Metabolite profiling of Calvin cycle intermediates by HPLC-MS using mixed-mode stationary phases

SUMMARY: A sensitive and robust mixed-mode high performance liquid chromatography-tandem mass spectrometry method was developed for the qualitative and quantitative determination of sugar phosphates, which are notoriously difficult to separate using reversed-phase materials. Sugar phosphates were separated on a Primesep SB column by gradient elution using aqueous ammonium formate and acetonitrile as mobile phases. Target analytes were identified by their precursor/product ions and retention times. Quantitative analysis was performed in negative ionization/multiple reaction monitoring mode with five different time segments. The method was validated by spiking authentic sugar phosphate standards into complex plant tissue extracts. Standard curves of neat authentic standards and spiked extracts were generated for concentrations in the low picomole to nanomole range, with correlation coefficients of R(2) > 0.991, and the degree of ion suppression in the presence of a plant matrix was calculated for each analyte. Analyte recoveries, which were determined by including known quantities of authentic standards in the sugar phosphate extraction protocol, ranged from 40.0% to 57.4%. The analytical reproducibility was assessed by determining the coefficient of variance based on repeated extractions/measurements (<20%). The utility of our method is demonstrated with two types of applications: profiling of Calvin cycle intermediates in (i) dark-adapted and light-treated tobacco leaves, and in (ii) antisense plants expressing reduced levels of the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase or ribulose-1,5-bisphosphate carboxylase/oxygenase (comparison with wild-type controls). The broader applicability of our method is illustrated by profiling sugar phosphates extracted from the leaves of five taxonomically diverse plants.     

Formation of sugar phosphates in colicin K-treated Escherichia coli.

Colicin K greatly decreased the incorporation of 32P-labeled inorganic orthophosphate into nucleotides and nucleic acids, causing a concomitant increase in the formation of 32P-labeled sugar phosphates in sensitive cells of Escherichia coli. These sugar phosphates were formed in aerobically growing cells, as well as in cells under stringent control of ribonucleic acid synthesis. The main 32P-labeled product was identified as sedoheptulose 7-phosphate in two strains (B1 and K-12 MK-1) and fructose 1,6-diphosphate in one strain (K-12 CP78). The formation of sugar phosphates induced by colicin K was inhibited by carbonyl cyanide m-chlorophenylhydrazone. It was also not observed in N,N'-dicyclohexylcarbodiimide-treated cells or Mg2+-(Ca2+)-adenosine triphosphatase-less mutant (strain K-12 AN120) cells. Thus, the formation of sugar phosphates in colicin K-treated cells is dependent on the formation of adenosine 5'-triphosphate by oxidative phosphorylation.     

Recent progress in artificial receptors for phosphate anions in aqueous solution

Phosphate esters exist ubiquitously in nature in the form of nucleoside phosphates (nucleotides) as components of RNA (or DNA), sugar nucleotides for glycosylation of oligosaccharides or proteins, activated form of proteins responding to extracellular signals, and chemical mediators playing central roles in intracellular signaling signals. Phosphorylation of anti-viral nucleoside analogues by intracellular kinases yields nucleoside phosphates (nucleotide) as biologically active forms as anti-viral agents. Development of artificial phosphate receptors would afford new methodologies for detection, separation, or transport of biologically important phosphates. Herein, a recent progress of artificial phosphate receptors is reviewed with special focus on macrocyclic polyamines and their metal complexes as a new prototype. In comparison to most of the previous artificial receptors (most of them are organic molecules), our system characteristically works in aqueous solution at neutral pH with extremely strong affinities with phosphate anions. Moreover, zinc(II)-macrocyclic tetraamine (cyclen) complexes were discovered to selectively bind thymine and uracil, so that nucleotides of these bases are specifically recognized by the bis(Zn2+-cyclen) complexes.     

Properties of two phosphatases and a cyclic phosphodiesterase of Salmonella typhimurium.

The properties of three phosphatases from Salmonella typhimurium have been examined. A cyclic 2',3'-nucleotide phosphodiesterase (EC 3.1.4.d) hydrolyzes cyclic 2',3'-purine and -pyrimidine nucleotides, as well as 3'-mononucleotides, and has a pH optimum of about 7.5. It requires divalent cations for activity and has a molecular weight of 67,000. Acid hexose phosphatase (EC 3.1.2.2) possesses activity towards hexose phosphates as well as other sugar phosphates. The enzyme is apparently a dimer of 37,000-dalton subunits. Nonspecific acid phosphatase (EC 3.1.3.2) hydrolyzes a variety of phosphate esters, including nucleotides and sugar phosphates. The enzyme also hydrolyzes the phosphoric anhydride bonds of pyrophosphate and nucleotides. Michaelis constants of the nonspecific acid phosphatase for several of its substrates are in the 1 to 2 mM range. Nonspecific acid phosphatase is a dimer of 27,000-dalton subunits.     

Leaf Phosphate Status,Photosynthesis, and Carbon Partitioning in Sugar Beet (IV. Changes with Time Following Increased Supply of Phosphate to Low-Phosphate Plants)

Changes in photosynthesis, carbon partitioning, and growth following resupply of orthophosphate (Pi) to moderately P-deficient plants (low-P) were determined for sugar beets (Beta vulgaris L. cv F58-554H1) cultured hydroponically in growth chambers. One set of plants was supplied with 1.0 mM Pi in half-strength Hoagland solution (control plants), and a second set (low-P plants) was supplied with 0.05 mM Pi. At the end of 2 weeks, the low-P plants were resupplied with 1.0 mM Pi. Low-P plants rapidly accumulated large amounts of Pi, and the photosynthesis rate increased to control values within 4 to 6 h. The rate of photosynthesis appeared to be controlled by ribulose-1,5-bisphosphate (RuBP); low P reduced photosynthesis and RuBP levels, and P resupply increased photosynthesis and RuBP in a manner parallel with time. Low-P treatment reduced adenylate levels substantially but not nicotinamide nucleotides; adenylate levels recovered to control values over 3 to 6 h. With low P, more photosynthate is allocated to non-P carbon compounds (e.g. starch, sucrose) than to sugar phosphates. When P is resupplied, sugar phosphates increase as starch and sucrose pools decrease; this increase in leaf (chloroplast) sugar phosphates was most likely responsible for the increases in RuBP and photosynthesis and may have increased adenylate levels (through enhanced levels of ribose-5-phosphate).     

Introduction and metabolism of pentose and hexose phosphates in permeabilized Morris hepatoma 5123TC cells

Metabolism of arabinose 5-P, ribose 5-P and glucose 6-P in permeabilized and resealed Morris hepatoma 5123TC cells was investigated by measuring the contribution of these compounds to nucleic acid biosynthesis. The level of [14C]-arabinose (non-phosphorylated) incorporation into nucleic acids was slight, presumably due to the low activity of the transport system or the absence or low activity of a specific 'kinase' enzyme. The permeabilizing procedure involved the brief treatment of Morris hepatoma 5123TC cells with lysolecithin and resulted in a cell population which was permeable to charged compounds i.e. sugar phosphates and nucleotides, that otherwise could not cross the plasma membrane. The permeabilized (and resealed cells) retained normal cellular morphology and intactness of specific organelles as judged by the maintenance of functional properties. Following permeabilization, these cells resealed when transferred back to normal growth medium, and continued to divide and increase at the same rates as control non-permeabilized cell cultures. The permeabilized cells incorporated deoxyribonucleotides ([methyl -3H]-TTP) into DNA at a linear rate of 0.047 nmol per 10(7) cells min-1, representing 90-100 per cent of the DNA synthesis rate in vivo. The permeabilization technique, when coupled with procedures to establish cell synchrony, permitted the comparative estimate of the contributions of [14C]-labelled arabinose 5-P, ribose 5-P and glucose 6-P to RNA, DNA, amino acids, CO2, lactate and sugar mono- and bisphosphates. The percentage of [14C]-isotope incorporated into total nucleic acids by these three labelled sugar phosphates were 2.3, 4.9 and 6.3 respectively. Possible reasons for the lower incorporation of 14C from arabinose 5-P are given. The results are consistent with the proposal that arabinose 5-P, an intermediate of the L-type pentose pathway activity of 5123TC cells, was incorporated into nucleic acids by its interconversion with ribulose 5-P and ribose 5-P and thus into PRPP. This study represents the first report of sugar phosphate as opposed to free sugar metabolism by tumour cells in culture.     

The control of synthesis of bacterial cell walls. Interaction in the synthesis of nucleotide precursors

Phosphoenolpyruvate-UDP-N-acetylglucosamine enolpyruvyltransferase, UDP-N-acetylglucosamine pyrophosphorylase and CDP-glycerol pyrophosphorylase activities were demonstrated in soluble extracts from Bacillus licheniformis A.T.C.C. 9945. The effect of various nucleotides, sugar nucleotides and sugar phosphates on the nucleotide pyrophosphorylases was investigated. UDP-N-acetylglucosamine pyrophosphorylase was inhibited by UDP-MurAc-pentapeptide (UDP-N-acetylmuramyl-l-alanyl-d-glutamyl- meso-diaminopimelyl-d-alanyl -d-alanine) and CDP-glycerol. CDP-glycerol pyrophosphorylase was inhibited by UDP-MurAc-pentapeptide and stimulated by UDP-N-acetylglucosamine. Interaction between a precursor of one cell-wall polymer and an enzyme involved in the synthesis of a precursor of a second polymer has therefore been demonstrated. The possible role of such interaction in the control of bacterial cell-wall synthesis is discussed. Of the other compounds investigated mono- and di-nucleotides were shown to be inhibitory, indicating that nucleotide pyrophosphorylase activities may be influenced by the energy charge of the cell.     

Measurement of Metabolites Associated with Nonaqueously Isolated Starch Granules from Immature Zea mays L. Endosperm

Starch granules with associated metabolites were isolated from immature Zea mays L. endosperm by a nonaqueous procedure using glycerol and 3-chloro-1,2-propanediol. The soluble extract of the granule preparation contained varying amounts of neutral sugars, inorganic phosphate, hexose and triose phosphates, organic acids, adenosine and uridine nucleotides, sugar nucleotides, and amino acids. Based on the metabolites present and on information about translocators in chloroplast membranes, which function in transferring metabolites from the chloroplast stroma into the cytoplasm, it is suggested that sucrose is degraded in the cytoplasm, via glycolysis, to triose phosphates which cross the amyloplast membrane by means of a phosphate translocator. It is further postulated that hexose phosphates and sugars are produced from the triose phosphates in the amyloplast stroma by gluconeogenesis with starch being formed from glucose 1-phosphate via pyrophosphorylase and starch synthase enzymes. The glucose 1-phosphate to inorganic phosphate ratio in the granule preparation was such that starch synthesis by phosphorylase is highly unlikely in maize endosperm.     

Chemical models and radiation damage

E.s.r. spectroscopy has been used in conjunction with an aqueous flow system to investigate both the metal-catalysed decomposition of hydrogen peroxide to OH. and the subsequent reactions of this radical with a variety of biomolecules. Particular emphasis is placed on the effects of pH and ligand on the FeII-H2O2 reaction and on the sites of attack by OH. in its reaction with pyranose and furanose sugars, sugar phosphates, nucleosides and nucleotides. Attention is focused on subsequent reactions (for example, of radicals formed by attack in the ribofuranose moiety of adenosine) which may be involved in radiation damage.     

Ion-exchange chromatography of biologically important phosphate esters and other compounds

Borate complexed sugars, sugar phosphates, and nucleotides present in tissue extracts were separated and quantitated in 4 hr. An anion-exchange resin column and a programmed borate/acetate buffer gradient were used. Sugar residues were determined by a very sensitive orcinol/H₂SO₄ reaction. Samples required little preparation, and recovery of standard compounds added to tissue extracts was quantitative.     

Effect of zinc nutrition on sucrose biosynthesis in maize

Zinc deficiency caused an accumulation of ¹⁴C into malic acid, sugar phosphates, sugar nucleotides, glucose, fructose, phosphoenolpyruvate, glycine and alanine, whereas the ¹⁴C labelling in sucrose decreased. The activity of sucrose synthetase (EC 2.4.1.13) was unaffected up to the 15th day and thereafter it declined. Severe Zn deficiency reduced the biosynthesis of total protein and sucrose synthetase by 50 and 20%, respectively.     

Changes in the intracellular concentrations of adenosine phosphates and nicotinamide nucleotides during the aerobic growth cycle of yeast on different carbon sources

1. Methods for the quantitative extraction of adenosine phosphates and nicotinamide nucleotides from yeast cells are described. 2. The intracellular concentrations of adenosine phosphates and nicotinamide nucleotides were measured during the aerobic growth cycle of yeast on glucose and galactose. 3. When sugars were still present in the media the intracellular concentrations of NADH and AMP were in general higher in glucose- than in galactose-grown cells, whereas ADP concentration was always lower in glucose-grown cells. 4. The adenylate-kinase reaction was found to be far from equilibrium in the glucose-grown cells and when glucose was still present in the growth medium. 5. The significance of the changes in the intracellular concentrations of adenosine phosphates and nicotinamide nucleotides observed during growth on either sugar is discussed in relation to the metabolism and growth of the cells. 6. The differences observed in the concentrations of these cofactors in glucose- and galactose-grown cells are also discussed in relation to the type of metabolism of these cells. Control of glycolysis at the level of phosphofructokinase in galactose-grown cells and at the level of phosphoglycerate kinase in glucose-grown cells is suggested. 7. ADP is suggested to be the inducer of formation of respiratory enzymes.     

Inhibition of Charonia lampas ascorbate-2-sulfate sulfohydrolase activity by adenosine 5'-diphosphate and related compounds.

1) ADP was a potent inhibitor of the ascorbic-2-sulfate sulfohydrolase activity of Charonia lampas liver. The inhibition was competitive with respect to ascorbate 2-sulfate. The Ki value was 5.9 muM. ADP did not inhibit arylsulfatase (EC 3.1.6.1) of the same organism. 2) Other nucleoside 5'-diphosphates and GTP showed similar inhibition of ascorbate-2-sulfate sulfohydrolase activity. 3) The effects of different nucleosides, nucleotides, and sugar phosphates on ascorbate-2-sulfate sulfohydrolase activity were investigated. Phosphate derivatives other than 3',5'-cyclic AMP were more or less inhibitory.     

The separation of [32P]inositol phosphates by ion-pair chromatography: optimization of the method and biological applications

We have developed an ion-pair reverse-phase HPLC method to measure inositol phosphates in 32P-labeled cells. The different chromatographic parameters were analyzed to optimize the resolution of the 32P-labeled metabolites. Analysis of inositol phosphates in biological samples was improved by a single charcoal pretreatment which eliminated interfering nucleotides without removing inositol phosphates. The kinetics of production of inositol phosphates in calcium-activated erythrocytes, vasopressin-stimulated hepatocytes, and thrombin-activated platelets were analyzed. Original data on the activation of phosphoinositide phospholipase C were obtained in intact erythrocytes by direct measurement of inositol (1,4,5)P3. Data from agonist-stimulated hepatocytes and platelets were consistent with those from previous studies. In conclusion, this technique offers many advantages over the methodologies currently employed involving anion-exchange chromatography and [3H]inositol labeling: (i) 32P labeling is less expensive and more efficient than 3H labeling and can be used with all types of cells without permeabilization treatments and (ii) ion-pair HPLC gives good resolution of inositol phosphates from nucleotides with shorter retention times, and long reequilibration periods are not required.     

Rat liver pyruvate carboxylase. Inhibition by chromium nucleotide complexes.

The effect of inert coordination complexes of chromium (III) with various nucleotides on the catalytic activity of rat liver pyruvate carboxylase was determined. The chromium nucleotides are effective initial inhibitors of pyruvate carboxylase and the inhibition becomes more severe with time. The initial rate decreases for several minutes, reaching a new slower rate that is then maintained until considerable net reaction occurs. Incubation of the enzyme with chromium nucleotides in the presence of Mg2+ and HCO3- causes maximal inhibition of the reaction and linear initial rates are then observed. This effect is similar to that found with yeast hexokinase (Dannenberg, K.D., and Cleland, W.W. (1975) Biochemistry 14, 28-39). The specificity of the carboxylase toward the nucleotide complexes suggests that the alpha and beta nucleotide phosphates are as important as the gamma phosphate in binding to the enzyme. A stable pyruvate carboxylase chromium nucleotide complex was not observed. These results are quite different from those found with yeast hexokinase where a stable complex between CrATP, sugar, and enzyme is found and hexokinase appears to be specific toward the beta, gamma phosphates of its nucleotide substrates.     

Chemical and enzymatic analysis of covalent bonds between peptides and chromosomal DNA.

DNA from Ehrlich ascites tumor (EAT) cells and from human placenta was examined for covalent bonds between hydroxy amino acid residues in peptides and nucleotide phosphate groups. The residual proteinaceous material in highly purified DNA was radiolabelled with 125Iodine and the linking-groups between peptides and nucleotides released by combined protease and nuclease treatment were investigated with respect to their chemical and enzymatic stabilities. The residual nucleotide(s)-peptide(s) fraction from DNA isolated after prolonged alkaline cell lysis and phenol extraction contains mainly alkali and acid-stable but phosphodiesterase-sensitive peptide-nucleotide complexes which indicates phosphodiesters between tyrosyl residues in peptides and nucleotide phosphates. In contrast, the linking-group fraction from DNA isolated under native conditions contains additional peptide components. (a) Phospho-peptides that co-purify with DNA but that are not covalently bound to nucleotides. (b) A fraction of peptides that is released from nucleotides by alkali in a time and concentration-dependent reaction. Evidence is presented indicating that the latter fraction involves phospho-triesters between hydroxy amino acid residues in peptides and internucleotide phosphates. The phosphodiesters between hydroxy amino acids and nucleotide phosphates representing the predominant class of peptide-nucleotide complexes in alkali-denatured DNA are most likely side products of peptide-nucleotide phospho-triester hydrolysis.     

Inactivation of the protease inhibitor phenylmethylsulfonyl fluoride in buffers.

Since the original work by Sweeley et al. (1) the silylation and subsequent gas-liquid chromatography of simple sugars has been well documented (2–5). The silylation of their biochemically important derivatives, notably sugar phosphates, has proven more difficult. Wells et al. (6) premethylated the phosphate with diazomethane in methanol before silylating the sugar group with the usual reagents [pyridine, hexamethyldisilazane (HMDS), and trimethylchlorosilane (TMCS)], Hashizume and Sasaki (7) refluxed the sugar phosphates in the reaction mixture for 1 hr to effect complete silylation, while Eisenberg and Bolden (8) achieved similar results by heating in a sealed vial at 100°C for 10 min. The latter researchers noted that glucose 1-phosphate tended to decompose under their conditions to give one major and two minor peaks. Horning et al. (9) and, later, Sherman et al. (10) used bis(trimethylsilyl)acetamide (BSA) to silylate sugar phosphates, but Pierce (11) has noted that BSA tends to give inconsistent silylation of simple sugars and we have also noted this in our work.In 1969, Ellis (12) reported on the use of a silylation system using dimethylsuifoxide (DMSO) or dimethylformamide (DMF) as the reaction solvent rather than pyridine. The silylated derivatives are not soluble in either of these solvents and they form a second, upper liquid layer (in 10 min in the case of DMSO, 18 hr for DMF). The silylated sample is thus concentrated and this avoids the necessity of removing the solvent [with its attendant problems (10)] after silylation.This paper reports a modification and extension of the silylation system described by Ellis which allows rapid, quantitative silylation of sugars and sugar phosphates at room temperature, i.e., the addition of cyclohexane to the silylation mixture to promote the silylation of sugar phosphates and other biologically important acids. Also reported is the first use of SE-52 stationary liquid phase for the glc of sugar phosphates.     

Specificity of enzymes of biosynthesis of Salmonella anatum O-antigen for polyprenyl derivatives of different chain length and saturation

Polyprenyl phosphates of different structure were prepared and their ability to serve as sugar acceptors in the biosynthesis of O-specific polysaccharides of Salmonella anatum was investigated. It was demonstrated that C30-C80-polyprenyl phosphates with unsaturated alpha-isoprene unit were as active as natural acceptor (undecaprenyl phosphate) in this enzymic system. C15- and C100-polyprenyl phosphates of this series were less effective in O-antigen repeating unit formation. Citronellyl and dolichyl phosphates (derivatives of C10- and C105-polyprenols, respectively, with saturated alpha-isoprene unit) were poor substrates. For polymerization of repeating units, the polyprenol chain-length is of utmost importance: its shortening results in a marked drop in the efficiency of respective compounds as substrates.     

Characterization of glucose transport mutants of Saccharomyces cerevisiae during a nutritional upshift reveals a correlation between metabolite levels and glycolytic flux

Saccharomyces cerevisiae shows a marked preference for glucose and fructose, revealed by the repression of genes whose products are involved in processing other carbon sources. This response seems to be driven by sugar phosphorylation in the first steps of glycolysis rather than by the external sugar concentration. To gain a further insight into the role of the internal sugar signalling mechanisms, were measured the levels of upper intracellular glycolytic metabolites and adenine nucleotides in three mutant strains, HXT1, HXT7 and TM6*, with progressively reduced uptake capacities in comparison with the wild type. Reducing the rate of sugar consumption caused an accumulation of hexose phosphates upstream of the phosphofructokinase (PFK) and a reduction of fructose-1,6-bisphosphate levels. Mathematical modelling showed that these effects may be explained by changes in the kinetics of PFK and phosphoglucose isomerase. Moreover, the model indicated a modified sensitivity of the pyruvate dehydrogenase and the trichloroacetic acid cycle enzymes towards the NAD/NADH in the TM6* strain. The activation of the SNF1 sugar signalling pathway, previously observed in the TM6* strain, does not correlate with a reduction of the ATP : AMP ratio as reported in mammals. The mechanisms that may control the glycolytic rate at reduced sugar transport rates are discussed.