Structure-based engineering of E. coli galactokinase as a first step toward in vivo glycorandomization

In vitro glycorandomization is a rapid chemoenzymatic strategy to diversify complex natural product scaffolds. The glycorandomization sugar activation pathway is dependent upon the efficient construction of diverse sugar-1-phosphate libraries. In the context of the previously evolved GalK Y371H "gatekeeper" mutation, the active site M173L mutation described herein presents a kinase with remarkably broadened substrate range to include 28 diverse natural and unnatural sugars. Among these new substrates, 6-azido-6-deoxy-galactose and 6-azido-6-deoxy-glucose present unique chemical probes to assess the utility of an E. coli Y371H/M173L-GalK-overproducing strain to generate unnatural sugar-1-phosphates in vivo. Remarkably, the in vivo conversion of both unnatural sugars rival that demonstrated in vitro. This notable in vivo success stands as the first step toward constructing short sugar-activation pathways in vivo and, ultimately, in vivo natural-product glycorandomization.     

Quantification of sugars and sugar phosphates in Arabidopsis thaliana tissues using porous graphitic carbon liquid chromatography-electrospray ionization mass spectrometry

This work reports the development and optimisation of a negative ion mode on-line LC-ESI-MS/MS method for the sensitive targeted analysis of the key glycolytic intermediates, sugars and sugar phosphates from plants, using a porous graphitic carbon (PGC) stationary phase and an MS compatible mobile phase. Using this newly developed method, separation and detection of a solution of standard compounds is achieved in less than 20min. Target metabolite compounds were identified in plant extracts from their characteristic retention times, and product ion spectra. This on-line PGC-ESI-MS/MS method shows good linearity over the concentration range 0-100microM, selectivity, short analysis time, and limits of detection of 0.1microM for disaccharides trehalose (Tre), sucrose (Suc), and maltose, and 1.5microM for hexose phosphates fructose-6-phosphate (Fru6P), glucose-1-phosphate (Glc1P), and glucose-6-phosphate (Glc6P), and phosphoenolpyruvate (PEP). This paper describes details of our method and its application to the simultaneous quantitative analysis of soluble sugars and sugar phosphates from Arabidopsis thaliana tissues. We have demonstrated the utility of our method for the analysis of biological samples by applying it to the simultaneous quantitation of changes in soluble sugars and sugar phosphates in A. thaliana Columbia-0 (Col-0) and its starchless phosphoglucomutase (pgm) mutant over a 12-h light/12-h dark growth cycle.     

Esters phosphoriques,phosphonates et oxydes de phosphine dérivés de sucres. Communication préliminaire

Some sugar phosphates, phosphonates and phosphine oxides, Preliminary communication Some new phosphates of 1, 2-O-isopropylidene-α-D-ribofuranose have been prepared. Reactions of 3-C-cyanomethylidene-3-deoxy-1, 2-O-isopropylidene-5-O-trityl-α-D -erythro-pentofuranose (9) have been studied. On treatment with phosphorus nucleophiles, 9 led to phosphorus bearing branched-chain sugar derivatives. Branched-chain cyanosugars as 15 and 16 prepared by cis-vic-dihydroxylation of 9 constitute interesting potential precursors of new types of cyclic sugar phosphates.     

Hydrophilic interaction chromatography/electrospray mass spectrometry analysis of carbohydrate-related metabolites from Arabidopsis thaliana leaf tissue

This work describes the development and application of an on-line liquid chromatography/mass spectrometry (LC/MS) method using hydrophilic interaction chromatography (HILIC) coupled to negative ion mode electrospray ionisation ion trap mass spectrometry (ESI-MS) for the analysis of highly polar carbohydrate-related metabolites commonly found in plants, ranging from reducing and non-reducing sugars and sugar alcohols to sugar phosphates. Using this method, separation and detection of a mixture of eight authentic standard compounds containing glucose (Glc), sucrose (Suc), raffinose, verbascose, mannitol, maltitol, glucose-6-phosphate (Glc6P) and trehalose-6-phosphate (Tre6P) were achieved in less than 15 min. The method is rapid, robust, selective, and sensitive, with limits of detection (LODs) ranging from 0.2 microM obtained for neutral sugars, to 1.0 microM obtained for sugar alcohols, and 2.0 microM obtained for negatively charged sugar phosphates. We have studied the negative ion collision-induced dissociation (CID) fragmentation behaviour of the non-reducing raffinose family oligosaccharides (RFOs) raffinose, stachyose, and verbascose. Mainly Bi and Ci glycosidic and Ai cross-ring structurally informative cleavages are observed. We have applied this HILIC/ESI-MS method for the analysis of Arabidopsis thaliana wild-type Columbia-0 (Col-0) and its starchless phosphoglucomutase mutant (pgm1) leaf extracts. The method was used to quantify Glc, Suc, raffinose, and Glc6P in A. thaliana extracts. Data obtained using this HILIC/ESI-MS method were compared with those obtained using a comparable porous graphitic carbon-based LC/ESI-MS method.     

Kinetic determination of the GTPase activity of Ras proteins by means of a luminescent terbium complex

Guanine nucleotide binding proteins, such as Ras proteins, play a pivotal role in maintaining the regular life cycle of cells. The involvement of Ras mutants in the progress of cancer has attracted many efforts to find detection methods for Ras activity. In this study we present a luminescent microwell plate assay for monitoring GTPase activity of Ras proteins. The luminescence intensity of the Tb–norfloxacin complex is influenced by nucleoside phosphates as well as by inorganic phosphates. Real-time kinetics of the GTPase activity of wild-type Ras and Ras mutants can be monitored online. The effect of a GTPase activating protein as well as of a downstream effector (Ras-binding domain of human Raf-1) on the GTPase activity of different Ras mutants is examined. In contrast to other methods, this assay does not require the use of radioactively labeled substrates or chromatographic separation steps. Moreover, the application of fluorescently labeled GTP substrates which often interfere with enzymatic activity can be avoided. This in vitro assay can serve as a model system for the screening of regulators affecting the GTPase activity of Ras proteins. Figure The emission of the lanthanide complex Tb(III)-norfloxacin is influenced by nucleoside phosphates as well as by inorganic phosphates. Ras proteins display a specific GTPase activity which converts protein-bound GTP to GDP and phosphate, the latter being released. The Ras activity can be monitored by a significant decrease in luminescence intensity of Tb(III)-norfloxacin owing to the strong quenching effect induced by the enzymatically hydrolyzed phosphate anions. This luminescent assay enables the monitoring of real-time kinetics of the GTPase activity of Ras proteins and Ras mutants and a fast screening of their regulators.     

Photoexcitation of dinucleoside radical cations: a time-dependent density functional study

The excited states of dinucleoside phosphates (dGpdG, dApdA, dApdT, TpdA, and dGpdT) in their cationic radical states were studied with time-dependent density functional theory (TD-DFT). The ground-state geometries of all the dinucleoside phosphate cation radicals considered, in their base stacked conformation, were optimized with the B3LYP/6-31G(d) method. Further, to take into account the effect of the aqueous environment surrounding the dinucleoside phosphates, the polarized continuum model (PCM) was considered and the excitation energies were computed by using the TD-B3LYP/6-31G(d) method. From this study, we find that the first transition in all the dinucleoside molecules involves hole transfer from base to base. dG*+pdG and dApdA*+ were found to have substantially lower first transition energies than others with two different DNA bases. Higher energy transitions involve base to sugar as well as base to base hole transfer. The calculated TD-B3LYP/6-31G(d) transition energies are in good agreement with previous calculations with CASSCF/CAS-PT2 level of theory. This TD-DFT work supports the experimental findings that sugar radicals formed upon photoexcitation of G*+ in gamma-irradiated DNA and suggests an explanation for the wavelength dependence found.     

Analysis of sugar phosphates in plants by ion chromatography on a titanium dioxide column with pulsed amperometric detection

This paper describes the development of a practical method for the analysis of sugar phosphates from the model higher plant Arabidopsis thaliana by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). The extraction method of sugar phosphates from higher plants was first optimized for HPAEC-PAD analysis. In order to improve the resolution in HPAEC-PAD, a column packed with titanium dioxide resin was used. The titanium dioxide column was used as a trap-column for sugar phosphates and nucleotides, for the removal of sample matrices. Sample pretreatment was achieved in-line and automatically using a six-port valve placed after the injection valve.     

Synthesis of Some Specifically Deoxygenated D-Hexopyranosyl Phosphates

Abstract

A number of diphenyl α-glucopyranosyl and xylopyranosyl phosphates (4, 7, 11. 15, 19, and 25) were prepared from their respective glycosyl chlorides by reaction with silver diphenyl phosphate. These sugar phosphates are of interest as enzyme substrates in deoxy sugar biosynthesis.     

Sugar determination via the homogeneous reduction of Au salts: A novel optical measurement

A novel optical assay for sugar determination based on the catalytic and biocatalytic growth of gold nanoparticles (AuNPs) is presented. The reaction of carbohydrates with these Au salts in alkaline media generates AuNPs at room temperature (RT) without the need for Au seeds in the solution or fibrous mesh. The optical properties of the resulting AuNPs relates to the total reducing sugar content of the samples analyzed. The development of such inexpensive optical assay was evaluated qualitatively and quantitatively on food beverages and honey samples. Its application can be of help to control the glucose content of the diet or easily extended in a host of industrial, biomedical and clinical fields.     

A practical method for the stereoselective generation of beta-2-deoxy glycosyl phosphates

Beta-2-Deoxy sugar nucleotides are substrates used by a variety of glycosyltransferases (Gtfs). We have developed a chemical route to synthesize beta-2-deoxy sugar phosphates that starts from alpha-glycosyl chlorides. Our approach reliably provides access to a range of NDP beta-2-deoxy sugars essential for studying glycosyltransferases involved in the synthesis of biologically active natural products.     

Mass spectrometric studies of the path of carbon in photosynthesis: positional isotopic analysis of (13)C-labelled C(4) to C(7) sugar phosphates

The (EIMS) electron ionization mass spectrometric fragmentation patterns of the methoxime- and ethoxime-trimethylsilyl (TMS) derivatives of C(4) to C(7) sugars involved as phosphates in the Calvin pathway of photosynthesis in plants were analysed by gas chromatography/EIMS using specifically labelled (13)C analogs. In general, most but not all of the major ions in the mass spectra arise from single carbon-carbon bond cleavages of the straight-chain derivatives. The results confirm that GC/MS of the alkoxime-TMS derivatives is a viable method for measuring (13)C incorporations at individual carbon atoms in each of the sugar phosphates during photosynthetic experiments with (13)CO(2).     

A radiotracer study of adsorption on activated carbon cloth from aqueous solution

A study has been made on the effect of pH upon the equilibrium adsorption capacity of triethyl phosphate, dimethyl phosphate and orthophosphate on to activated carbon cloth. It is shown that for molecular phosphates no dependence upon pH exists, whilst the adsorption of ionic phosphates exhibit a strong pH dependence. These adsorption trends may be explained in terms of pKa values, ionic strength and the surface charge of the activated carbon cloth is aqueous solution.     

Phenyl radicals react with dinucleoside phosphates by addition to purine bases and H-atom abstraction from a sugar moiety

Laser-induced acoustic desorption combined with mass spectrometry has been used to demonstrate that phenyl radicals can attack dinucleoside phosphates at both the sugar and base moieties, that purine bases are more susceptible to the attack than pyrimidine bases, and that the more electrophilic the radical, the more efficient the damage to dinucleoside phosphates.     

Determination of nitrite, nitrate, and glucose-6-phosphate in muscle tissues and cured meat by IC/MS

The endogenous nitrate concentration in fresh meat and the residual nitrate and nitrite contents after curing are related to food quality and safety. Most ion chromatography (IC) methods suffer from interferences, especially in fresh meat samples, in which the endogenous nitrate content is low, and in cured meat products, in which other nitrogenous compounds can interfere with the separation of inorganic anions. One of the major classes of interfering compounds in fresh meat are sugar phosphates, which originate from glycolysis during the conversion of muscle glycogen to lactic acid. Nitrate can be separated from interfering compounds with a high-capacity anion-exchange column that was manufactured for use with hydroxide eluents (i.e., hydroxide-selective). This column has a different selectivity than traditional IC columns that use carbonate eluents and facilitates the determination of nitrate in both fresh and cured meats. Nitrate was detected by both suppressed conductivity measurement and mass spectrometry (MS). The identifications of nitrate and glucose-6-phosphate were confirmed by MS detection. The described IC/MS method is robust, sensitive to nitrate concentrations as low as 0.10 mg/kg, and can determine sugar phosphates that are useful for monitoring meat freshness. We successfully used this method to determine nitrate in nearly 100 muscle tissues and cured meat samples.     

Oxide formation in the synthesis and hydrolysis of some fluorides and phosphate esters

Investigation of several routes to fluoro-carbohydrates and sugar phosphates has shown that appreciable formation of internal ethers may occur in certain cases.     

Metabolite profiling of sucrose effect on the metabolism of Melissa officinalis by gas chromatography-mass spectrometry

The effect of sugar on plant metabolism, which is known to be similar to hormone-like signaling, was metabolomically studied using Melissa officinalis (lemon balm). The metabolite profiles of M. officinalis treated with sucrose were analyzed by gas chromatography-mass spectrometry (GC-MS) and principal component analysis (PCA). A total of 64 metabolites from various chemical classes including alcohols, amines, amino acids, fatty acids, inorganic acids, organic acids, phosphates, and sugars were identified by GC-MS. Three groups treated with different sucrose concentrations were clearly separated by PCA of their metabolite profiles, indicating changes in the levels of many metabolites depending on the sucrose concentration. Metabolite profiling revealed that treatment with a higher sucrose level caused an increase in the levels of metabolites such as sugars, sugar alcohols, and sugar phosphates, which are related to the glycolytic pathway of M. officinalis. Furthermore, proline and succinic acid, which are associated with the proline-linked pentose phosphate pathway, the shikimic acid pathway, and the biosynthesis of phenylpropanoids, also increased with increasing sucrose concentration. Therefore, these metabolic changes induced by sucrose ultimately led to the increased production of flavonoids such as caffeic acid via the biosynthetic pathway of phenylpropanoids. This study demonstrated that the abundance changes in some primary and secondary metabolites were somewhat interlocked with each other in response to sucrose.     

Production of condensed phosphate by plasma chemical treatment of phosphate raw material

Thermodynamic calculations and experimental studies have demonstrated that dissociation of natural phosphates in a low-temperature plasma involves partial calcium oxide evaporation. As a result, upon cooling gaseous products of the dissociated phosphate raw material, compounds containing condensed calcium phosphate are formed. The composition and properties of condensed calcium phosphates, which can be used as fertilizers, are discussed.     

Simple and rapid visual sensing of saccharides

Solutions of compound 1 exhibit dramatic, characteristic color changes in response to sugar analytes. Structurally related saccharides including glucose phosphates and amino and carboxylic acid sugars can be readily distinguished by visual inspection. These findings should promote the design of unique color sensory materials based on readily available, functional macrocyclic hosts.     

Determination of the anomeric configuration of glycosyl esters of nucleoside pyrophosphates and polyisoprenyl phosphates by fast-atom bombardment tandem mass spectrometry

Collision-induced dissociation of the deprotonated molecules of glycosyl esters of nucleoside pyrophosphates and polyisoprenyl (dolichyl and polyprenyl) phosphates results in distinct fragmentation patterns that depend on cis-trans configuration of the phosphodiester and 2″ (or 2′, respectively)-hydroxyl groups of the glycosyl residue. At the collision-offset voltage of 0. 5 V, sugar nucleotides with cis configuration produce only one very abundant fragment of nucleoside monophosphate, whereas compounds with trans configuration give weak signals for nucleoside di- and mono-phosphates and their dehydration products. These fragmentation patterns are largely preserved at higher collision energy, with the exception that, for sugar nucleotides with trans configuration, the characteristic signals are much more abundant and a novel diagnostic fragment of [ribosyl(deoxyribosyl)-5′-P₂O₅ — H]^? is generated. In the case of polyisoprenyl-P-sugars, polyisoprenyl phosphate ion is the only fragment observed for compounds with trans configuration, whereas in compounds with cis configuration, this ion is accompanied by another abundant fragment, which is derived from the cleavage across the sugar ring and corresponds to [polyisoprenyl-PO₄-(C₂H₃O)]^?. The relative intensity ratio of the latter ion to the [polyisoprenyl-HPO₄]^? ion is close to 1 for compounds with cis configuration, but it is only about 0. 01 for compounds with trans configuration. This ratio may serve, therefore, as a diagnostic value for determination of the anomeric configuration of glycosyl esters of polyisoprenyl phosphates. It is proposed that the observed differences in fragmentation patterns of cis-trans sugar nucleotides and polyisoprenyl-P-sugars could be explained in terms of kinetic stereoelectronic effect, and a speculative mechanism of fragmentation of compounds with trans configuration is presented. For compounds with cis configuration, formation of a hydrogen bond between the C-2″(2′) hydroxyl and the phosphate group could play a crucial role in directing the specific fragmentation reactions. Consequently, the described empirical rules would hold only for compounds that have a free 2″(2′)-hydroxyl group and no alternative charge location. Owing to its simplicity, sensitivity, and tolerance of impurities, fast-atom bombardment-tandem mass spectrometry represents a suitable method for determination of the anomeric linkage of glycosyl esters of nucleoside pyrophosphates and polyisoprenyl phosphates if the absolute configuration of glycosyl residue is known and the compound fulfills the above-mentioned requirements.     

Metabolic profiling of intracellular metabolites in fermentation broths from β-lactam antibiotics production by liquid chromatography–tandem mass spectrometry methods

An analytical platform comprising three LC–ESI-MS/MS methods is presented for qualitative and quantitative profiling of more than 200 intracellular metabolites. Employing a silica based zwitterionic stationary phase in the HILIC mode, in total 223 hydrophilic metabolites can be determined. In particular, amino acids, organic acids as well as nucleotide sugars were found to be well separable and detectable under acidic mobile phase conditions, while in comparison especially phosphates such as nucleotides, coenzymes or sugar phosphates as well as sugars and sugar acids performed better at higher pH. Additionally, 21 less polar analytes turned out to be amenable for separation and analysis on a pentafluorophenyl modified silica stationary phase in RP mode. Solutes were detected by tandem mass spectrometry on a triple quadrupole instrument in the selected reaction monitoring (SRM) mode and specific SRM transitions for 258 metabolites are provided. All three methods were validated with respect to the limit of quantification, linear dynamic range, precision and accuracy. Applicability of the analytical platform was evaluated by analysis of the targeted metabolites in extracts of β-lactam antibiotics fermentation broths. Thereby, 87 metabolites were determined qualitatively in penicillin fermentation broths, and 94 compounds were found in cephalosporin extracts. In addition, a number of selected metabolites that can be determined by at least two of the presented LC–MS/MS methods was analyzed quantitatively by both, external calibration using pure standards as well as by matrix-matched calibration performing standard addition. Quantitative results obtained with the different methods agreed well, however, for some analytes external calibration was found to be ill-suited due to matrix effects.