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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.

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.

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 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.

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