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Nonaqueous phase liquids (NAPL, e.g., hydrocarbons and chlorinated compounds) are common groundwater pollutants. Electrokinetic remediation of NAPLs uses electric fields to draw them toward electrodes and remove them from groundwater. The treatment requires NAPL mobility. Emulsification increases mobility, but at a risk for downstream receptors. We propose using alkaline aqueous solutions of zein and graphene nanoparticles (GNP) to form conductive materials, which could also act as barriers to control NAPL migration. Alkaline zein-GNP solutions can be injected in the polluted soil and solidified by neutralizing the pH (e.g., with glacial acetic acid, GAA). Shear rheology experiments showed that zein-GNP composites were cohesive, and voltammetry showed that GNP increased electrical conductivity of zein-based materials by 3.5 times. Gas chromatography-mass spectroscopy (GC-MS) demonstrated that the electrokinetic treatment of model sandy aquifers yielded >60% and ∼47% removal of emulsified toluene in freshwater and in salt solutions, respectively (with 30 min treatment using a 10 V differential voltage between a zein-GNP and an aluminum electrode. NaCl was used as model salt contaminant. The conductivity of surfactant solutions was lower in saline water than in freshwater, explaining differences in toluene removal. Toluene-water emulsions were stabilized using the natural surfactants lecithin and saponin. These surfactants acted synergistically in stabilizing emulsions in either freshwater or salt solutions. Lecithin and saponin likely interacted at toluene-water interfaces, as indicated by the morphology, interfacial tension and compressional rigidity of toluene-water interfaces with both components (relative to interfaces of either lecithin or saponin alone). The compressional behavior of interfacial films was well-described by the Marczak model. Electrokinetic treatment of saturated model sandy aquifers also decreased the turbidity of emulsions of water and either tricholoroethylene (TCE, by ∼41%) or diesel (by ∼75%), in the presence of a bacterial biosurfactant. This decrease was used as semiquantitative indicator of NAPL removal from water.

Environmental water monitoring is an important responsibility of municipal governments. In this study, we partnered with several municipalities in an extensive sampling program to investigate the effects of spatiotemporal and environmental factors on bacterial diversity in a complex watershed ecosystem containing specific environments including creeks, a river, canals, stormwater outfalls and freshwater lakes of the Niagara Peninsula. Samples were collected using standard municipal protocols and bacterial DNA extracted from these samples was sequenced using high-throughput DNA sequencing targeting the V3–V4 regions of the 16S rRNA gene. Average taxonomic richness and alpha diversity differed significantly between samples collected from lakes and creeks (P

Residents in rural communities across Canada collect potable water from aquifers. Fecal contaminants from sewage and agricultural runoffs can penetrate aquifers, posing a public health risk. Standard methods for detecting fecal contamination test for fecal indicator bacteria (FIB), but the presence of these do not identify sources of contamination. In contrast, DNA-based diagnostic tools can achieve this important objective. We employed quantitative polymerase chain reaction (qPCR) and high-throughput DNA sequencing to trace fecal contamination sources in Wainfleet, a rural Ontario township that has been under the longest active boil water advisory in Canada due to FIB contamination in groundwater wells. Using traditional methods, we identified FIBs indicating persistent fecal pollution in well waters. We used 16S rRNA sequencing to profile groundwater microbial communities and identified Campylobacteraceae as a fecal contamination DNA marker in septic tank effluents (STEs). We also identified Turicibacter and Gallicola as a potential cow and chicken fecal contamination marker, respectively. Using human specific Bacteroidales markers, we identified leaking septic tanks as the likely primary fecal contamination source in some of Wainfleet's groundwater. Overall, the results support the use of sequencing-based methods to augment traditional water quality testing methods and help end-users assess fecal contamination levels and identify point and non-point pollution sources. This article has been made Open Access thanks to the generous support of a global network of libraries as part of the Knowledge Unlatched Select initiative.

This study proposes injectable polymeric filters to prevent diesel migration during its bioremediation. Pseudomonas aeruginosa (Gram negative bacterium) was isolated from forest soil and used to biodegrade diesel. P. aeruginosa produced biosurfactants that emulsified diesel in water while degrading it, by decreasing the interfacial tension and forming skins around diesel droplets. In lab experiments, emulsified diesel droplets could migrate through model soil columns (sand and limestone) saturated with water (to mimic aquifers). These results indicate that clean aquifers downstream of diesel spills are at risk of becoming contaminated during diesel bioremediation by P. aeruginosa. Injectable filters were developed to mitigate this risk. Injectable filters were obtained by injecting into model soils aqueous solutions of quaternized hydroxyethylcellulose (HEC+, with a positive electrostatic charge). HEC + adsorbed onto model soils, yielding positively charged surfaces. Diesel droplets stabilized by P. aeruginosa had a negative electrostatic charge (as demonstrated through zeta potential measurements) and adhered onto HEC + coated soil, likely due to attractive electrostatic forces. As a result, diesel droplet mobility through soil columns decreased. Our proof of concept indicates that injectable HEC + filters can protect clean regions of aquifers during the bioremediation of diesel spills by P. aeruginosa.

Pseudomonas sp. bacteria were incorporated into a double emulsion system (water in oil in water, W/O/W), which can be injected in the subsurface to trap and biotreat naphthalene. The outermost phase of the W/O/W emulsion was an aqueous solution of chitosan (1.65 wt.%). Naphthalene could be dispersed in the aqueous chitosan phase of W/O/W emulsions. Two separate primary water in oil (W/O) emulsions were emulsified in chitosan, using Tween 20 as emulsifier. W/O emulsions were prepared with canola oil (containing ethylcellulose and calcium stearate as emulsifiers), and aqueous solutions of either Pseudomonas sp. in minimal broth or sodium citrate (crosslinker). The formation of W/O/W double emulsions was verified with optical and confocal microscopy. Without addition of triggers able to induce gelation on demand, W/O/W emulsions were stable and mainly viscous under shear. The shear elastic modulus (G’ = 1.90 ± 0.39 Pa) and the shear viscous modulus (G” = 5.76 ± 0.06 Pa) were low, to facilitate pumping in the subsurface. With addition of the surfactant cocamidopropyl betaine, W/O/W emulsions were destabilized on demand, thereby releasing citrate (crosslinker) and Pseudomonas sp. in the chitosan phase, where naphthalene was dispersed. Mixing chitosan with citrate led to its gelation, trapping naphthalene. Mixing naphthalene with Pseudomonas sp. led to its bioremediation. Gelation was demonstrated by the increase in the viscoelastic moduli, with G’ = 111.02 ± 1.67 Pa > G” = 8.66 ± 0.10 Pa. With naphthalene, Pseudomonas sp. survival in gelled chitosan was confirmed by plating bacteria sampled from the gel. Without naphthalene, Pseudomonas sp. did not survive in chitosan.

Enterohemorrhagic Escherichia coli O157:H7 is responsible for many outbreaks of gastrointestinal illness and hemolytic uremic syndrome worldwide. Monitoring this pathogen in food and water supplies is an important public health issue. Highly conserved genetic markers, which are characteristic for specific strains, can provide direct identification of target pathogens. In this study, we examined a new detection strategy for pathogenic strains of E. coli O157:H7 serotype based on a conserved signature insertion/deletion (CSI) located in the ybiX gene using TaqMan-probe-based quantitative PCR (qPCR). The qPCR assay was linear from 1.0 × 10(2) to 1.0 × 10(7) genome copies and was specific to O157:H7 when tested against a panel of 15 non-O157:H7 E. coli. The assay also maintained detection sensitivity in the presence of competing E. coli K-12, heterologous nontarget DNA spiked in at a 1000-fold and 800-fold excess of target DNA, respectively, demonstrating the assay's ability to detect E. coli O157:H7 in the presence of high levels of background DNA. This study thus validates the use of strain-specific CSIs as a new class of diagnostic marker for pathogen detection.

As bacterial pathogens develop resistance against most currently used antibiotics, novel alternatives for treatment of microbial infectious diseases are urgently needed. Targeting bacterial virulence functions in order to disarm pathogens represents a promising alternative to classical antibiotic therapy. Type IV secretion systems, which are multiprotein complexes in the cell envelope that translocate effectors into host cells, are critical bacterial virulence factors in many pathogens and excellent targets for such “antivirulence” drugs. The VirB8 protein from the mammalian pathogen Brucella was chosen as a specific target, since it is an essential type IV secretion system component, it participates in multiple protein-protein interactions, and it is essential for the assembly of this translocation machinery. The bacterial two-hybrid system was adapted to assay VirB8 interactions, and a high-throughput screen identified specific small-molecule inhibitors. VirB8 interaction inhibitors also reduced the levels of VirB8 and of other VirB proteins, and many of them inhibited virB gene transcription in Brucella abortus 2308, suggesting that targeting of the secretion system has complex regulatory effects in vivo . One compound strongly inhibited the intracellular proliferation of B. abortus 2308 in a J774 macrophage infection model. The results presented here show that in vivo screens with the bacterial two-hybrid assay are suited to the identification of inhibitors of Brucella type IV secretion system function.

The hydrogenase maturation proteins HypF and HypE catalyze the synthesis of the CN ligands of the active site iron of the NiFe-hydrogenases using carbamoylphosphate as a substrate. HypE protein from Escherichia coli was purified from a transformant overexpressing the hypE gene from a plasmid. Purified HypE in gel filtration experiments behaves predominantly as a monomer. It does not contain statistically significant amounts of metals or of cofactors absorbing in the UV and visible light range. The protein displays low intrinsic ATPase activity with ADP and phosphate as the products, the apparent K(m) being 25 micro m and the k(cat) 1.7 x 10(-3) s(-1). Removal of the C-terminal cysteine residue of HypE which accepts the carbamoyl moiety from HypF affected the K(m) (47 micro m) but not significantly the k(cat) (2.1 x 10(-3) s(-1)). During the carbamoyltransfer reaction, HypE and HypF enter a complex which is rather tight at stoichiometric ratios of the two proteins. A mutant HypE variant was generated by amino acid replacements in the nucleoside triphosphate binding region, which showed no intrinsic ATPase activity. The variant was active as an acceptor in the transcarbamoylation reaction but did not dehydrate the thiocarboxamide to the thiocyanate. The results obtained with the HypE variants and also with mutant HypF forms are integrated to explain the complex reaction pattern of protein HypF.

NiFe-hydrogenases have an Ni-Fe site in which the iron has one CO and two CN groups as ligands. Synthesis of the CN ligands requires the activity of two hydrogenase maturation proteins: HypF and HypE. HypF is a carbamoyltransferase that transfers the carbamoyl moiety of carbamoyladenylate to the COOH-terminal cysteine of HypE and thus forms an enzyme-thiocarbamate. HypE dehydrates the S -carbamoyl moiety in an adenosine triphosphate–dependent process to yield the enzyme thiocyanate. Chemical model reactions corroborate the feasibility of this unprecedented biosynthetic route and show that thiocyanates can donate CN to iron. This finding underscores a striking parallel between biochemistry and organometallic chemistry in the formation of an iron-cyano complex.

The synthesis and the insertion of the metallo-centre of NiFe-hydrogenases is a complex process, in which seven maturation enzymes plus ATP, GTP and carbamoyl phosphate are involved. The review summarizes what is known about the properties and activities of these auxiliary proteins, and postulates a pathway along which maturation may take place.

The interaction of the hydrogenase maturation endopeptidase HycI with its substrate, the precursor of the large subunit, was studied. Replacement of conserved amino-acid residues in HycI, which have been shown to bind a cadmium ion from the crystallization buffer in crystals of HybD (endopeptidase for hydrogenase 2), abolished or strongly reduced processing activity. Atomic absorption spectroscopy of purified HycI and HybD proteins showed the absence of nickel. In vitro processing assays showed that the reaction requires nickel to be bound to the precursor and the protease does not have a function in nickel delivery to the substrate. Radioactive labelling of cells with 63Ni, devoid of endopeptidase, resolved several forms of the precursor which are possibly intermediates in the maturation pathway. It is concluded that the endopeptidase uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif.

The maturation of [NiFe]-hydrogenases is a catalysed process in which the activities of at least seven proteins are involved. The last step consists of the endoproteolytic cleavage of the precursor of the large subunit after the [NiFe]-metal centre has been assembled. The amino acid sequence requirements for the endopeptidase HycI involved in the C-terminal processing of HycE, the large subunit of the hydrogenase 3 from Escherichia coli, were investigated. Mutational alteration of the amino acid residues neighbouring the cleavage site showed that proteolysis still occurred when chemically similar amino acids were exchanged. Processing was blocked, however, in a variant in which the methionine at the C-terminal side was replaced by a glutamate residue. Truncation of the precursor from the C-terminal end rendered variants amenable to maturation even when two-thirds of the extension were removed but abolished proteolysis upon further deletion of a cluster of six basic amino acids. A construct in which the C-terminal extension from the large subunit of the hydrogenase 2 was fused to the mature part of the large subunit of hydrogenase 3 was neither processed by HycI nor by HybD, the endopeptidase specific for the large subunit of hydrogenase 2. The maturation endopeptidase, therefore, exhibits a relaxed sequence constraint in recognition of its cleavage site and does not require the entire C-terminal extension. The results point to an interaction of the C-terminus with some domain of the large subunit, rendering a conformation amenable to recognition by the endopeptidase.

Chemical and biochemical methods were used to unravel the unprecedented pathway by which the CN ligands of iron in [NiFe] hydrogenase are introduced. Carbamoyl phosphate is the one carbon precursor of these ligands, and reactions involving a protein cysteinyl sulfur are key for processing this precursor into CN ligands.

Type IV secretion systems are macromolecular assemblies in the cell envelopes of bacteria that function in macromolecular translocation. Structural biology approaches have provided insights into the interaction of core complex components, but information about proteins that undergo transient interactions with membrane components has not been forthcoming. We have pursued an unbiased approach using peptide arrays and phage display to identify interaction partners and interaction domains of type IV secretion system assembly factor VirB8. These approaches identified the globular domain from the VirB5 protein to interact with VirB8. This interaction was confirmed in cross-linking, pull-down, and fluorescence resonance energy transfer (FRET)-based interaction assays. In addition, using phage display analysis, we identified different regions of VirB6 as potential interaction partners of VirB8. Using a FRET-based interaction assay, we provide the first direct experimental evidence of the interaction of a VirB6 periplasmic domain with VirB8. These results will allow us to conduct directed structural biological work and structure-function analyses aimed at defining the molecular details and biological significance of these interactions with VirB8 in the future.

SummarySecretion systems translocate virulence factors of many bacterial pathogens, enabling their survival inside the host organism. Consequently, inhibition strongly attenuates pathogenicity and can be considered a target for novel antimicrobial drugs. The type IV secretion system (T4SS) of the intracellular pathogen Brucella is a prerequisite for its virulence, and in this work we targeted the interactions of the essential assembly factor protein, VirB8, using small-molecule inhibitors. High-throughput screening identified several potent and specific inhibitors, and the target-binding site of these inhibitors was identified by X-ray crystallography, in silico docking, and analysis of the derivates of the inhibitor B8I-2. VirB8 interaction inhibitors bind to a surface groove opposite to the dimerization interface, and by varying the binding-site residues, we were able to determine which residues are required for inhibitor activity. E115 and K182 were found to be especially important, and changes at R114, Y229, and L151 also reduced inhibitor efficiency.

The hydrogenase maturation proteins HypF and HypE catalyze the synthesis of the CN ligands of the active site iron of the NiFe-hydrogenases using carbamoylphosphate as a substrate. HypE protein from Escherichia coli was purified from a transformant overexpressing the hypE gene from a plasmid. Purified HypE in gel filtration experiments behaves predominantly as a monomer. It does not contain statistically significant amounts of metals or of cofactors absorbing in the UV and visible light range. The protein displays low intrinsic ATPase activity with ADP and phosphate as the products, the apparent K(m) being 25 micro m and the k(cat) 1.7 x 10(-3) s(-1). Removal of the C-terminal cysteine residue of HypE which accepts the carbamoyl moiety from HypF affected the K(m) (47 micro m) but not significantly the k(cat) (2.1 x 10(-3) s(-1)). During the carbamoyltransfer reaction, HypE and HypF enter a complex which is rather tight at stoichiometric ratios of the two proteins. A mutant HypE variant was generated by amino acid replacements in the nucleoside triphosphate binding region, which showed no intrinsic ATPase activity. The variant was active as an acceptor in the transcarbamoylation reaction but did not dehydrate the thiocarboxamide to the thiocyanate. The results obtained with the HypE variants and also with mutant HypF forms are integrated to explain the complex reaction pattern of protein HypF.

Publisher Summary This chapter elaborates the structural chemistry and the biological aspects of hydrogenase maturation endopeptidase. [NiFe]Hydrogenases consist of subunits of 30–35 kDa and of 60–65 kDa, depending on the organism. The large subunit carries the [NiFe]metallocenter, and it is synthesized in a precursor form and proteolytically processed to the form present in the mature enzyme. Hycl and HybD endopeptidases are monomeric proteins with molecular masses of 17 kDa and 17.5 kDa, respectively. There is no primary structure motifs characteristic of serine, cysteine or metalloproteases. Hycl lacks the N-terminal methionine. The crystal structure of HybD, which cleaves off 15 amino acid peptide from the C-terminus of the precursor of the large subunit of hydrogenase 2 from E. coli, has been solved at 2.2 A resolutions. HybD crystallizes with a cadmium ion from the crystallization buffer whereby the metal is pentacoordinated by Glul6, Asp62 and His93, and a water molecule. These residues are strictly conserved amongst other members of the hydrogenase maturation endopeptidase family. Their replacement either abolishes processing activity completely or it impairs activity. The function of Hycl and HybD endopeptidases is the formation of active hydrogenase 3 and 2, respectively, in E. coli.

HypF has been characterized as an auxiliary protein whose function is required for the synthesis of active [NiFe] hydrogenases in Escherichia coli and other bacteria. To approach the functional analysis, in particular the involvement in CO/CN ligand synthesis, HypF was purified from an overproducing strain to apparent homogeneity. The purified protein behaves as a monomer on size exclusion chromatography, and it is devoid of nickel or other cofactors. As indicated by the existence of a sequence motif also present in several O-carbamoyltransferases, HypF interacts with carbamoyl phosphate as a substrate and releases inorganic phosphate. In addition, HypF also possesses ATP cleavage activity that gives rise to AMP and pyrophosphate as products and that is dependent on the presence of carbamoyl phosphate. This and the fact that HypF catalyzes a carbamoyl phosphate-dependent pyrophosphate ATP exchange reaction suggest that the protein catalyzes activation of carbamoyl phosphate. Extensive mutagenesis of the putative functional motifs deduced from the derived amino acid sequence showed a full correlation of the resulting variants between their activity in hydrogenase maturation and the in vitro reactivity with carbamoyl phosphate. The results are discussed in terms of the involvement of HypF in the conversion of carbamoyl phosphate to the CN ligand.

The iron of the binuclear active center of [NiFe]-hydrogenases carries two CN and one CO ligands which are thought to confer to the metal a low oxidation and/or spin state essential for activity. Based on the observation that one of the seven auxiliary proteins required for the synthesis and insertion of the [NiFe] cluster contains a sequence motif characteristic of O-carbamoyl-transferases it was discovered that carbamoyl phosphate is essential for formation of active [NiFe]-hydrogenases in vivo and is specifically required for metal center synthesis suggesting that it is the source of the CO and CN ligands. A chemical path for conversion of a carbamoyl group into cyano and carbonyl moieties is postulated

The maturation of [NiFe] hydrogenases includes formation of the nickel metallocenter, proteolytic processing of the metal center carrying large subunit, and its assembling with other hydrogenase subunits. The hydrogenase maturating enzyme HYBD from Escherichia coli, a protease of molecular mass 17.5 kDa, specifically cleaves off a 15 amino acid peptide from the C terminus of the precursor of the large subunit of hydrogenase 2 in a nickel-dependent manner. Here we report the crystal structure of HYBD at 2.2 A resolution. It consists of a twisted five-stranded β-sheet surrounded by four and three helices, respectively, on each side. A cadmium ion from the crystallization buffer binds to the proposed nickel-binding site and is penta-coordinated by Glu16, Asp62, His93, and a water molecule in a pseudo-tetragonal arrangement. HYBD is topologically related to members of the metzincins superfamily of zinc endoproteinases, sharing the central β-sheet and three helices. In contrast to the metzincins, the metal-binding site of HYBD is localized at the C-terminal end of the β-sheet. Three helical insertions unique to HYBD pack against one side of the sheet, build up the active site cleft, and provide His93 as ligand to the metal. From this structure, we derive molecular clues into how the protease HYBD is involved in the hydrogenase maturation process.

The hypoxic and glycolytic environment of malignant cells facilitates high levels of reactive oxygen species (ROS) production. Breast, ovarian and prostate cancer etiology is associated with the ROS production, which are thought to play an important role in regulating the cancers cell growth, survival and metastasis. A potent and major cellular, however functional limited characterized source of ROS, is the mitochondrial FAD-linked glycerol-3-phosphate dehydrogenase (GPD2). GPD2 is an essential component of the glycerol-3-phosphate shuttle and necessarily expressed in all tissues. In several cancer cell lines, GPD2 is highly expressed and we estimated it accounts for up to 70% of the total ROS production within the prostate cancer cell line PC3. In this study we have utilized this knowledge, to complete a cell-based high throughput-screening (HTS) assay, aimed to identify small molecule inhibitors of the GPD2 dependent ROS formation in PC3 cell lines. We employed the amplex red hydrogen peroxidase detection assay and adapted it to the HTS format. 133 inhibitory compounds from the Canadian Compound Collection were identified to reduce the ROS production activity within the PC3 cells. In order to validate these hits and to determine their mode of action, we PCR amplified GPD2 form PC3-cell cDNA and purified recombinant human GPD2 from a bacterial overproducing strain to homogeneity by employing Strep-tactin affinity-chromatography. The heterologously expressed enzyme, devoid of its mitochondrial target sequence, displayed glycerol-3-phosphate dependent resazurin, dichlorophenolindophenol, as well as tetrazole/phenazine methosulfate oxidoreductase activity. Follow up enzymatic assays of the primary HTS hits with the artificial electron acceptors identified several GPD2 activity specific inhibitors. Subsequent concentration response studies of the HTS derived inhibitors elucidated their in vitro half maximal inhibitory concentration at the range of 10 μM. In order to map GPD2's ROS production site and determine the inhibitor binding sites within the enzyme, we bioinformatically derived the proteins tertiary structure. Considering that GPD2 dependent ROS formation may drive the prostate cancer proliferation, we aim by exploiting the results of this work to generate novel lead molecules as promising potential anti-proliferating cancer drug candidates. (This work was supported by a grant from the Canadian Institutes of Health Research to Gurmit Singh) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3694.