Analysis of <Emphasis Type="Italic">Escherichia coli</Emphasis> nicotinate mononucleotide adenylyltransferase mutants <Emphasis Type="Italic">in vivo</Emphasis> and <Emphasis Type="Italic">in vitro</Emphasis>

Background  

Adenylation of nicotinate mononucleotide to nicotinate adenine dinucleotide is the penultimate step in NAD⁺ synthesis. In Escherichia coli, the enzyme nicotinate mononucleotide adenylyltransferase is encoded by the nadD gene. We have earlier made an initial characterization in vivo of two mutant enzymes, NadD72 and NadD74. Strains with either mutation have decreased intracellular levels of NAD⁺, especially for one of the alleles, nadD72.     

Quercetin Glucoside Production by Engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

Escherichia coli strains expressing the O-glucosyltransferases UGT73B3 or UGT84B1 were compared for the production of glucosides from quercetin supplied into a defined medium. The formation of quercetin-3-glucoside (Q3G) by UGT73B3 showed a maximum at 33 °C, while the formation of quercetin-7-glucoside by UGT84B1 increased with increasing temperature to 37 °C. The highest concentrations of Q3G were attained by strains having a deletion in the pgi gene-coding phosphoglucose isomerase, which effectively blocked the entry of glucose-6P into the Embden–Meyerhof–Parnas pathway. Formation of Q3G was improved in 1-L controlled bioreactors compared to shake flask cultures, a result attributed to the greater oxygen transfer rate in bioreactors. Under batch conditions with 30 g/L glucose as the sole carbon source, E. coli MEC367 (MG1655 pgi) expressing UGT73B3 generated 3.9 g/L Q3G in 56 h.     

Liquid chromatography/mass spectrometry characterization of <Emphasis Type="Italic">Escherichia coli</Emphasis> and <Emphasis Type="Italic">Shigella</Emphasis> species

Liquid chromatography/quadrupole time of flight mass spectrometry (LC/QTOF MS) utilizing electrospray ionization was employed to monitor protein expression in Escherichia coli and Shigella organisms. Comparison with MALDI/TOF-MS revealed more proteins, particularly above 15 kDa. A combination of automated charge state deconvolution, spectral mirroring, and spectral subtraction was used to reveal subtle differences in the LC/MS data. Reproducible intact protein biomarker candidates were discovered based on their unique mass, retention time, and relative intensity. These marker candidates were implemented to differentiate closely related strain types, (e.g., two distinct isolates of E. coli O157:H7) and to correctly identify unknown pathogens. This LC/MS approach is less labor-intensive than pulsed-field gel electrophoresis, affords greater specificity than real-time PCR, and requires no primers or antibodies. Additionally, this approach would be beneficial during outbreaks of foodborne disease or bioterrorism investigations by complementing methods typically used in diagnostic microbiology laboratories.     

Functional Analysis of Ribonucleotide Reductase from <Emphasis Type="Italic">Cordyceps militaris</Emphasis> Expressed in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Cordyceps militaris produces cordycepin (3′-deoxyadenosine), which has various activities, including anti-oxidant, anti-tumoral, anti-viral, and anti-inflammatory. Ribonucleotide reductase (RNR) seems to be a candidate to produce cordycepin in C. militaris because RNR catalyzes the reduction of nucleotides to 2′-deoxynucleotides, whose structures are similar to that of cordycepin. However, the role of RNR has not been confirmed yet. In this study, complementary DNAs (cDNAs) of C. militaris RNR (CmRNR) large and small subunits (CmR1 and CmR2) were cloned from C. militaris NBRC9787 to investigate the function of CmRNR for its cordycepin production. C. militaris NBRC9787 began to produce cordycepin when grown in a liquid surface culture in medium composed of glucose and yeast extract for 15 days. CmR1 cDNA and CmR2 cDNA were obtained from its genomic DNA and from total RNA extracted from its mycelia after cultivation for 21 days, respectively. Recombinant CmR1 and CmR2 were expressed individually in Escherichia coli and purified. Purified recombinant CmR1 and CmR2 showed RNR activity toward adenosine diphosphate (ADP) only when two subunits were mixed but only show the reduction of ADP to 2′-deoxyADP. These results indicate that the pathway from ADP to 3′deoxyADP via CmRNR does not exist in C. militaris and cordycepin production in C. militaris may be mediated by other enzymes.     

Strain-Dependent Carotenoid Productions in Metabolically Engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

Seven Escherichia coli strains, which were metabolically engineered with carotenoid biosynthetic pathways, were systematically compared in order to investigate the strain-specific formation of carotenoids of structural diversity. C30 acyclic carotenoids, diaponeurosporene and diapolycopene were well produced in all E. coli strains tested. However, the C30 monocyclic diapotorulene formation was strongly strain dependent. Reduced diapotorulene formation was observed in the E. coli strain Top10, MG1655, and MDS42 while better formation was observed in the E. coli strain JM109, SURE, DH5a, and XL1-Blue. Interestingly, C40 carotenoids, which have longer backbones than C30 carotenoids, also showed strain dependency as C30 diapotorulene did. Quantitative analysis showed that the SURE strain was the best producer for C40 acyclic lycopene, C40 dicyclic β-carotene, and C30 monocyclic diapotorulene. Of the seven strains examined, the highest volumetric productivity for most of the carotenoids structures was observed in the recombinant SURE strain. In conclusion, we showed that recombinant hosts and carotenoid structures influenced carotenoid productions significantly, and this information can serve as the basis for the subsequent development of microorganisms for carotenoids of interest.     

<Emphasis Type="Italic">Z</Emphasis>-and <Emphasis Type="Italic">E</Emphasis>-conformers of <Emphasis Type="Italic">N</Emphasis>-chloroacetylcytisine

N-Chloroacetylcytisine was synthesized by acylation of (–)-cytisine. Stable Z- and E-conformers with respect to rotational isomerism around the N-12–CO bond were found in PMR spectra at room temperature. The point at which PMR resonances of the Z- and E-conformers coalesced upon heating was measured. The transition barrier between the conformers was estimated.     

Study of the growth of <Emphasis Type="Italic">Enterococcus faecalis</Emphasis>, <Emphasis Type="Italic">Escherichia coli</Emphasis> and their mixtures by microcalorimetry

In a majority of environments, microbes live as interacting communities. Microbial communities are composed of a mix of microbes with often unknown functions. Polymicrobial diseases represent the clinical and pathological manifestations induced by the presence of multiple infectious agents. These diseases are difficult to diagnose and treat and usually are more severe than monomicrobial infections. The interaction relationship between Enterococcus faecalis and Escherichia coli was researched using a Calvet calorimeter. Three mixtures of both bacteria were prepared in the following proportions: 20 + 80 % (0.2 mL E. faecalis + 0.8 mL E. coli), 50 + 50 % (0.5 mL E. faecalis + 0.5 mL E. coli) and 80 + 20 % (0.8 mL E. faecalis + 0.2 mL E. coli). Experiments were carried out at concentration of 10⁶ CFU mL^?1 and a constant temperature of 309.65 K. The differences in shape of graph of E. faecalis, E. coli and their mixtures were compared. Also, the thermokinetic parameters such as detection time (t _d), growth constant (k), generation time (G) and the amount of heat released (Q) were calculated.     

Rapid Determination of <Emphasis Type="SmallCaps">l</Emphasis>-Glutamine using Engineered <Emphasis Type="Italic">Escherichia coli</Emphasis> Overexpressing Glutamine Synthetase

A genetically engineered Escherichia coli was developed as the source of enzyme for rapidly quantifying glutamine. E. coli BL21 (DE3) cells overexpressing a glutamine synthetase from Bacillus subtilis were prepared as tube aliquots and used in a small volume of nontoxic mixture. The current method was compared to high performance liquid chromatography analysis, Sigma kit (GLN-1) and Mecke method. The method is applicable to a wide range of glutamine concentrations (0.05–2.5 mM) and correlates well to the detection results obtained from high performance liquid chromatography (Pearson correlation is 0.978 at the 0.01 level). Moreover, the whole assay procedure takes less than 15 min and uses nontoxic reagents, so it can be applied to monitor glutamine production and utilization conveniently.     

CO<Subscript>2</Subscript> Biofixation and Growth Kinetics of <Emphasis Type="Italic">Chlorella vulgaris</Emphasis> and <Emphasis Type="Italic">Nannochloropsis gaditana</Emphasis>

CO₂ biofixation was investigated using tubular bioreactors (15 and 1.5 l) either in the presence of green algae Chlorella vulgaris or Nannochloropsis gaditana. The cultivation was carried out in the following conditions: temperature of 25 °C, inlet-CO₂ of 4 and 8 vol%, and artificial light enhancing photosynthesis. Higher biofixation were observed in 8 vol% CO₂ concentration for both microalgae cultures than in 4 vol%. Characteristic process parameters such as productivity, CO₂ fixation, and kinetic rate coefficient were determined and discussed. Simplified and advanced methods for determination of CO₂ fixation were compared. In a simplified method, it is assumed that 1 kg of produced biomass equals 1.88 kg recycled CO₂. Advance method is based on empirical results of the present study (formula with carbon content in biomass). It was observed that application of the simplified method can generate large errors, especially if the biomass contains a relatively low amount of carbon. N. gaditana is the recommended species for CO₂ removal due to a high biofixation rate—more than 1.7 g/l/day. On day 10 of cultivation, the cell concentration was more than 1.7?×?10⁷ cells/ml. In the case of C. vulgaris, the maximal biofixation rate and cell concentration did not exceed 1.4 g/l/day and 1.3?×?10⁷ cells/ml, respectively.     

Expression of a <Emphasis Type="Italic">hemA</Emphasis> Gene from <Emphasis Type="Italic">Agrobacterium radiobacter</Emphasis> in a Rare Codon Optimizing <Emphasis Type="Italic">Escherichia coli</Emphasis> for Improving 5-aminolevulinate Production

The 5-aminolevulinate (ALA) synthase gene (hemA) from Agrobacterium radiobacter zju-0121, which was cloned previously in our laboratory, contains several rare codons. To enhance the expression of this gene, Escherichia coli Rosetta(DE3), which is a rare codon optimizer strain, was picked out as the host to construct an efficient recombinant strain. Cell extracts of the recombinant E. coli were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis under the appropriate conditions. The results indicated that the activity of ALA synthase expressed in Rosetta(DE3)/pET-28a(+)-hemA was about 20% higher than that in E. coli BL21(DE3). Then the effects of precursors (glycine and succinate) and glucose, which is an inhibitor for ALA dehydratase as well as the carbon sources for cell growth, on the production of 5-aminolevulinate were investigated. Based on an optimal fed-batch culture system described in our previous work, up to 6.5 g/l (50 mM) ALA was produced in a 15-l fermenter.     

Functional Expression of <Emphasis Type="Italic">Bacillus anthracis</Emphasis> Protective Antigen in <Emphasis Type="Italic">E. coli</Emphasis>

The protective antigen (PA) of Bacillus anthracis is a potent immunogen and an important candidate vaccine. In addition, it is used in monitoring systems like enzyme-linked immunosorbent assay to assess antibodies against PA in immunized subjects. The low level of PA production in B. anthracis and the difficulty of separating it from other bacterial components have made the researchers do different studies with the aim of producing recombinant PA (rPA). In this study, to produce rPA as a recombinant protein vaccine, the partial sequence of protective antigen of B. anthracis, amino acids 175–764, as a potent immunogenic target was inserted in pET21b(+). This is a prokaryotic plasmid that carries an N-terminal T7.tag sequence. The integrity of constructed plasmid was confirmed using restriction enzyme mapping. rPA was expressed after induction with isopropyl β-d-1-thiogalactopyranoside in Escherichia coli BL21. Purification of rPA was done with an affinity system using anti T7.tag antibody. Electrophoresis and Western blotting confirmed the specificity of the expressed protein. BALB/c mice were immunized with obtained PA protein and evaluation of specific immunoglobulin G antibodies against PA in sera using Western blotting method and showed that rPA is immunogenic. The challenge of immunized mice with virulent strain of B. anthracis showed that rPA is functional to protect against pathogenic strain.     

Spatial structure and stability of Mo<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Si<Subscript><Emphasis Type="Italic">m</Emphasis></Subscript> nanoparticles

By means of the ab initio DMol³ method Mo _n Si _m nanoparticles and fragments of Mo₃Si and MoSi₂ crystal lattices are theoretically modeled. For both crystals a few neutral Mo₄Si₆ and Mo₆Si₆ fragments of different shapes and symmetry are considered. In each case, after cluster separation its geometry is optimized, as a result of which the geometric structure noticeably changes and its stability increases. In order to theoretically search for the spatial configurations of Mo₄Si₆ and Mo₆Si₆ nanoparticle, two approaches are used: 1) in the most stable Fe₄C₆ and Fe₆C₆ isomers found previously, iron and carbon atoms are replaced by molybdenum and silicon respectively and then the geometry is optimized to obtain new equilibrium distances and angles; 2) the search for main Mo₄Si₆ and Mo₆Si₆ configurations is performed using the binominal scheme, starting from Mo₂, MoSi, and Si₂ dimers. The nanoparticle structures are found to contain metal atom chains and isolated pairs and triples of silicon atoms. In most cases, the nanoparticle stability proves to be higher than that of the crystal clusters.     

Solid-phase microbead array for multiplex O-serotyping of <Emphasis Type="Italic">Escherichia coli</Emphasis>

Typing and classification of Escherichia coli (E. coli) according to cell wall components, like polysaccharides, is routinely done by serotyping. Given the presence of 188 known O-antigens, this process is complex. The authors present a proof-of-concept planar microbead array for multiplexed O-serotyping. Ten clinically relevant E. coli serotypes associated with high risk for diarrhea in humans were examined (O26, O55, O78, O118, O124, O127, O128, O142, O145 and O157). Antisera were assigned to specific microbead populations, which can be differentiated by size and fluorescence color. Automatted image processing and data analysis were conducted by a microscopic interpretation platform. Homogenous antiserum coating of the microbeads was demonstrated by an intra-population CV that ranges from 3.3 to 6.3% and by an inter-population CV of 9.5%. Typical detections limits are in the range from 0.31 to 0.71 refMFI. Significantly elevated fluorescence signals revealed that E. coli of a certain serogroup bound specifically to microbeads with the matching antiserum (p < 0.001). In our perception, the method represents a viable diagnostic tool for automated multiplex serotyping of E. coli. It enables simultaneous and high-throughput screening for different O-antigens by a simple staining and binding protocol.

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Graphical abstract Schematic of a planar microbead array for the typing and classification of E. coli according to cell wall components. Based on coated fluorescent microbeads, multiplex O-serotyping of E. coli is accomplished via fluorescence imaging.

     

Electrodeposition of Fe<Subscript> <Emphasis Type="Italic">x</Emphasis> </Subscript>Se<Subscript> <Emphasis Type="Italic">y</Emphasis> </Subscript> films from acidic solutions

Iron selenide (Fe_xSe_y) thin films were electrodeposited on a glassy carbon electrode (GCE) surface under constant potential and pulse potential modes. The deposition mechanism was investigated using cyclic voltammetry. Electrochemical processes at room temperature are accompanied by adsorption of selenium on the electrode surface and complicated by chemical reactions in the solution bulk. Several approaches to control the film stoichiometry were applied: varying of electrodeposition potential; the use of elevated temperatures (60–80°C) to decrease the electrode passivation and electrodissolution of interfering elements under pulse mode. The composition of Fe_xSe_y thin films was analyzed using an energy dispersive X-rays (EDX) analysis.     

Accelerating <Emphasis Type="Italic">k</Emphasis><Subscript>0</Subscript>

Combining the powers of a fast pneumatic transport system and the Automatic Activation Analyzer (AAA) of the Atominstitut in Vienna with the newest version of the IAEA k ₀-Software, the application of the k ₀-method to the determination of short-lived radionuclides becomes easily possible. By calculating Asp-values with the IAEA software, the often expensive and time-consuming measurement of Asp-values using certified reference materials is reduced to quality control checks. Measurements clearly show that the two approaches are equivalent, especially since both take self-absorption and neutron self-shielding into account. In this way it is possible to expand the library of the AAA with many hitherto unobtainable Asp-values. At the same time, using highly accurate Asp-values already measured for many short-lived radionuclides, k ₀-values for those can be produced with a simple procedure.     

Comparison of bacteriolytic activity of human interleukin-2 and chicken egg lysozyme on <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> and <Emphasis Type="Italic">Escherichia coli</Emphasis> cells

The article continues studies of the recently discovered bacteriolytic activity of interleukin-2. It was detected earlier that interleukin (IL-2) possesses greater substrate specificity in comparison with chicken egg lysozyme. IL-2 disrupted the cell wall of Escherichia coli but did not lyse lysozyme substrates such as the cell walls of Micrococcus luteus and Bacillus subtilis. In the present study it is demonstrated for the first time that both IL-2 and chicken egg lysozyme are capable of lysing Lactobacillus plantarum. The effects of IL-2 and chicken egg lysozyme on Lactobacillus plantarum are compared with those on Escherichia coli. The dependences of the rate of lysis on the concentration of bacteriolytic factors and pH are studied.     

Evaluation of the <Emphasis Type="Italic">Q</Emphasis><Subscript><Emphasis Type="Italic">y</Emphasis></Subscript> absorption band maximum in a light-harvesting complex of the bacterial photosynthetic center <Emphasis Type="Italic">Thermochromatium tepidum</Emphasis>

Excitation energies of the bacteriochlorophyll (BChl) chromophores embedded in the photosynthetic light-harvesting complex of the purple bacterium Thermochromatium tepidum are computed using the time-dependent density functional theory based upon the fragmental molecular orbital (FMO-TDDFT) method. The results are correlated with the empirically based estimates of the Q _y absorption maximum, as well as with the observed large red shift induced by the binding of calcium.     

Halogenophilic and classical <Emphasis Type="Italic">Ad</Emphasis><Subscript><Emphasis Type="Italic">N</Emphasis></Subscript><Emphasis Type="Italic">E</Emphasis> mechanisms in nucleophilic vinylic substitution reactions involving the anions of transition metal carbonyls

The mechanism of the reaction of carbonylate anions ([M(CO) _n L]^–) with highly activated vinyl halides (Hal = Cl, Br, I) was investigated by the method of “anion traps” – the effect of proton donors on the composition of the reaction products. It was demonstrated that the reactions with PhCHal=C(Z)₂ (Hal = Br, I;Z=CN, CO₂Et) and PhCN=CClI take place through initial attack by the carbonylate at the halogen atom, the reactions with PhCCl=C(CO₂Et)₂ and PhCOCH=CHHal (Hal = Cl, I) take place through attack by the carbonylate at the π bond (Ad_NE mechanism), and in the case of E-and Z-PhCN=CHI the two mechanisms operate concurrently. The main laws determining the reaction mechanisms are analyzed.     

Quantum dot-based array for sensitive detection of <Emphasis Type="Italic">Escherichia coli</Emphasis>

A fluorescent quantum dot-based antibody array, used in sandwich format, has been developed to detect Escherichia coli O157:H7. Numerous parameters such as solid support, optimal concentration of immunoreagents, blocking reagents, and assay time were optimized for array construction. Quantum dot-conjugated anti-IgG was used as the detecting system. The array allows the detection of E. coli O157:H7 at concentrations below 10 CFU mL⁻¹ without sample enrichment, exhibiting an increase of three orders of magnitude in the limit of detection compared to ELISA. The interference caused by Gram (+) and Gram (−) bacteria was negligible at low concentrations of bacteria.     

Optimization of Fermentation Conditions for the Biosynthesis of <Emphasis Type="SmallCaps">l</Emphasis>-Threonine by <Emphasis Type="Italic">Escherichia coli</Emphasis>

In this study, the fed-batch fermentation technique was applied to improve the yield of l-threonine produced by Escherichia coli TRFC. Various fermentation substrates and conditions were investigated to identify the optimal carbon source, its concentration and C/N ratio in the production of l-threonine. Sucrose was found to be the optimal initial carbon source and its optimal concentration was determined to be 70 g/L based on the results of fermentations conducted in a 5-L jar fermentor using a series of fed-batch cultures of E. coli TRFC. The effects of glucose concentration and three different feeding methods on the production of l-threonine were also investigated in this work. Our results showed that the production of l-threonine by E. coli was enhanced when glucose concentration varied between 5 and 20 g/L with DO-control pulse fed-batch method. Furthermore, the C/N ratio was a more predominant factor than nitrogen concentration for l-threonine overproduction and the optimal ratio of ammonium sulfate to sucrose (g/g) was 30. Under the optimal conditions, a final l-threonine concentration of 118 g/L was achieved after 38 h with the productivity of 3.1 g/L/h (46% conversion ratio from glucose to threonine).