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Pseudomonas aeruginosa (PA) is an electrogenic bacterium, in which extracellular electron transfer (EET) is mediated by microbially-produced phenazines, especially pyocyanin. Increasing EET rate in electrogenic bacteria is key for the development of biosensors and bioelectrofermentation processes. In this work, the production of pyocyanin, Nicotinamide Adenine Dinucleotide (NAD) and NAD synthetase by the electrogenic strain PA-A4 is determined using a Microbial Fuel Cell (MFC). Effects of metabolic inhibition and enhancement of pyocyanin and NAD synthetase on NAD/NADH levels and electrogenicity was demonstrated by short chronoamperometry measurements (0–48 h). Combined overexpression of two intermediate NAD synthetase production genes—nicotinic acid mononucleotide adenyltransferase (nadD) and quinolic acid phosphoribosyltransferase (nadC) genes, which are distant on the PA genomic map, enabled co-transcription and increased NAD synthetase activity. The resulting PA-A4 nadD + nadC shows increases in pyocyanin concentration, NAD synthetase activity, NAD/NADH levels, and MFC potential, all significantly higher than its wild type. Extracellular respiratory mechanisms in PA are linked with NAD metabolism, and targeted increased yield of NAD could directly lead to enhanced EET. A previous attempt at enhancing NAD synthetase for electrogenicity by targeting the terminal NAD synthetase gene (nadE) in standard P. aeruginosa PA01 had earlier been reported. Our work however, poses another route to electrogenicity enhancement in PA using; a combination of nadD and nadC. Further experiments are needed to understand specific intracellular mechanisms governing how over-expression of nadD and nadC induced activity of NadE protein. These findings significantly advance the knowledge of the versatility of NAD biosynthetic genes in PA electrogenicity. [ABSTRACT FROM AUTHOR]

Ammonia dependent NAD+ synthetase from multi drug resistance Staphylococcus aureus catalyzes ATP dependent formation of NAD+ from deamido-NAD+ and ammonia at the synthetase active site. Binding of ATP accompanies a large movement of flexible loop region (205-225) acting as a lid to the catalytic core. A 17 Å long ammonia tunnel with an entry and exit radius of 3.5 Å and 3.2 Å respectively allows transfer of ammonia from surface to the active site of the enzyme in each monomer to attack the C7N=O7N linkage of transient intermediate NAD-adenylate thus releasing NAD+. In this study, we report structural details of ammonia transport tunnel in Staphylococcus aureus NH 3 -dependent NAD synthetase and compared their architecture and dynamics with other bacterial and eukaryotic enzymes. Tunnel shows conformational variations in apo and substrate complexes and is less intricate compared to glutamine dependent counterparts. We have also performed steered molecular dynamic simulations of ammonia transport across the tunnel in enzyme-intermediate complex which reveals critical bottleneck residues and structural determinants during ammonium migration. Ordered water molecules and conserved charged residues form a network of hydrogen bonds and electrostatic interaction which facilitate the ammonium movement towards the active center. Analysis of the sMD simulated structural snapshots delineates the conformational reshaping of ammonia tunnel at the different step of the enzymatic reaction. Tunnel architecture and environment could offer the new target site to design novel small molecule inhibitors for the development of more efficient therapeutics against multi drug resistant S. aureus strains. [ABSTRACT FROM AUTHOR]

NAD synthetase (NadE) catalyzes the last step in NAD biosynthesis, transforming deamido-NAD+ into NAD+ by a two-step reaction with co-substrates ATP and amide donor ammonia. In this study, we report the crystal structure of Staphylococcus aureus NAD synthetase enzyme (sa NadE) at 2.3 Å resolution. We used this structure to perform molecular dynamics simulations of apo-enzyme, enzyme-substrate (NadE with ATP and NaAD) and enzyme-intermediate complexes (NadE with NaAD-AMP) to investigate key binding interactions and explore the conformational transitions and flexibility of the binding pocket. Our results show large shift of N-terminal region in substrate bound form which is important for ATP binding. Substrates drive the correlated movement of loop regions surrounding it as well as some regions distal to the active site and stabilize them at complex state. Principal component analysis of atomic projections distinguish feasible trajectories to delineate distinct motions in enzyme-substrate to enzyme-intermediate states. Our results suggest mixed binding involving dominant induced fit and conformational selection. MD simulation extracted ensembles of NadE could potentially be utilized for in silico screening and structure based design of more effective Methicillin Resistant Staphylococcus aureus (MRSA) inhibitors. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is an important human and animal pathogen that causes a wide range of infections. The prevalence of multidrug-resistant S. aureus strains in both hospital and community settings makes it imperative to characterize new drug targets to combat S. aureus infections. In this context, enzymes involved in NAD metabolism and synthesis are significant drug targets as NAD is a central player in several cellular processes. NAD synthetase catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide, making it a crucial intermediate enzyme linked to the biosynthesis of several amino acids, purine and pyrimidine nucleotides, coenzymes and antibiotics. [ABSTRACT FROM AUTHOR]

Abstract: Microbial fuel cells (MFCs) are promising for harnessing bioenergy from various organic wastes. However, low electricity power output (EPT) is one of the major bottlenecks in the practical application of MFCs. In this study, EPT improvement by cofactor manipulation was explored in the Pseudomonas aeruginosa-inoculated MFCs. By overexpression of nadE (NAD synthetase gene), the availability of the intracellular cofactor pool (NAD(H/+)) significantly increased, and delivered approximately three times higher power output than the original strain (increased from 10.86μW/cm2 to 40.13μW/cm2). The nadE overexpression strain showed about a onefold decrease in charge transfer resistance and higher electrochemical activity than the original strain, which should underlie the power output improvement. Furthermore, cyclic voltammetry, HPLC, and LC–MS analysis showed that the concentration of the electron shuttle (pyocyanin) increased approximately 1.5 fold upon nadE overexpression, which was responsible for the enhanced electrochemical activity. Thus, the results substantiated that the manipulation of intracellular cofactor could be an efficient approach to improve the EPT of MFCs, and implied metabolic engineering is of great potential for EPT improvement. [Copyright &y& Elsevier]

Abstract: The effects of combining two strategies, recycling NAD and improving the availability of NADH, on hydrogen production in Enterobacter aerogenes were investigated. The NAD synthetase encoded by nadE gene was homologously overexpressed in AB91002-O, which had been obtained previously, to increase the intracellular concentration of the NAD(H/+) pool. This overexpression was duplicated in mutant strains in which the phosphoenolpyruvate carboxylase (PEPC) gene (ppc) and hybO gene were knocked out, yielding AB91102-OP (ΔhybO/Δppc), AB91102-ON (ΔhybO/nadE), and AB91102-OP/N (ΔhybO/Δppc/nadE). Chemostat experiments showed that the total NAD(H) pool size in AB91102-ON increased 2-fold compared with the control strain AB91102-OC, but the NADH/NAD+ ratio decreased by 24%. Metabolic analysis of batch experiments indicated that a larger NAD(H/+) pool and inactivation of PEPC led to a significant shift in metabolic patterns, whereas a smaller NADH/NAD+ ratio improved glucose uptake. Thus, compared with the control strain, the hydrogen yields per glucose of the mutant strains AB91102-OP, AB91102-ON, and AB91102-OP/N were enhanced by 36.2%, 66.0%, and 149%, respectively, and the total volumes of hydrogen production increased by 27%, 165%, and 301%, respectively. The maximum hydrogen production of 5.1 L/L was achieved by AB91102-OP/N, suggesting that the double modification strategy exhibits markedly positive synergistic effects on hydrogen production. [Copyright &y& Elsevier]

Abstract: Virtual screening was employed to identify new drug-like inhibitors of NAD synthetase (NADs) as antibacterial agents. Four databases of commercially available compounds were docked against three subsites of the NADs active site using FlexX in conjunction with CScore. Over 200 commercial compounds were purchased and evaluated in enzyme inhibition and antibacterial assays. 18 compounds inhibited NADs at or below 100μM (7.6% hit rate), and two were selected for future SAR studies. [Copyright &y& Elsevier]

Abstract: Nicotinic acid adenine dinucleotide phosphate (NAADP) has been shown to mobilize Ca2+ from intracellular stores in a wide variety of organisms, ranging from plants to humans. We have developed a novel enzyme cycling assay for NAADP that involves coupled reactions catalyzed by four enzymes. In this system, NAADP is first converted into nicotinic acid adenine dinucleotide (NAAD) by alkaline phosphatase, after which the NAAD is converted to NAD, AMP, and PPi by NAD synthetase (NADS) in the presence of ATP and ammonia. The NAD is then amplified using an enzyme cycling system driven by glucose dehydrogenase and diaphorase. The resultant formation of formazan dye is measured spectrophotometrically based on the increase in absorbance at 450nm. Using this method, NAADP (20–400nM) was assayed, and a highly linear correlation was obtained between the NAADP concentration and the increase in absorbance at 450nm. The cycling rate was approximately 95cycles/min. In addition, the within-run coefficients of variation (CVs) for 25, 50, and 100nM NAADP solutions were 9.33, 4.86, and 3.13%, respectively. Interference by NAD analogs (e.g., NAAD, NADP) in the sample was eliminated prior to running the assay by treating the sample with NADS and NAD nucleosidase (NADase). In sum, our findings indicate this enzyme cycling assay to be readily applicable for determination for NAADP in a variety of biological samples and to be particularly appropriate for use with an autoanalyzer. [Copyright &y& Elsevier]

Abstract: Background: Ammonia is an important marker for liver diseases such as hepatitis and hepatic cirrhosis. Several methods have been developed for ammonia analysis. In particular, the enzymatic assay using glutamate dehydrogenase has been widely used. However, this method is not necessarily high in sensitivity and accuracy due to inhibition by interferences in plasma and instability over long-term storage. Methods: We developed an ammonia assay using a system consisting of three enzymes, NAD synthetase (NADS; EC 6.3.1.5), glucose dehydrogenase (GlcDH; EC 1.1.1.47), and diaphorase (DI; EC 1.6.99.2). Results: The calibration curve for ammonia with the cycling method was linear (r=0.999) up to 300 μmol/l. The within-run CVs of 10 and 20 μmol/l NH4Cl solutions and 24.1 μmol/l ammonia in human plasma were 2.3%, 1.5%, and 2.8%, respectively. The between-run CVs of them were 4.5%, 3.1%, and 2.8%, respectively. The recovery was between 96.3% and 105%, and the limit of detection was 2.4 μmol/l. No significant interference was observed with addition of the following components: hemoglobin, bilirubin, chyle, EDTA, heparin, and sodium citrate. Due to the high degree of specificity of NAD synthetase to ammonia, no amino compounds exhibited any effect on the ammonia assay. A high correlation was obtained between results of the present method (y) and a conventional glutamate dehydrogenase method in regression analysis; y=0.944x−6.160 with r=0.993 (n=125). However, an addition error was observed from Bland–Altman analysis (the 95% limits of agreement between the two methods; 9.51±5.92 μmol/l). Conclusion: This new enzymatic method is more sensitive, precise, and accurate than the conventional method. In particular, accurate assay for ammonia can be performed without interference in the presence of various compounds. [Copyright &y& Elsevier]