Studies on the kinetic mechanism and the phosphoryl-enzyme compound of the Escherichia coli acetate kinase reaction.

The Escherichia coli acetate kinase was further examined to determine whether a phosphoryl-enzyme intermediate (or compound) was kinetically discernible or chemically essential in the catalysis of that reaction. The extent of phosphoryl-enzyme formation as monitored by gel filtration of the enzyme-phosphoryl donor substrate complex (E-P) was found to be quite variable. Isolated E-P could be reduced with sodium borohydride and the extent of formation of α-amino-δ-hydroxyvalerate paralleled the observed degree of phosphorylation of the acetate kinase. Incubation with 1 m neutral hydroxylamine of the enzyme, which had been preincubated with acetyl-P for 30–60 min, led to parallel loss of the enzyme's ability to catalyze the net reaction and the ADP ATP exchange reaction. The percentage of activity loss depended upon the concentration of acetyl-P with which the enzyme was preincubated. These observations point toward a requirement for an unmodified active site carboxyl group which may be phosphorylated during the reaction course. The theoretical basis for a new and simple alternative substrate protocol for segregating sequential and ping-pong mechanisms is presented. When applied to acetate kinase, the findings clearly rule out a ping-pong kinetic mechanism. This was also confirmed by initial rate measurements with propionyl-P and ADP, and the weight of the evidence now clearly favors a modified random substrate addition pathway as presented herein. The data do not in any way exclude E-P formation as a requirement for catalysis. Finally, the rates of cold inactivation at 0 °C and reactivation at 29 °C were determined in order to minimize the possible influence of this phenomenon on the kinetic studies.     

In vitro characterization of a phosphate starvation-independent carbon-phosphorus bond cleavage activity in Pseudomonas fluorescens 23F.

A novel, metal-dependent, carbon-phosphorus bond cleavage activity, provisionally named phosphonoacetate hydrolase, was detected in crude extracts of Pseudomonas fluorescens 23F, an environmental isolate able to utilize phosphonoacetate as the sole carbon and phosphorus source. The activity showed unique specificity toward this substrate; its organic product, acetate, was apparently metabolized by the glyoxylate cycle enzymes of the host cell. Unlike phosphonatase, which was also detected in crude extracts of P. fluorescens 23F, phosphonoacetate hydrolase was inducible only in the presence of its sole substrate and did not require phosphate starvation.     

Evidence against the physiological role of acetyl phosphate in the phosphorylation of the ArcA response regulator in <Emphasis Type="Italic">Escherichia coli</Emphasis>

The Arc two-component signal transduction system of Escherichia coli comprises the ArcB sensor kinase and the ArcA response regulator. Under anoxic growth conditions, ArcB autophosphorylates and transphos-phorylates ArcA, which, in turn, represses or activates its target operons. ArcA has been shown to be able to autophosphorylate in vitro at the expense of acetyl-P. Here, the in vivo effect of acetyl phosphate on the redox signal transduction by the Arc system was assessed. Our results indicate that acetyl phosphate can modulate the expression of ArcA-P target genes only in the absence of ArcB. Therefore, the acetyl phosphate dependent ArcA phosphorylation route does not seem to play a significant role under physiological conditions.     

A novel method for the purification of inositol phosphates from biological samples reveals that no phytate is present in human plasma or urine

Inositol phosphates are a large and diverse family of signalling molecules. While genetic studies have discovered important functions for them, the biochemistry behind these roles is often not fully characterized. A key obstacle in inositol phosphate research in mammalian cells has been the lack of straightforward techniques for their purification and analysis. Here we describe the ability of titanium dioxide (TiO₂) beads to bind inositol phosphates. This discovery allowed the development of a new purification protocol that, coupled with gel analysis, permitted easy identification and quantification of InsP₆ (phytate), its pyrophosphate derivatives InsP₇ and InsP₈, and the nucleotides ATP and GTP from cell or tissue extracts. Using this approach, InsP₆, InsP₇ and InsP₈ were visualized in Dictyostelium extracts and a variety of mammalian cell lines and tissues, and the effects of metabolic perturbation on these were explored. TiO₂ bead purification also enabled us to quantify InsP₆ in human plasma and urine, which led to two distinct but related observations. Firstly, there is an active InsP₆ phosphatase in human plasma, and secondly, InsP₆ is undetectable in either fluid. These observations seriously question reports that InsP₆ is present in human biofluids and the advisability of using InsP₆ as a dietary supplement.     

Different mechanisms of acetate activation in Desulfurella acetivorans and Desulfuromonas acetoxidans

Desulfurella acetivorans and Desulfuromonas acetoxidans are both acetate oxidizing sulfur reducing eubacteria. The two organisms differ in G+C content of DNA (31.4% versus 50–52%) and in growth temperature optimum (55°C versus 30°C) and in that D. acetivorans does not contain cytochromes. Both organisms are shown to be similar in that they metabolize acetate via the citric acid cycle rather than via the carbon monoxide dehydrogenase pathway. They were found to differ, however, in the mechanism of acetate activation and of succinate formation. In D. acetoxidans acetyl-CoA and succinate are formed from acetate and succinyl-CoA involving only one enzyme, succinyl-CoA: acetate CoA-transferase. In D. acetivorans acetyl-CoA is generated from acetate via acetyl phosphate involving acetate kinase and phosphate acetyltransferase; succinate is formed from succinyl-CoA via succinyl-CoA synthetase. Both sulfur reducers were found to contain menaquinone.Abbreviations HPLC high performance liquid chromatography - acetyl-P acetyl phosphate     

Initial in vitro characterisation of phosphonopyruvate hydrolase, a novel phosphate starvation-independent, carbon-phosphorus bond cleavage enzyme in Burkholderia cepacia Pal6

A novel, inducible carbon-phosphorus bond cleavage enzyme, phosphonopyruvate hydrolase, was detected in cell-free extracts of Burkholderia cepacia Pal6, an environmental isolate capable of mineralising L-phosphonoalanine as carbon, nitrogen and phosphorus source. The activity was induced only in the presence of phosphonoalanine, did not require phosphate starvation for induction and was uniquely specific for phosphonopyruvate, producing equimolar quantities of pyruvate and inorganic phosphate. The native enzyme had a molecular mass of some 232 kDa and showed activation by metal ions in the order Co2+ > Ni2+ > Mg2+ > Zn2+ > Fe2+ > Cu2+. Temperature and pH optima in crude cell extracts were 50 degrees C and 7.5, respectively, and activity was inhibited by EDTA, phosphite, sulfite, mercaptoethanol and sodium azide. Phosphonopyruvate hydrolase is the third bacterial C-P bond cleavage enzyme reported to date that proceeds via a hydrolytic mechanism.     

Purification of recombinant flavanone 3beta-hydroxylase from petunia hybrida and assignment of the primary site of proteolytic degradation

Flavanone 3beta-hydroxylase catalyzes the Fe(II)/oxoglutarate-dependent hydroxylation of (2S)-flavanones to (2R,3R)-dihydroflavonols in the course of flavonol/anthocyanin or catechin biosynthesis. The enzyme from Petunia hybrida consists of a 41,655-Da polypeptide that is prone to rapid proteolysis in crude plant extracts as well as on expression in Escherichia coli, and commercial protease inhibitors were inefficient in stopping the degradation. To pinpoint the primary site of proteolysis and to improve the activity yields, two revised schemes of purification were developed for the recombinant polypeptides. Applying a four-step protocol based on extraction and ion-exchange chromatography at pH 7.5, the primary, catalytically inactive proteolytic enzyme fragment (1.1 mg) was isolated and shown to cross-react on Western blotting as one homogeneous band of about 38 kDa. Mass spectrometric analysis assigned a mass of 37,820 +/- 100 Da to this fragment, and partial sequencing revealed an unblocked amino terminus identical to that of the native 3beta-hydroxylase. Thus, the native enzyme had been degraded by proteolysis of a small carboxy-terminal portion, and the primary site of cleavage must be assigned most likely to the Glu 337-Leu 338 bond, accounting for a loss of about 3800 Da. Alternatively, the enzyme degradation was greatly reduced when the extraction of recombinant bacteria was carried out with phosphate buffer at pH 5.5 followed by size exlusion and anion-exchange chromatography. This rapid, two-step purification resulted in a homogeneous 3beta-hydroxylase of high specific acitivity (about 32 mkat/kg) at roughly 5% yield, and the procedure is a major breakthrough in mechanistic investigations of this class of labile dioxygenases.     

Transfection of adherent and suspended cells by calcium phosphate

DNA-calcium phosphate coprecipitates have been used for 30 years as an efficient method to introduce genetic material into cells. The method involves simple solutions that can be prepared or purchased by the experimentalist. All the numerous variations of the protocol found in the literature are based on the same principle--a spontaneous precipitation that occurs in supersaturated solutions. When DNA is present during this process, it is readily incorporated into the forming calcium phosphate precipitate. Although a wide range of conditions will lead to precipitates, high transfection efficiencies are only obtained within a narrow range of optimized parameters that assure certain properties of the precipitate. This paper describes several physico-chemical parameters that are critical to adapt the method to a particular cell line and/or cultivation condition. Examples of protocols that were established and tested within the authors' laboratory are presented. The article also emphasizes differences between transfections of adherent and suspended cells.     

Surface phosphophilicity of aluminum-containing adjuvants probed by their efficiency for catalyzing the P--O bond cleavage with chromogenic and fluorogenic substrates

Aluminum-containing adjuvants are widely used in a variety of vaccine products, such as recombinant proteins, virus-like particles, conjugated polysaccharides, and recently DNA vaccines. Aluminum-containing adjuvants are also known to have a high affinity to inorganic phosphate and its mono- or diesters. Since phosphate groups are present in many antigens as well as the natural physiological environment, a better understanding of the interactions between phosphate and phospho-containing species could help in the design of improved vaccines. This report describes a convenient and novel continuous procedure to measure the avidity denoted by the new term "phosphophilicity" of phosphate and phosphate esters to the surface of aluminum-containing adjuvants. The assay measures the rate of hydrolysis of a fluorogenic substrate-6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP)-with a microplate reader. This method was based on the fundamental bioorganic phenomenon that when a tight binding event occurs, the effective concentration of nucleophile(s) will be significantly increased in the proximity of the P atom for a nucleophilic reaction (i.e., the cleavage of the P&bond;O bond) to take place. A very good leaving group (pK(a) of DiFMU approximately 4.7) in the phosphate monoester substrate makes the assay highly sensitive. Top reading of the nascent fluorescence makes the assay very convenient with no need to separate the particulate adjuvants from the reaction mixtures. The results from this assay are consistent with catalysis of the chromogenic phosphate mono- or diesters.     

Ternary borate–nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry

Phosphate esters play a central role in cellular energetics, biochemical activation, signal transduction and conformational switching. The structural homology of the borate anion with phosphate, combined with its ability to spontaneously esterify hydroxyl groups, suggested that phosphate ester recognition sites on proteins might exhibit significant affinity for nonenzymatically formed borate esters. ¹¹B NMR studies and activity measurements on ribonuclease A (RNase A) in the presence of borate and several cytidine analogs demonstrate the formation of a stable ternary RNase A·3′-deoxycytidine–2′-borate ternary complex that mimics the complex formed between RNase A and a 2′-cytidine monophosphate (2′-CMP) inhibitor. Alternatively, no slowly exchanging borate resonance is observed for a ternary RNase A, borate, 2′-deoxycytidine mixture, demonstrating the critical importance of the 2′-hydroxyl group for complex formation. Titration of the ternary complex with 2′-CMP shows that it can displace the bound borate ester with a binding constant that is close to the reported inhibition constant of RNase A by 2′-CMP. RNase A binding of a cyclic cytidine-2′,3′-borate ester, which is a structural homolog of the cytidine-2′,3′-cyclic phosphate substrate, could also be demonstrated. The apparent dissociation constant for the cytidine-2′,3′-borate·RNase A complex is 0.8 mM, which compares with a Michaelis constant of 11 mM for cytidine-2′,3′-cyclic phosphate at pH 7, indicating considerably stronger binding. However, the value is 1,000-fold larger than the reported dissociation constant of the RNase A complex with uridine–vanadate. These results are consistent with recent reports suggesting that in situ formation of borate esters that mimic the corresponding phosphate esters supports enzyme catalysis.     

Optimization of oxidative folding methods for cysteine‐rich peptides: a study of conotoxins containing three disulfide bridges

The oxidative folding of small, cysteine‐rich peptides to selectively achieve the native disulfide bond connectivities is critical for discovery and structure‐function studies of many bioactive peptides. As the propensity to acquire the native conformation greatly depends on the peptide sequence, numerous empirical oxidation methods are employed. The context‐dependent optimization of these methods has thus far precluded a generalized oxidative folding protocol, in particular for peptides containing more than two disulfides. Herein, we compare the efficacy of optimized solution‐phase and polymer‐supported oxidation methods using three disulfide‐bridged conotoxins, namely µ‐SIIIA, µ‐KIIIA and ω‐GVIA. The use of diselenide bridges as proxies for disulfide bridges is also evaluated. We propose the ClearOx‐assisted oxidation of selenopeptides as a fairly generalized oxidative folding protocol. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Nature and mode of action of NAD and ATP dephosphorylating enzyme from Aspergillus terreus DSM 826

NAD and ATP were dephosphorylated by Aspergillus terreus extracts optimally at pH 8 and 40 °C. The data obtained indicate that one phosphohydrolase was involved in the cleavage of all the phosphate linkages of these two energy-carrying molecules, and also indicate that this enzyme can be classified as a non-specific alkaline phosphatase. This is based on the following criteria: during fractionation of the enzymes of the extracts, using Sephadex G-200 column chromatography, the recorded elution diagram showed only one phosphohydrolase activity peak and this peak was the same with NAD, ATP, inorganic pyrophosphate and phenyl phosphate as substrates; the activity profiles with these four substrates were similar; and these four substrates were hydrolyzed at almost constant relative rates. Moreover, the activities of the pooled fractions with these different substrates responded similarly on changing some experimental conditions, such as addition of fluoride to the reaction mixtures or exposing the enzyme preparation to temperatures above 40 °C. Chromatographic detection of the intermediates and the products formed during the progression of NAD and ATP dephosphorylation by the most purified fraction of this enzyme was found to be consistent with the following mode of its action: This revised version was published online in June 2006 with corrections to the Cover Date.     

Parameters affecting substance P measurement in heart, lung, and skin

Substance P (SP), a neuropeptide that is widely distributed both peripherally and centrally, mediates several pathophysiological processes. Among current assays for SP, enzyme-linked immunosorbent assay (ELISA) and radioimmunoassay (RIA) have been most widely used. Several previous studies, mostly performed with nerve extracts or organ perfusates, determined that acidity of the extraction buffer as well as the number extractions performed constitute factors influencing accurate measurements. We used an ELISA protocol in this study to analyze methodological aspects of SP measurement in extracts from heart, skin, and lung. The extraction procedure had two steps, an acid extraction followed by a column extraction. We could effectively measure SP with extract from as little as 10 mg of tissue. For each tissue examined, different variables influenced the SP measured. For all tissues, the weight of tissue extracted was critical; the more tissue extracted, the lower the sensitivity of the assay. This problem could be overcome in skin by omitting the column extraction. When mechanical loses were considered (e.g., loss during extraction and SP retained by the column after elution), column extraction improved SP measurements only with lung tissue. The amount of SP remaining in the sample after the first extraction also varied among tissues. The first acid extraction effectively isolated 80% of total SP from skin. In contrast, the first extraction with lung tissue recovered only 58%. Because both acid and heat effectively release SP from nerve endings, this could reflect the presence of non-neuronal SP, especially in lung. High-dose capsaicin treatment, which depletes SP in nerve endings, caused 42% loss of SP in skin independent of amount of tissue extracted Our results suggest that a second acid extraction of tissue should be performed and that column extraction is clearly detrimental with skin samples.     

Two forms of farnesyl pyrophosphate synthetase from hog liver

Two forms of farnesyl pyrophosphate synthetase were separated from hog liver extracts by DEAE-Sephadex chromatography. They were designated as farnesyl pyrophosphate synthetase A and B, in order of elution. Both enzymes catalyzed the exclusive formation of E,E-farnesyl pyrophosphate from isopentenyl pyrophosphate and either dimethylallyl pyrophosphate or geranyl pyrophosphate. They also showed no detectable differences in pH optima, molecular weights, and susceptibilities to metal ions. However, the catalytic activity of the synthetase B was greatly stimulated by the addition of common sulfhydryl reagents. This stimulation was the result of conversion of the synthetase B into the synthetase A. Conversely the synthetase A was converted into form B when it was dialyzed against a buffer solution containing cupric ions. It is suggested that the formation and cleavage of disulfide bond(s) is involved in the interconversion between the two forms.     

Fluorimetric HPLC detection of endogenous riboflavin 4',5'-cyclic phosphate in rat liver at nanomolar concentrations

We have investigated the biological occurrence of riboflavin 4',5'-cyclic phosphate (cyclic FMN or cFMN), the flavin product known to be formed in vitro from FAD by the rat liver enzyme FAD-AMP lyase (cyclizing) or FMN cyclase (EC 4.6.1.15). The expected difficulties were the low concentration of the compound, the tendency of the more abundant FAD to decompose chemically to cFMN, and the acid lability of cFMN itself. A protocol was devised to prepare deproteinized rat liver extracts, avoiding conditions prone to the chemical formation of cFMN and making exposure to conditions of cFMN degradation as short as possible. In these extracts, cFMN was assayed by HPLC with fluorimetric detection. The identity of liver cFMN was confirmed by its HPLC separation from other known flavins, its coelution with authentic cFMN, and its susceptibility to acid degradation, yielding a mixture of 5'-FMN and 4'-FMN. The amount of total cFMN recovered in the liver extracts was 22+/-11 pmol/g fresh tissue. Careful control experiments were performed to rule out the possibility that this could be a chemical product of FAD degradation during extract preparation. These controls indicated that, on average, 97% of the measured extract concentration of cFMN, i.e., about 21+/-10 pmol/g, was already present in the liver at the beginning of the process and was extracted from the tissue. This figure is likely to be an underestimation of the hepatic content, as indicated by control experiments.     

Polynucleotide phosphorylase-based photometric assay for inorganic phosphate

Polynucleotide phosphorylase is a prokaryotic enzyme that catalyzes phosphorolysis of polynucleotides with release of nucleotide diphosphates. By taking advantage of this property, we developed a photometric assay for inorganic phosphate. In the presence of polyadenylic acid, phosphate is converted into adenosine 5'-diphosphate (ADP) by this enzyme. ADP then reacts with phosphoenolpyruvate in a pyruvate kinase-catalyzed reaction, thus giving rise to adenosine 5'-triphosphate and pyruvate. Finally, pyruvate oxidizes reduced nicotinamide adenine dinucleotide (NADH) through the action of L-lactate dehydrogenase, with concomitant decrease in absorbance at 340 nm. As expected, in this detection system 1 mol of NADH was oxidized per mole of phosphate. The assay showed an excellent reproducibility, as the standard deviations never exceeded 5%. It also was shown to be unaffected by several compounds that are regarded as major interferents of the traditional colorimetric assays. Absence of interference was also demonstrated when determining phosphate content in different biological samples, such as human serum and perchloric acid extracts from Escherichia coli, yeast, and bovine liver. An E. coli strain overexpressing His-tagged polynucleotide phosphorylase developed in our laboratories allowed quick and straightforward purification of enzyme, making the assay feasible and convenient. Since all other reagents required are inexpensive, the assay represents a cheaper alternative to commercially available phosphate assay kits.     

Activation of an insulin-stimulated S6 kinase in 3T3 L1 cell-free extracts by proteolysis

Using chromatography on a Fast S-Sepharose column, the insulin-stimulated S6 kinase can be resolved from other S6 kinases present in 3T3 L1 cell extracts. Only one S6 kinase is greatly activated by insulin (4-5-fold) and phosphorylates S6 with a high stoichiometry (4-5 mol phosphate per mol S6). This insulin-dependent S6 kinase can be activated in cell-free extracts by incubation with high concentrations of Ca2+. This activation is blocked by protease inhibitors such as leupeptin and is mimicked by trypsin. The stimulation does not require the presence of the protein kinase dependent on phospholipids and calcium (PK-C) in the cell extracts. The level of stimulation produced by proteolysis in the cell extracts is comparable to that reached in vivo by incubation with insulin.     

High-performance liquid chromatography of phospholipids: quantitation by phosphate analysis

Quantitation of individual phospholipids separated by HPLC from tissue extracts by colorimetric analysis of phosphate was investigated. Elution of inorganic phosphate and breakthrough of lecithin were determined using radioisotopes. A substance which interfered with sample phosphate determinations was found in the column eluant, and a method to minimize its effect was developed. This method allows accurate quantitation of individual phospholipids present at a minimum of 20 nmol phosphate.     

Characterization of the newly-formed internucleotide bond of in vitro spliced mRNAs

Precursor RNAs were synthesized in vitro from a plasmid in which the early region 2 (E2) of adenovirus 2 is fused to an efficient bacteriophage promoter (Salmonella phage 6). The RNAs were purified and utilized as substrates for in vitro splicing in the presence of nuclear extracts prepared from MOPC-315 mouse myeloma cells. We have shown previously (Goldenberg, C.J., PNAS, August, in press, 1984) that in vitro splicing in those extracts was accurate at the nucleotide level. We now show that: i) the new internucleotide bond at the splice junction generated in vitro is a 3',5'-phosphodiester bond; and ii) the phosphate that forms the splice between the exons is derived from the pre-mRNA.