degradation in anaerobic granular sludge bioreactors

The effect of nickel deprivation from the influent of a mesophilic (30 degrees C) methanol fed upflow anaerobic sludge bed (UASB) reactor was investigated by coupling the reactor performance to the evolution of the Methanosarcina population of the bioreactor sludge. The reactor was operated at pH 7.0 and an organic loading rate (OLR) of 5-15 g COD l(-1) day(-1) for 191 days. A clear limitation of the specific methanogenic activity (SMA) on methanol due to the absence of nickel was observed after 129 days of bioreactor operation: the SMA of the sludge in medium with the complete trace metal solution except nickel amounted to 1.164 (+/-0.167) g CH(4)-COD g VSS(-1) day(-1) compared to 2.027 (+/-0.111) g CH(4)-COD g VSS(-1) day(-1) in a medium with the complete (including nickel) trace metal solution. The methanol removal efficiency during these 129 days was 99%, no volatile fatty acid (VFA) accumulation was observed and the size of the Methanosarcina population increased compared to the seed sludge. Continuation of the UASB reactor operation with the nickel limited sludge lead to incomplete methanol removal, and thus methanol accumulation in the reactor effluent from day 142 onwards. This methanol accumulation subsequently induced an increase of the acetogenic activity in the UASB reactor on day 160. On day 165, 77% of the methanol fed to the system was converted to acetate and the Methanosarcina population size had substantially decreased. Inclusion of 0.5 muM Ni (dosed as NiCl(2)) to the influent from day 165 onwards lead to the recovery of the methanol removal efficiency to 99% without VFA accumulation within 2 days of bioreactor operation.

Cloning, sequencing and characterization of a urease gene operon from urease-positive thermophilic Campylobacter (UPTC)

AIMS

To clone, sequence and characterize the genetic organization of urease genes within urease-positive thermophilic Campylobacter (UPTC).

METHODS AND RESULTS

An approx. 5.1-kbp region encoding a urease gene operon was identified, when recombinant plasmid DNAs from a genomic DNA library of a Japanese isolate (CF89-12) of UPTC were analysed.

CONCLUSIONS

Six closely spaced and putative open reading frames (ORFs) for ureA, ureB, ureE, ureF, ureG and ureH were detected. ATG codons initiated each ORF of the UPTC urease operon except for ureB and ureH, which commenced with the most probable TTG codon. Overlaps were detected between ureA and ureB and also between ureB and ureE. Probable ribosome-binding sites and a putative rho-independent transcriptional termination region were identified. Two putative promoter structures, consisting of consensus sequences at the -35 like and -10 regions were also identified.

SIGNIFICANCE AND IMPACT OF THE STUDY

Construction of a neighbour-joining tree based on the nucleotide sequence data of urease genes indicated that UPTC formed a cluster with some Helicobacter organisms separate from the other urease-producing bacteria, suggesting a commonly shared ancestry between UPTC and Helicobacter urease genes.

Development and characterization of nickel accumulating mutants of Aspergillus nidulans

Stable mutants of Aspergillus nidulans, resistant to 1 mM Ni were developed by step-by-step repeated culturing of the fungus on the medium containing increasing concentrations of nickel chloride. Characterization of mutants could differentiate them into two categories Ni(R) I and Ni(R) II. Each category of mutants exhibited alterations in growth, conidial germination and melanin secretion both in Ni-free and Ni-containing media. Ni(R) II mutants were little slow in growth with sparse mycelia and conidiation but showed high melanin secretion and higher Ni-uptake in comparison to Ni(R) I mutant. Studies involving metabolic and translational inhibitors could prove that Ni-accumulation was biphasic. The initial energy independent surface accumulation was found to be followed by energy dependent intarcellular uptake. Increase in the concentration of the metal in the medium or the time of exposure did not proportionately increase the metal uptake by the mutants. Ni-uptake followed Michaelis-Menton saturation kinetics, which was enhanced under optimum pH of 6.5-7.5 and reduced complexity of the medium due to free availability of ions. Resistance to Ni was found to be constitutive in Ni(R)I mutant, and could be induced in Ni(R)II mutant.

Fluctuation in recoverable nickel and zinc resistant copiotrophic bacteria explained by the varying zinc ion content of Torsa River in different months

Heavy metal content analysis of River Torsa in India did not indicate any alarming level of toxicity for human consumption but revealed variation at the ppb level in different months. The variation in recoverable nickel and zinc resistant copiotrophic (or eutrophic) bacterial counts was explained by the variation of the zinc content (34.0-691.3 ppb) of the river water in different sampling months. Growth studies conducted with some purified nickel and/or zinc resistant strains revealed that pre-exposure of the cells to ppb levels of Zn(2+), comparable to the indigenous zinc ion concentration of the river, could induce the nickel or zinc resistance. A minimum concentration of 5-10 microM Zn(2+ )(325-650 ppb) was found effective in inducing the Nickel resistance of the isolates. Zinc resistance of the isolates was tested by pre-exposing the cells to 4 microM Zn(2+ )(260 ppb). The lag phase was reduced by 6-8 h in all the cases. Biochemical characteristics and phylogenetic analysis based on 16S rDNA sequence indicated that some of the Torsa River isolates, having inducible nickel and zinc resistance, are members of the genus Pseudomonas, Acinetobacter, Bacillus, Enterobacter, Serratia and Moraxella.

Intrinsically disordered structure of Bacillus pasteurii UreG as revealed by steady-state and time-resolved fluorescence spectroscopy

UreG is an essential protein for the in vivo activation of urease. In a previous study, UreG from Bacillus pasteurii was shown to behave as an intrinsically unstructured dimeric protein. Here, intrinsic and extrinsic fluorescence experiments were performed, in the absence and presence of denaturant, to provide information about the form (fully folded, molten globule, premolten globule, or random coil) that the native state of BpUreG assumes in solution. The features of the emission band of the unique tryptophan residue (W192) located on the C-terminal helix, as well as the rate of bimolecular quenching by potassium iodide, indicated that, in the native state, W192 is protected from the aqueous polar solvent, while upon addition of denaturant, a conformational change occurs that causes solvent exposure of the indole side chain. This structural change, mainly affecting the C-terminal helix, is associated with the release of static quenching, as shown by resolution of the decay-associated spectra. The exposure of protein hydrophobic sites, monitored using the fluorescent probe bis-ANS, indicated that the native dimeric state of BpUreG is disordered even though it maintains a significant amount of tertiary structure. ANS fluorescence also indicated that, upon addition of a small amount of GuHCl, a transition to a molten globule state occurs, followed by formation of a pre-molten globule state at a higher denaturant concentration. The latter form is resistant to full unfolding, as also revealed by far-UV circular dichroism spectroscopy. The hydrodynamic parameters obtained by time-resolved fluorescence anisotropy at maximal denaturant concentrations (3 M GuHCl) confirmed the existence of a disordered but stable dimeric protein core. The nature of the forces holding together the two monomers of BpUreG was investigated. Determination of free thiols in native or denaturant conditions, as well as light scattering experiments in the absence and presence of dithiothreitol as a reducing agent, under native or denaturing conditions, indicates that a disulfide bond, involving the unique conserved cysteine C68, is present under native conditions and maintained upon addition of denaturant. This covalent bond is therefore important for the stabilization of the dimer under native conditions. The intrinsically disordered structure of UreG is discussed with respect to the role of this protein as a chaperone in the urease assembly system.

Nickel resistance in fission yeast associated with the magnesium transport system

We isolated and characterized a nickel (Ni2+)-resistant mutant (GA1) of Schizosaccharomyces pombe. This mutant strain displayed resistance to both Ni2+ and Zn2+, but not to Cd2+, Co2+, and Cu2+. The growth rate of GA1 increased proportionally with increasing Mg2+ concentrations until 50 mM Mg2+. The GA1 mutation phenotype suggests a defect in Mg2+ uptake. Sequence analysis of the GA1 open reading frame (ORF) O13779, which is homologous to the prokaryotic and eukaryotic CorA Mg2+ transport systems, revealed a point mutation at codon 153 (ccc to acc) resulting in a Pro153Thr substitution in the N-terminus of the CorA domain. Our results provide novel genetic information about Ni2+ resistance in fission yeast. Specifically, that reducing Mg2+ influx through the CorA Mg2+ transport membrane protein confers Ni2+ resistance in S. pombe. We also report that Ni2+ ion detoxification of the fission yeast is related to histidine metabolism and pH.

Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli

Bacteria have evolved a number of tightly controlled import and export systems to maintain intracellular levels of the essential but potentially toxic metal nickel. Nickel homeostasis systems include the dedicated nickel uptake system nik found in Escherichia coli, a member of the ABC family of transporters, that involves a periplasmic nickel-binding protein, NikA. This is the initial nickel receptor and mediator of the chemotactic response away from nickel. We have solved the crystal structure of NikA protein in the presence and absence of nickel, showing that it behaves as a "classical" periplasmic binding protein. In contrast to other binding proteins, however, the ligand remains accessible to the solvent and is not completely enclosed. No direct bonds are formed between the metal cation and the protein. The nickel binding site is apolar, quite unlike any previously characterized protein nickel binding site. Despite relatively weak binding, NikA is specific for nickel. Using isothermal titration calorimetry, the dissociation constant for nickel was found to be approximately 10 microm and that for cobalt was approximately 20 times higher.

External nickel inhibits epithelial sodium channel by binding to histidine residues within the extracellular domains of alpha and gamma subunits and reducing channel open probability

Epithelial sodium channels (ENaC) are regulated by various intracellular and extracellular factors including divalent cations. We studied the inhibitory effect and mechanism of external Ni(2+) on cloned mouse alpha-beta-gamma ENaC expressed in Xenopus oocytes. Ni(2+) reduced amiloride-sensitive Na(+) currents of the wild type mouse ENaC in a dose-dependent manner. The Ni(2+) block was fast and partially reversible at low concentrations and irreversible at high concentrations. ENaC inhibition by Ni(2+) was accompanied by moderate inward rectification at concentrations higher than 0.1 mm. ENaC currents were also blocked by the histidine-reactive reagent diethyl pyrocarbonate. Pretreatment of the oocytes with the reagent reduced Ni(2+) inhibition of the remaining current. Mutations at alphaHis(282) and gammaHis(239) located within the extracellular loops significantly decreased Ni(2+) inhibition of ENaC currents. The mutation alphaH282D or double mutations alphaH282R/gammaH239R eliminated Ni(2+) block. All mutations at gammaHis(239) eliminated Ni(2+)-induced inward current rectification. Ni(2+) block was significantly enhanced by introduction of a histidine at alphaArg(280). Lowering extracellular pH to 5.5 and 4.4 decreased or eliminated Ni(2+) block. Although alphaH282C-beta-gamma channels were partially inhibited by the sulfhydryl-reactive reagent [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET), alpha-beta-gamma H239C channels were insensitive to MTSET. From patch clamp studies, Ni(2+) did not affect unitary current but decreased open probability when perfused into the recording pipette. Our results suggest that external Ni(2+) reduces ENaC open probability by binding to a site consisting of alphaHis(282) and gammaHis(239) and that these histidine residues may participate in ENaC gating.

PrpE, a PPP protein phosphatase from Bacillus subtilis with unusual substrate specificity

Bacillus subtilis is a Gram-positive bacterium with a relatively large number of protein phosphatases. Previous studies have shown that some Ser/Thr phosphatases play an important role in the life cycle of this bacterium [Losick and Stragier (1992) Nature (London) 355, 601-604; Yang, Kang, Brody and Price (1996) Genes Dev. 10, 2265-2275]. In this paper, we report the biochemical properties of a putative, previously uncharacterized phosphatase, PrpE, belonging to the PPP family. This enzyme shares homology with other PPP phosphatases as well as with symmetrical diadenosine tetraphosphatases related to ApaH (symmetrical Ap(4)A hydrolase) from Escherichia coli. A His-tagged recombinant PrpE was purified from E. coli and shown to have Ni(2+)-dependent and okadaic acid-resistant phosphatase activity against a synthetic phosphorylated peptide and hydrolase activity against diadenosine 5',5"'-tetraphosphate. Unexpectedly, PrpE was able to remove phosphate from phosphotyrosine, but not from phosphothreonine or phosphoserine.

NreB from Achromobacter xylosoxidans 31A Is a nickel-induced transporter conferring nickel resistance

There are two distinct nickel resistance loci on plasmid pTOM9 from Achromobacter xylosoxidans 31A, ncc and nre. Expression of the nreB gene was specifically induced by nickel and conferred nickel resistance on both A. xylosoxidans 31A and Escherichia coli. E. coli cells expressing nreB showed reduced accumulation of Ni(2+), suggesting that NreB mediated nickel efflux. The histidine-rich C-terminal region of NreB was not essential but contributed to maximal Ni(2+) resistance.

Identification of the nik gene cluster of Brucella suis: regulation and contribution to urease activity

Analysis of a Brucella suis 1330 gene fused to a gfp reporter, and identified as being induced in J774 murine macrophage-like cells, allowed the isolation of a gene homologous to nikA, the first gene of the Escherichia coli operon encoding the specific transport system for nickel. DNA sequence analysis of the corresponding B. suis nik locus showed that it was highly similar to that of E. coli except for localization of the nikR regulatory gene, which lies upstream from the structural nikABCDE genes and in the opposite orientation. Protein sequence comparisons suggested that the deduced nikABCDE gene products belong to a periplasmic binding protein-dependent transport system. The nikA promoter-gfp fusion was activated in vitro by low oxygen tension and metal ion deficiency and was repressed by NiCl(2) excess. Insertional inactivation of nikA strongly reduced the activity of the nickel metalloenzyme urease, which was restored by addition of a nickel excess. Moreover, the nikA mutant of B. suis was functionally complemented with the E. coli nik gene cluster, leading to the recovery of urease activity. Reciprocally, an E. coli strain harboring a deleted nik operon recovered hydrogenase activity by heterologous complementation with the B. suis nik locus. Taking into account these results, we propose that the nik locus of B. suis encodes a nickel transport system. The results further suggest that nickel could enter B. suis via other transport systems. Intracellular growth rates of the B. suis wild-type and nikA mutant strains in human monocytes were similar, indicating that nikA was not essential for this step of infection. We discuss a possible role of nickel transport in maintaining enzymatic activities which could be crucial for survival of the bacteria under the environmental conditions encountered within the host.

Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation

The metalloenzyme glyoxalase I (GlxI) converts the nonenzymatically produced hemimercaptal of cytotoxic methylglyoxal and glutathione to nontoxic S-D-lactoylglutathione. Human GlxI, for which the structure is known, is active in the presence of Zn(2+). Unexpectedly, the Escherichia coli enzyme is inactive in the presence of Zn(2+) and is maximally active with Ni(2+). To understand this difference in metal activation and also to obtain a representative of the bacterial enzymes, the structure of E. coli Ni(2+)-GlxI has been determined. Structures have also been determined for the apo enzyme as well as complexes with Co(2+), Cd(2+), and Zn(2+). It is found that each of the protein-metal complexes that is catalytically active has octahedral geometry. This includes the complexes of the E. coli enzyme with Ni(2+), Co(2+), and Cd(2+), as well as the structures reported for the human Zn(2+) enzyme. Conversely, the complex of the E. coli enzyme with Zn(2+) has trigonal bipyramidal coordination and is inactive. This mode of coordination includes four protein ligands plus a single water molecule. In contrast, the coordination in the active forms of the enzyme includes two water molecules bound to the metal ion, suggesting that this may be a key feature of the catalytic mechanism. A comparison of the human and E. coli enzymes suggests that there are differences between the active sites that might be exploited for therapeutic use.