Enzymology in vivo using NMR and molecular genetics

Models of metabolic flux regulation are frequently based on an extrapolation of the kinetic properties of enzymes measured in vitro to the intact cell. Such an extrapolation assumes a detailed knowledge of the intracellular environment of these enzymes in terms of their free substates and effectors concentrations and possible interaction with other cellular macromolecules, which may modify their kinetic properties. These is a considerable incentive, therefore, to study the properties of enzymes directly in vivo. We have been using non-invasive NMR techniques, in conjunction with molecular genetic manipulation of enzyme levels, to study the kinetic properties of individual enzymes in vivo. We have also developed a novel strategy which has allowed us to monitor, by NMR, the ligand binding properties and mobilities of enzymes in the intact cell. This technique may also allow us to measured the diffusion coefficients of these proteins in the cell. These studies should give new insight into the properties of enzymes in vivo     

Developmental regulation of multiple forms of UDPglucose pyrophosphorylase of Dictyostelium

Uridine diphosphoglucose pyrophosphorylase (UTP:α-d-glucose-1-phosphate uridylyltransferase, EC 2.7.7.9) is a developmentally regulated enzyme in Dictyostelium discoideum essential for the completion of its life cycle. During vegetative growth and the early stages of differentiation the specific activity of the enzyme remains constant. However, it increases threefold by the time fruiting bodies are formed. We have identified a developmentally specific form of uridine diphosphoglucose pyrophosphorylase, altered in both isoelectric point and apparent molecular weight, by resolving crude extracts of cells on two-dimensional denaturing polyacrylamide gels, renaturing the protein in situ, and localizing active enzyme with a histochemical stain. Quantitation of the amount of enzyme stain deposited in the gels shows that the activity in the new form can account for the increase observed in development. The appearance of the developmental form of the enzyme requires de novo protein synthesis since it is inhibited by cycloheximide. Immunoprecipitation of uridine diphosphoglucose pyrophosphorylase from in vivo and in vitro synthesized proteins has revealed heterogeneity not previously detected in the enzyme from both vegetative and developed cells. Two different proteins are synthesized in vitro by mRNA from either vegetative or developed cells. These two proteins are also found in vivo in developed cells. Only one of the two proteins is found in vegetative cells. Enzyme protein synthesized in vivo appears to be modified after translation. Therefore, the observed heterogeneity in uridine diphosphoglucose pyrophosphorylase found in vivo appears due both to post-translational modification and to synthesis of two polypeptides from one or more species of mRNA.     

Distribution of Phenylalanine Ammonia Lyase and Chalcone Synthase within Trunks of Robinia pseudoacacia L.

During heartwood formation, a kind of apoptosis in the inner parts of woody axes, phenolic substances are accumulated by in situ biosynthesis. In Robinia pseudoacacia L, these compounds are mainly flavonoids. In the present work, we performed a study to show if there is a correlation between measurable activities and detectable protein levels of phenylalanine ammonia lyase (PAL; EC 4.3.1.5) and chalcone synthase (CHS; EC 2.3.1.74), key enzymes of general phenylpropanoid metabolism and flavonoid biosynthesis, respectively. After separation of total protein extracts by one-dimensional micro-gel electrophoresis, newly emerging polypeptides were detectable within the sapwood-heartwood transition zone, pointing toward a transient activation of metabolism shortly before cell death occurs. Most prominent was a polypeptide around 46 kDa. By immunoblotting, this band was identified as a CHS subunit. Thus, the exclusive presence of both enzyme protein and extractable enzyme activity of CHS in the heartwood bordering tissue was shown. In contrast, levels of PAL protein were similar in all xylem tissues which contain living cells. PAL activity, however, was measurable only in the differentiating xylem and the sapwood-heartwood transition zone. From these results we conclude that during heartwood formation, CHS and PAL differ in their mode of regulation. It seems likely that CHS activity is regulated at the level of enzyme protein while PAL regulation is most probably post-translational.     

Immunolocalization of S-nitrosoglutathione, S-nitrosoglutathione reductase and tyrosine nitration in pea leaf organelles

S-Nitrosoglutathione (GSNO) is a nitrosothiol which plays a major role in the metabolism of NO in higher plants mediating signaling processes. Protein tyrosine nitration (NO₂–Tyr) is a post-translational modification which contributes to protein regulation. The subcellular localization of GSNO, S-nitrosoglutathione reductase (GSNOR), an enzyme which catalyzes its decomposition and protein tyrosine nitration was studied in pea (Pisum sativum L.) leaf plants with the aid of the electron microscopy immunogold-labeling technique. Our findings show that GSNO, GSNOR and nitrated proteins are present in the different subcellular compartments of leaf cells which include chloroplasts, cytosol, mitochondria, and peroxisomes. Given that pea peroxisomes are one of the cell compartments where nitric oxide (NO) has been thoroughly studied, our results provide additional insights into the metabolism of NO in this organelle where NO and GSNO could function as signal molecules in cross talk between the different cell compartments.     

Regulation of Escherichia coli phosphofructokinase in situ

The activity of E. coli phosphofructokinase in situ has been studied in cells permeabilized to its substrates, products and effectors by a toluene-freezing treatment. The in situ enzyme exhibits moderate cooperativity in respect to F6P (n_H up to 2.0), rather low affinity for ATP (with Km up to 1 mM when saturated with F6P), activation by ADP, and inhibition, within the physiological range of concentrations, by high ATP and phosphoenolpyruvate. This behaviour of the enzyme in situ at concentrations of the effector metabolites as those reported in intact cells in glycolytic and gluconeogenic conditions could account for the changes of phosphofructokinase activity needed for metabolic regulation in vivo.     

Direct isolation of flavonoids from plants using ultra‐small anatase TiO2 nanoparticles

Surface functionalization of nanoparticles has become an important tool for in vivo delivery of bioactive agents to their target sites. Here we describe the reverse strategy, nanoharvesting, in which nanoparticles are used as a tool to isolate bioactive compounds from living cells. Anatase TiO₂ nanoparticles smaller than 20 nm form strong bonds with molecules bearing enediol and especially catechol groups. We show that these nanoparticles enter plant cells, conjugate enediol and catechol group‐rich flavonoids in situ, and exit plant cells as flavonoid‐nanoparticle conjugates. The source plant tissues remain viable after treatment. As predicted by the surface chemistry of anatase TiO₂ nanoparticles, quercetin‐based flavonoids were enriched amongst the nanoharvested flavonoid species. Nanoharvesting eliminates the use of organic solvents, allows spectral identification of the isolated compounds, and opens new avenues for use of nanomaterials for coupled isolation and testing of bioactive properties of plant‐synthesized compounds.     

Assessment of lysosomal function by quantitative histochemical and cytochemical methods

Summary Quantitative histochemistry and cytochemistry enables a direct link to be made between metabolic functions such as the activity of lysosomal enzymes and the morphology of a tissue or a type of cell. Several approaches exist such as microchemistry based on (bio)chemical analysis of a single cell or a small piece of tissue dissected from a freeze-dried section. This technique has been routinely used for prenatal diagnosis of inherited enzyme defects and especially of lysosomal storage diseases. Other approaches are cytofluorometry or cytophotometry, which are based on the principle that a fluorescent or coloured final reaction product is precipitated at the site of the enzyme. The amount of final reaction product is analysed per cell or per unit volume of tissue using either a microscope cytofluorometer or flow cytometer for fluorescence measurements or an image analysing system or scanning and integrating cytophotometer for absorbance measurements.In principle, fluorescence methods are to be preferred over chromogenic methods because they are more sensitive and enable multiparameter analysis. However, only a limited number of fluorogenic methods are at hand that give a final reaction product which is sufficiently water-insoluble to guarantee good localisation. The best results have been obtained with methods based on naphthol AS-TR derivatives and with methods for the demonstration of protease activity using methoxynaphthylamine derivatives as substrates and 5-nitrosalicylaldehyde as coupling reagent. Chromogenic methods are far better with respect to localisation properties and, therefore, most commonly used for quantitative histochemical analysis of lysosomal enzyme activities. Besides the measurement of enzyme reactions in tissues and cells, chromogenic methods have been applied for the analysis of kinetic parameters of lysosomal enzymesin situ which could be a better reflection of enzyme kineticsin vivo than those obtainedin vitro with biochemical means in diluted solutions. Chromogenic methods have also been used in the lysosomal fragility test which is based on the lag phase occurring when a lysosomal enzyme reaction is analysed against time. The duration of the lag phase is a parameter for the stability of the lysosomal membrane and is affected by toxic compounds or under pathological conditions. This paper reviews briefly fundamental aspects and applications of quantitative histochemical and cytochemical methods in the study of lysosomes.     

Reporter genes in transgenic mice

Althoughin vivo models utilizing endogenous reporter genes have been exploited for many years, the use of reporter transgenes to dissect biological issues in transgenic animals has been a relatively recent development. These transgenes are often, but not always, of prokaryotic origin and encode products not normally associated with eukaryotic cells and tissues. Some encode enzymes whose activities are detected in cell and tissue homogenates, whereas others encode products that can be detectedin situ at the single cell level. Reporter genes have been used to identify regulatory elements that are important for tissue-specific gene expression or for development; they have been used to producein vivo models of cancer; they have been employed for the study ofin vivo mutagenesis; and they have been used as a tool in lineage analysis and for marking cells in transplanation experiments. The most commonly usedin situ reporter gene islacZ, which encodes a bacterial -galactosidase, a sensitive histochemical marker. Although it has been used with striking success in cultured cells and in transgenic mouse embryos, its postnatalin vivo expression has been unreliable and disappointing. Nevertheless, the ability to express reporter genes in transgenic mice has been an invaluable resource, providing insights intoin vivo biological mechanisms. The development of newin vivo models, such as those in which expression of transgenes can be activated or repressed, should produce transgenic animal systems that extend our capacity to address heretofore unresolved biological questions.     

植物酶的组织和细胞化学定位研究方法

酶是参与植物体内生化反应的特殊蛋白质。在保持活组织和细胞结构完整性的条件下,利用组织化学、细胞化学、免疫学和显微检测等技术研究酶的即位定位,是了解酶在组织、细胞和亚细胞中的分布、活性动态与定量及酶功能等的重要途径。对植物体中酶定位的组织化学和细胞化学方法的概念、原理与研究进展进行了综述,并根据国际酶化学分类编号顺序,分别介绍了25种酶的组织化学染色定位所用的反应介质和染色方法及46种酶的细胞化学定位方法的参考文献。     

Redox interconversion of Escherichia coli glutathione reductase. A study with permeabilized and intact cells

Summary The redox interconversion of Escherichia coli glutathione reductase has been studied both in situ, with permeabilized cells treated with different reductants, and in vivo, with intact cells incubated with compounds known to alter their intracellular redox state.The enzyme from toulene-permeabilized cells was inactivated in situ by NADPH, NADH, dithionite, dithiothreitol, or GSH. The enzyme remained, however, fully active upon incubation with the oxidized forms of such compounds. The inactivation was time-, temperature-, and concentration-dependent; a 50% inactivation was promoted by just 2 M NADPH, while 700 M NADH was required for a similar effect. The enzyme from permeabilized cells was completely protected against redox inactivation by GSSG, and to a lesser extent by dithiothreitol, GSH, and NAD(P)⁺. The inactive enzyme was efficiently reactivated in situ by physiological GSSG concentrations. A significant reactivation was promoted also by GSH, although at concentrations two orders of magnitude below its physiological concentrations. The glutathione reductase from intact E. coli cells was inactivated in vivo by incubation with DL-malate, DL-isocitrate, or higher L-lactate concentrations. The enzyme was protected against redox inactivation and fully reactivated by diamide in a concentration-dependent fashion. Diamide reactivation was not dependent on the synthesis of new protein, thus suggesting that the effect was really a true reactivation and not due to de novo synthesis of active enzyme. The glutathione reductase activity increased significantly after incubation of intact cells with tert-butyl or cumene hydroperoxides, suggesting that the enzyme was partially inactive within such cells. In conclusion, the above results show that both in situ and in vivo the glutathione reductase of Escherichia coli is subjected to a redox interconversion mechanism probably controlled by the intracellular NADPH and GSSG concentrations.     

Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana

Availability of plant‐specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measured in vitro, often under non‐physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximal in vivo catalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome‐b6f complex, ATP‐citrate synthase, sucrose‐phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition‐specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements from Arabidopsis thaliana rosette with and fluxes through canonical pathways in a constraint‐based model of leaf metabolism. In comparison to findings in Escherichia coli, we demonstrate weaker concordance between the plant‐specific in vitro and in vivo enzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximal in vivo catalytic rates, and available quantitative metabolomics data are below reported values and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome‐wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.     

Lipid Metabolizing Enzyme Activities Modulated by Phospholipid Substrate Lateral Distribution

Biological membranes contain many domains enriched in phospholipid lipids and there is not yet clear explanation about how these domains can control the activity of phospholipid metabolizing enzymes. Here we used the surface dilution kinetic theory to derive general equations describing how complex substrate distributions affect the activity of enzymes following either the phospholipid binding kinetic model (which assumes that the enzyme molecules directly bind the phospholipid substrate molecules), or the surface-binding kinetic model (which assumes that the enzyme molecules bind to the membrane before binding the phospholipid substrate). Our results strongly suggest that, if the enzyme follows the phospholipid binding kinetic model, any substrate redistribution would increase the enzyme activity over than observed for a homogeneous distribution of substrate. Besides, enzymes following the surface-binding model would be independent of the substrate distribution. Given that the distribution of substrate in a population of micelles (each of them a lipid domain) should follow a Poisson law, we demonstrate that the general equations give an excellent fit to experimental data of lipases acting on micelles, providing reasonable values for kinetic parameters—without invoking special effects such as cooperative phenomena. Our theory will allow a better understanding of the cellular-metabolism control in membranes, as well as a more simple analysis of the mechanisms of membrane acting enzymes.     

Quantitative assessment of primary cerium reaction product formed by glucose-6-phosphatase activity in a male rat liver: an image analysis study

 Glucose-6-phosphatase (G6Pase) activity has been determined in periportal and pericentral areas of the liver of normal male rats. Measurements were performed on unfixed cryostat sections mounted on semipermeable membranes. In the present study, the oxidized primary reaction product of a cerium-based histochemical method [Ce(IV)perhydroxyphosphate] instead of the final reaction product after a second-step incubation was measured. For quantification of the amount of Ce(IV)perhydroxyphosphate formed the digital image analyzing system Quantimet 500+ was used. Estimated values of optical densities of Ce(IV)perhydroxyphosphate over test areas were employed for calculation of kinetic parameters of (G6Pase). Highest activities of G6Pase (higher K _m and V _max levels) were found in periportal areas of the rat liver, indicating a higher amount of active enzyme molecules and a lower affinity for the substrate. Differences in values for both K _m and V _max between periportal and pericentral zones were highly significant and closely comparable to those for male fed rats. Correlations between K _m and V _max were significant for periportal as well for pericentral liver areas. The results of the present study thus allow the same biological implications as histochemical methods employing a final reaction for quantification of enzyme activities. The present method avoids the drawbacks of enhancement reactions and demonstrates the feasibility of in situ analysis of enzyme kinetic parameters by quantification of oxidized primary cerium reaction products. Accepted: 8 January 1996     

Acid β-Glucosidase: Enzymology and Molecular Biology of Gaucher Diseas

Abstract

Human lysosomal β-glucosidase (D-glucosyl-acylsphingo-sine glucohydrolase, EC 3.2.1.45) is a membrane-associated enzyme that cleaves the β-glucosidic linkage of glucosylcer-amide (glucocerebroside), its natural substrate, as well as synthetic β-glumsides. Experiments with cultured cells suggest that in vivo this glycoprotein requires interaction with negatively charged lipids and a small acidic protein, SAP-2, for optimal glucosylceramide hydrolytic rates. In vitro, detergents (Triton? X-100 or bile acids) or negatively charged gangliosides or phos-pholipids and one of several “activator proteins” increase hydrolytic rate of lipid and water-soluble substrates. Using such in vitro assay systems and active site-directed covalent inhibitors, kinetic and structural properties of the active site have been elucidated. The defective activity of this enzyme leads to the variants of Gaucher disease, the most prevalent lysosomal storage disease. The nonneuronopathic (type 1) and neuronopathic (types 2 and 3) variants of this inherited (autosomal recessive) disease but panethnic, but type 1 is most prevalent in the Ashkenazi Jewish population. Several missense mutations, identified in the structural gene for lysosomal β-glucosidase from Gaucher disease patients, are presumably casual to the specifically altered post-translational oligosaccharide processing or stability of the enzyme as well as the alterecA in vitro kinetic properties of the residual enzyme from patient tissues.     

Enzyme histochemistry and immunohistochemistry with freeze-dried or freeze-substituted resin-embedded tissue

Summary Freeze-drying or freeze-substitution, combined with low-temperature resin-embedding, represents a new approach to the optimum preservation of tissue for enzyme histochemistry and immunohistochemistry. This method, which avoids tissue fixation, combines excellent tissue morphology with the preservation of enzyme activity and immunoreactivity and allows high-resolution enzyme histochemical and immunohistochemical studies to be performed. The activity of a wide range of enzymes can be demonstrated in sections of freeze-dried or freeze-substituted resin-embedded tissue. Enzymes are retainedin situ with high activity, accurate localization and no diffusion. Immunohistochemical studies can also be performed on resin sections, and antigens—especially labile antigens — are immobilizedin situ without denaturation and can be demonstrated with high sensitivity and accurately localized. This method allows the localization and distribution of enzymes and antigens to be studied in relation to excellent histological and cytological detail.     

INHIBITION OF BACTERIAL AND MAMMALIAN CHOLINE ACETYLTRANSFERASES BY STYRYLPYRIDINE ANALOGUES

—Choline acetyltransferase was extracted from Lactobacillus plantarum by relatively gentle procedures involving penicillin treatment, osmotic shock and passage through a French pressure cell. After partial purification, the extract was compared with choline acetyltransferase of calf caudate nucleus for kinetic properties and response to a class of inhibitors which consists of analogues of styrylpyridine. Both enzymes obeyed a sequential mechanism with Michaelis constants for the bacterial enzyme, K_m= 8 μm vs. acetyl-CoA and 0·44 mm vs. choline; and for the caudate nucleus enzyme, K_m= 15 μm vs. acetyl-CoA and 0·8 mm vs. choline. Both were stabilized by dithiothreitol and EDTA. The extracts differed in that the bacterial enzyme was more labile and apparently was susceptible to conformational changes, which modified its response to the styrylpyridinetype inhibitors. The use of intact cells of Lactobacillus plantarum as an in vivo system for studying the inhibition of choline acetyltransferase by styrylpyridines was possible only for non-quaternary analogues, which exist as an equilibrium mixture of charged and uncharged species.     

Seasonal variation in enzyme activities and temperature sensitivities in Arctic tundra soils

Arctic soils contain large amounts of organic matter due to very slow rates of detritus decomposition. The first step in decomposition results from the activity of extracellular enzymes produced by soil microbes. We hypothesized that potential enzyme activities are low relative to the large stocks of organic matter in Arctic tundra soils, and that enzyme activity is low at in situ temperatures. We measured the potential activity of six hydrolytic enzymes at 4 and 20 °C on four sampling dates in tussock, intertussock, shrub organic, and shrub mineral soils at Toolik Lake, Alaska. Potential activities of N‐acetyl glucosaminidase, β‐glucosidase, and peptidase tended to be greatest at the end of winter, suggesting that microbes produced enzymes while soils were frozen. In general, enzyme activities did not increase during the Arctic summer, suggesting that enzyme production is N‐limited during the period when temperatures would otherwise drive higher enzyme activity in situ. We also detected seasonal variations in the temperature sensitivity (Q₁₀) of soil enzymes. In general, soil enzyme pools were more sensitive to temperature at the end of the winter than during the summer. We modeled potential in situβ‐glucosidase activities for tussock and shrub organic soils based on measured enzyme activities, temperature sensitivities, and daily soil temperature data. Modeled in situ enzyme activity in tussock soils increased briefly during the spring, then declined through the summer. In shrub soils, modeled enzyme activities increased through the spring thaw into early August, and then declined through the late summer and into winter. Overall, temperature is the strongest factor driving low in situ enzyme activities in the Arctic. However, enzyme activity was low during the summer, possibly due to N‐limitation of enzyme production, which would constrain enzyme activity during the brief period when temperatures would otherwise drive higher rates of decomposition.     

Xanthine dehydrogenase from Drosophila melanogaster: a comparison of the kinetic parameters of the pure enzyme from two wild-type isoalleles differing at a putative regulatory site.

Summary Xanthine dehydrogenase (XDH) from Drosophila melanogaster has been purified to homogeneity by immunoaffinity chromatography, and its kinetic parameters determined. Drosophila XDH exhibits ordered binding for substrate and NAD⁺, analogous to the corresponding enzymes from vertebrate sources. The wild-type enzyme exhibits a K_m for xanthine of 2.4x10^-5 M, and for NAD⁺ of 4.0x10^-5 M. XDH purified from a genetic variant exhibiting elevated levels of enzyme activity has similar kinetic constants. The results provide further evidence that the site of variation in the latter strain results in higher steady state numbers of XDH molecules per fly.     

Metabolic control at the cytosol–mitochondria interface in different growth phases of CHO cells

Metabolism at the cytosol–mitochondria interface and its regulation is of major importance particularly for efficient production of biopharmaceuticals in Chinese hamster ovary (CHO) cells but also in many diseases. We used a novel systems-oriented approach combining dynamic metabolic flux analysis and determination of compartmental enzyme activities to obtain systems level information with functional, spatial and temporal resolution. Integrating these multiple levels of information, we were able to investigate the interaction of glycolysis and TCA cycle and its metabolic control. We characterized metabolic phases in CHO batch cultivation and assessed metabolic efficiency extending the concept of metabolic ratios. Comparing in situ enzyme activities including their compartmental localization with in vivo metabolic fluxes, we were able to identify limiting steps in glycolysis and TCA cycle. Our data point to a significant contribution of substrate channeling to glycolytic regulation. We show how glycolytic channeling heavily affects the availability of pyruvate for the mitochondria. Finally, we show that the activities of transaminases and anaplerotic enzymes are tailored to permit a balanced supply of pyruvate and oxaloacetate to the TCA cycle in the respective metabolic states. We demonstrate that knowledge about metabolic control can be gained by correlating in vivo metabolic flux dynamics with time and space resolved in situ enzyme activities.