The kinetic behavior of xanthine oxidase containing chemically modified flavins

The steady-state and rapid kinetic properties of xanthine oxidase containing a series of FAD analogs of varying reduction potential have been investigated. From steady-state analysis, Vmax is found to exhibit a sigmoidal dependence on the flavin midpoint potential in the homologous series. This dependence is accurately described by a model in which the rate of catalysis is attenuated by the amount of partially reduced enzyme generated during turnover possessing an unfavorable distribution of reducing equivalents among the several redox-active centers of the protein. The model assumes that reducing equivalents equilibrate among these centers rapidly compared to the limiting rates for the reductive and oxidative half-reactions. This assumption is borne out by a quantitative analysis of the reductive and oxidative half-reactions of the several enzyme forms investigated in detail. It is demonstrated in these studies that xanthine oxidase containing low potential flavin derivatives such as 1-deaza, 6-hydroxy, or 8-hydroxy FAD exhibits low turnover not because of inherently slow rates of reduction by xanthine or oxidation by molecular oxygen, but because in partially reduced enzyme generated in the course of turnover reducing equivalents are distributed within the enzyme in such a way that the enzyme can participate in neither the reductive nor oxidative half-reactions. These results provide confirmation of the operation of a thermodynamic control mechanism in a simple electron-transferring system.     

Growth of Saccharomyces cerevisiae is controlled by its limited respiratory capacity: Formulation and verification of a hypothesis

A novel mechanistic model for the growth of baker's yeast on glucoseis presented. It is based on the fact that glucose degradation proceeds via two pathways under conditions of aerobic ethanol formation. Part is metabolized oxidatively and part reductively, with ethanol being the end product of reductive energy metabolism. The corresponding metabolic state is designated oxidoreductive. Ethanol can be used oxidatively only. Maximum rates of oxidative glucose and ethanol degradation are governed by the respiratory capacity of the cells. The model is formulated by using the stoichiometric growth equations for pure oxidative and reductive (fermentative) glucose and ethanol metabolism. Together with the experimentally determinable yield coefficients (Y(X/S)) for the respective metabolic pathways, the resulting equation system is sufficiently determined. The superiority of the presented model over hitherto published ones is based on two essential novelities. (1) The model was developed on experimentally easily accessible parameters only. (2) For the modeling of aerobic ethanol formation, the substrate flow was split into two simultaneously operating (i.e., in parallel) metabolic pathways that exhibit different but constant energy-generating efficiencies (respiration and fermentation) and consequently different and constant biomass yields (Y(X/S)). The model allows the prediction of experimental data without parameter adaption in a biologically dubious manner.     

Metabolic pathways and biotechnological production of l-cysteine

l-Cysteine is an important amino acid both biologically and commercially. Although most amino acids are commercially produced by fermentation, cysteine is mainly produced by protein hydrolysis. However, synthetic or biotechnological products have been preferred in the market. Biotechnological processes for cysteine production, both enzymatic and fermentative processes, are discussed. Enzymatic process, the asymmetric hydrolysis of dl-2-amino-Δ²-thiazoline-4-carboxylic acid to l-cysteine, has been developed and industrialized. The l-cysteine biosynthetic pathways of Escherichia coli and Corynebacterium glutamicum, which are used in many amino acid production processes, are also described. These two bacteria have basically same l-cysteine biosynthetic pathways. l-Cysteine-degrading enzymes and l-cysteine-exporting proteins both in E. coli and C. glutamicum are also described. In conclusion, for the effective fermentative production of l-cysteine directly from glucose, the combination of enhancing biosynthetic activity, weakening the degradation pathway, and exploiting the export system seems to be effective.     

Fermentation metabolism of the unicellular cyanobacterium Cyanothece PCC 7822

The hydrogenase-catalyzed hydrogen production exhibited by the unicellular cyanobacterium Cyanothece 7822 during anoxic incubation in the dark is a result of the fermentative degradation of carbon reserves. Simultaneously with hydrogen production, evolution of carbon dioxide was detected, and excretion of ethanol, lactate, formate and acetate was demonstrated. The fermentation balance indicates that carbohydrates are fermented via a branched pathway, in which both the pentose phosphate pathway and glycolysis appear to be involved. It is proposed that the physiological function of hydrogen production is the introduction of protons as terminal electron acceptors. This removal of reducing equivalents might give rise to continuation of the pyruvate decarboxylation and consequently of the acetate formation, thereby increasing the efficiency of fermentative energy generation.     

Balancing oxidative protein folding: The influences of reducing pathways on disulfide bond formation

Oxidative protein folding is confined to few compartments, including the endoplasmic reticulum, the mitochondrial intermembrane space and the bacterial periplasm. Conversely, in compartments in which proteins are translated such as the cytosol, the mitochondrial matrix and the chloroplast stroma proteins are kept reduced by the thioredoxin and glutaredoxin systems that functionally overlap. The highly reducing NADPH pool thereby serves as electron donor that enables glutathione reductase and thioredoxin reductase to keep glutathione pools and thioredoxins in their reduced redox state, respectively. Notably, also compartments containing oxidizing machineries are linked to these reducing pathways. Reducing pathways aid in proofreading of disulfide bond formation by isomerization or they provide reducing equivalents for the reduction of disulfides prior to degradation. In addition, they contribute to the thiol-dependent regulation of protein activities, and they help to counteract oxidative stress. The existence of oxidizing and reducing pathways in the same compartment poses a potential problem as the cell has to avoid futile cycles of oxidation and subsequent reduction reactions. Thus, compartments that contain oxidizing machineries have developed sophisticated ways to spatiotemporally balance and regulate oxidation and reduction. In this review, we discuss oxidizing and reducing pathways in the endoplasmic reticulum, the periplasm and the mitochondrial intermembrane space and highlight the role of glutathione especially in the endoplasmic reticulum and the intermembrane space. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.     

Enzymology of Phanerochaete chrysosporium with respect to the degradation of recalcitrant compounds and xenobiotics

The archetypal white-rot fungus Phanerochaete chrysosporium has been shown to degrade a variety of persistent environmental pollutants. Many of the enzymes responsible for pollutant degradation, which are normally involved in the degradation of wood, are extracellular. Thus, P. chrysosporium is able to degrade toxic or insoluble chemicals more efficiently than other microorganisms. P. chrysosporium has a range of oxidative and reductive mechanisms and uses highly reactive, nonspecific redox mediators which increase the number of chemicals that can be effectively degraded. This review gives an overview of the enzymes that are believed to be important for bioremediation and briefly discusses the degradation of some individual chemicals. Received: 25 April 2000 / Received revision: 05 June 2000 / Accepted: 04 July 2000     

Detection of peroxyl and alkoxyl radicals produced by reaction of hydroperoxides with rat liver microsomal fractions.

E.s.r. spin trapping using the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) was used to detect peroxyl, alkoxyl and carbon-centred radicals produced by reaction of t-butyl hydroperoxide (tBuOOH) with rat liver microsomal fraction. The similarity of the hyperfine coupling constants of the peroxyl and alkoxyl radical adducts to those obtained previously with isolated enzymes suggests that these species are the tBuOO. and tBuO. adducts. The effects of metal-ion chelators, heat denaturation, enzyme inhibitors and reducing equivalents demonstrate that these species arise from reaction of tBuOOH with a haem enzyme such as cytochrome P-450 or cytochrome b5. In the absence of NADPH or NADH the previously undetected peroxyl radical adduct is the major species observed. In the presence of these reducing equivalents the alkoxyl and carbon-centred radical adducts predominate, which is in accord with product studies on similar systems. These results demonstrate that both reductive and oxidative decomposition of tBuOOH can occur in rat liver microsomal fraction with the reductive pathway favoured in the presence of NADH or NADPH.     

Propanol as an end product of threonine fermentation

Clostridium sp. strain 17cr1 was able to ferment l-threonine to propionate and propanol. Electrons arising in the oxidation of 2-oxobutyrate to propionyl-CoA were apparently used in reductive pathway leading to propanol formation. Part of the propionyl-CoA was used to form propionate in an ATP-forming pathway via a propionate kinase, so that the final ATP yield was 0.5 mol per mol of l-threonine metabolised. Other growth substrates were fermented mainly to acetate and butyrate, and the reductive formation of butyrate, from 2 mol of acetyl-CoA or from crotonate or 3-hydroxybutyrate, was the main route for recycling reduced electron carriers arising during oxidative pathways for most substrates.     

Acetate as a source of reducing equivalents in the reductive dechlorination of 2,5-dichlorobenzoate

Desulfomonile tiedjei is the key dechlorinating organism in a three-tiered bacterial consortium that grows on the methanogenic degradation of 3-chlorobenzoate. 2,5-Dichlorobenzoate, however, is only converted to 2-chlorobenzoate and is not a methanogenic substrate for the consortium. The dechlorinator uses hydrogen produced from benzoate by the benzoate degrading member of consortium as its source of reducing equivalents for the dechlorination reaction. Incubation of 3-chlorobenzoate grown consortium cells with 2,5-dichlorobenzoate resulted in the consumption of acetate concurrent with the formation of 2-chlorobenzoate indicating that acetate can serve as an alternative source of reducing equivalents for reductive dechlorination. This interpretation was confirmed by the finding that the formation of ¹⁴CO₂ from 2-¹⁴C-labeled acetate was stoichiometric. The addition of hydrogen to 2,5-dichlorobenzoate metabolizing cells resulted in (i) an 2.7-fold increase in the rate of dechlorination, and (ii) a drop in the amount of label recovered as CO₂+CH₄ from methyl ¹⁴C-labeled acetate, indicating that hydrogen was the preferred source of reducing equivalents for reductive dechlorination. Benzoate, an indirect source of H₂ in the consortium, also inhibited the oxidation of acetate, while glucose, methanol, and butyrate did not affect labeled gas production and therefore were not suitable electron donors. Concomittant to dechlorination of 2,5-dichlorobenzoate 3- and 4-methoxybenzoate were converted to 3- and 4-hydroxybenzoate respectively. These conversions stimulated the rate of dechlorination 2-fold. Demethylation of 4-methoxybenzoate stimulated, but demethylation of 3-methoxybenzoate inhibited the oxidation of benzoate during the dechlorination of 2,5-dichlorobenzoate, suggesting that these isomers are metabolized through different pathways. Experiments with benzoate, 3-chlorobenzoate and 2,5-dichlorobenzoate metabolizing cells amended with ¹⁴CO₂ showed that actively dechlorinating cells catalyzed an exchange reaction between CO₂ and acetate.     

Isolation and characterization of a bacterium possessing L-phenylalanine dehydrogenase activity

The new enzyme phenylalanine dehydrogenase [L-phenylalanine: NAD⁺-oxidoreductase (deaminating)] was detected in the crude extract of a strain of Brevibacterium spec. The bacterium was isolated from a soil sample by enrichment with phenylalanine. This strain was the only one containing phenylalanine dehydrogenase out of 173 tested strains, among them 22 of the genus Brevibacterium, 74 strains from soil samples and 77 strains from a culture collection belonging to several genera. The enzyme is involved in the degradation of phenylalanine and could be induced by addition of L-, D-, D,l-phenylalanine or L-histidine, the optimum inducer concentration of phenylalanine being 1%.The reaction mechanism of a reductive amination was confirmed by demonstrating the close coupling between NADH-consumption and phenylalanine production; ammonia could not be replaced by L-glutamate or L-aspartate as amino donor. The -keto acid of L-tyrosine was converted too, while the corresponding compound of histidine was inactive. The optimum pH value for reductive amination in the crude extract was 8.5 and for oxidative desamination 10.5.     

Sequential anaerobic/aerobic biodegradation of chloroethenes--aspects of field application

Because of a range of different industrial activities, sites contaminated with chloroethenes are a world-wide problem. Chloroethenes can be biodegraded by reductive dechlorination under anaerobic conditions as well as by oxidation under aerobic conditions. The tendency of chloroethenes to undergo reductive dechlorination decreases with a decreasing number of chlorine substituents, whereas with less chlorine substituents chloroethenes more easily undergo oxidative degradation. There is currently a growing interest in aerobic metabolic degradation of chloroethenes, which demonstrates advantages compared to cometabolic degradation pathways. Sequential anaerobic/aerobic biodegradation can overcome the disadvantages of reductive dechlorination and leads to complete mineralization of the chlorinated pollutants. This approach shows promise for site remediation in natural settings and in engineered systems.     

Methanogenic transformation of aromatic hydrocarbons and phenols in groundwater aquifers

Fermentative and methanogenic bacteria have been found repeatedly as important members of microbial flora in anoxic zones of the subsurface—in pristine as well as in contaminated groundwater aquifers. These bacteria, which together with obligate proton reducers form complex methanogenic communities, are significant as decomposers of organic matter under conditions of exogenous electron acceptor depletion. Their metabolic activity has been demonstrated in laboratory microcosms derived from aquifer material, and also in the subsurface in situ. Methanogenic communities have been shown to transform numerous organic pollutants, or even to completely degrade these compounds with the production of carbon dioxide and methane. Depending on the chemical structure of the pollutant, such a compound can be used as an electron donor and a carbon/energy source for fermentative microorganisms (which is typically the case with highly reduced compounds); alternatively, a highly oxidized pollutant can be used as a potential electron acceptor or electron sink. This review addresses fermentative/methanogenic degradation of chlorinated and nonchlorinated aromatic hydrocarbons and phenols by subsurface microorganisms; for comparison, it briefly relates also other types of anaerobic transformations (under sulfate‐reducing, iron‐reducing, and denitrifying conditions). Furthermore, it outlines transformation pathways, those that are proposed as well as those that are already partially proved, for aromatic hydrocarbons and phenols under fermentative/methanogenic conditions; finally, it discusses the relevance of these processes to bioremediation of contaminated groundwater aquifers.     

Cellular utilization of cytosolic NADPH in kidney and liver cells from rats fed a normal or a vitamin D-deficient diet

The amount of reducing equivalents from NADPH generated by glucose 6-phosphate dehydrogenase activity (G6PD) used in mixed function oxidation (pathway I) or in reductive biosynthesis (pathway II) has been determined by cytochemical methods and microdensitometry in cells from the pars recta (PR) and distal convoluted tubule (DCT) of the kidney and from centrilobular (CL) and periportal (PP) hepatocytes from rats fed a normal or a vitamin D-deficient diet. In the kidney, pathway I activity was similar to that of pathway II in PR, whereas in DCT pathway II was markedly predominant. Feeding a vitamin D-deficient diet resulted in an increase in the total amount of reducing equivalents in PR and DCT. This increase was due to a rise in pathway I activity in the PR, whereas in the DCT the increase resulted from a stimulation of pathway II activity. Pathway I activity in PR was inversely correlated with plasma calcium, and was significantly decreased when calcium (1 mM) was added in vitro. In the liver the total amount of reducing equivalents generated by G6PD and both hydrogen pathways, was higher in CL than in PP hepatocytes. In CL cells, a vitamin D-deficient diet induced a significant increase in both NADPH pathways. Furthermore, in these cells pathway I activity was inversely related to plasma calcium and was significantly lowered when 1 mM calcium was added in vitro. It is concluded that vitamin D status and calcium influence the production and utilization of cytosolic reducing equivalents both in kidney and liver.     

The anaerobic degradation of l-serine and l-threonine in enterobacteria: networks of pathways and regulatory signals

The mechanisms controlling the biosynthesis and degradation of l-serine and l-threonine are remarkably complex. Their metabolism forms a network of pathways linking several amino acids, central primary metabolites such as pyruvate, oxaloacetate and 3-phosphoglycerate, and C₁ metabolism. Studies on the degradation of these amino acids in Escherichia coli have revealed the involvement of fascinating enzymes that utilise quite diverse catalytic mechanisms. Moreover, it is emerging that both environmental and metabolic signals have a major impact in controlling enzyme synthesis. This is exemplified by the anaerobically regulated tdc operon, which encodes a metabolic pathway for the degradation of serine and threonine. Studies on this pathway are beginning to provide insights into how an organism adapts its genetic makeup to meet the physiological demands of the cell. Received: 30 August 1998 / Accepted: 9 October 1998     

Elucidating Turnover Pathways of Bioactive Small Molecules by Isotopomer Analysis: The Persistent Organic Pollutant DDT

The persistent organic pollutant DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) is still indispensable in the fight against malaria, although DDT and related compounds pose toxicological hazards. Technical DDT contains the dichloro congener DDD (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethyl]benzene) as by-product, but DDD is also formed by reductive degradation of DDT in the environment. To differentiate between DDD formation pathways, we applied deuterium NMR spectroscopy to measure intramolecular deuterium distributions (²H isotopomer abundances) of DDT and DDD. DDD formed in the technical DDT synthesis was strongly deuterium-enriched at one intramolecular position, which we traced back to ²H/¹H fractionation of a chlorination step in the technical synthesis. In contrast, DDD formed by reductive degradation was strongly depleted at the same position, which was due to the incorporation of ²H-depleted hydride equivalents during reductive degradation. Thus, intramolecular isotope distributions give mechanistic information on reaction pathways, and explain a puzzling difference in the whole-molecule ²H/¹H ratio between DDT and DDD. In general, our results highlight that intramolecular isotope distributions are essential to interpret whole-molecule isotope ratios. Intramolecular isotope information allows distinguishing pathways of DDD formation, which is important to identify polluters or to assess DDT turnover in the environment. Because intramolecular isotope data directly reflect isotope fractionation of individual chemical reactions, they are broadly applicable to elucidate transformation pathways of small bioactive molecules in chemistry, physiology and environmental science.     

Evidence of a new metabolic pathway of 5-fluorouracil in Escherichia coli from in vivo 19F-NMR spectroscopy

Two distinct metabolic pathways of 5-fluorouracil are proposed in Escherichia coli. The first metabolic pathway is a reductive degradation with the formation of dihydrofluorouracil as the first metabolite. The second metabolic pathway is shown to be a hydroxylating degradation, possibly with the formation of 5-hydro-6-hydroxy-5-fluorouracil as the first metabolite. The metabolites of both pathways undergo subsequent hydrolytic degradation with fluoride ion as the common final product. The chemical structures of these metabolites were partially identified by 19F-NMR. The results show a close resemblance between these two metabolic pathways with in vivo pyrimidine biodegradation. The reductive degradation has been proposed by several laboratories, whereas the hydroxy degradation has not been reported before. Both the reductive and hydroxy pathways are demonstrated in this report, to be independent reactions.     

The role of phosphatidylcholine and choline metabolites to cell proliferation and survival

The reorganization of metabolic pathways in cancer facilitates the flux of carbon and reducing equivalents into anabolic pathways at the expense of oxidative phosphorylation. This provides rapidly dividing cells with the necessary precursors for membrane, protein and nucleic acid synthesis. A fundamental metabolic perturbation in cancer is the enhanced synthesis of fatty acids by channeling glucose and/or glutamine into cytosolic acetyl-CoA and upregulation of key biosynthetic genes. This lipogenic phenotype also extends to the production of complex lipids involved in membrane synthesis and lipid-based signaling. Cancer cells display sensitivity to ablation of fatty acid synthesis possibly as a result of diminished capacity to synthesize complex lipids involved in signaling or growth pathways. Evidence has accrued that phosphatidylcholine, the major phospholipid component of eukaryotic membranes, as well as choline metabolites derived from its synthesis and catabolism, contribute to both proliferative growth and programmed cell death. This review will detail our current understanding of how coordinated changes in substrate availability, gene expression and enzyme activity lead to altered phosphatidylcholine synthesis in cancer, and how these changes contribute directly or indirectly to malignant growth. Conversely, apoptosis targets key steps in phosphatidylcholine synthesis and degradation that are linked to disruption of cell cycle regulation, reinforcing the central role that phosphatidylcholine and its metabolites in determining cell fate.     

Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle

Cellular metabolic demands change throughout the cell cycle. Nevertheless, a characterization of how metabolic fluxes adapt to the changing demands throughout the cell cycle is lacking. Here, we developed a temporal‐fluxomics approach to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle. This is achieved by combining pulse‐chase LC‐MS‐based isotope tracing in synchronized cell populations with computational deconvolution and metabolic flux modeling. We find that TCA cycle fluxes are rewired as cells progress through the cell cycle with complementary oscillations of glucose versus glutamine‐derived fluxes: Oxidation of glucose‐derived flux peaks in late G1 phase, while oxidative and reductive glutamine metabolism dominates S phase. These complementary flux oscillations maintain a constant production rate of reducing equivalents and oxidative phosphorylation flux throughout the cell cycle. The shift from glucose to glutamine oxidation in S phase plays an important role in cell cycle progression and cell proliferation.     

Degradation of Sulphonated Azo Dye Red HE7B by Bacillus sp. and Elucidation of Degradative Pathways

Bacteria capable of degrading the sulfonated azo dye Red HE7B were isolated from textile mill effluent contaminated soil. The most efficient isolate was identified as Bacillus sp. Azo1 and the isolate could successfully decolorize up to 89 % of the dye. The decolorized cultural extract analyzed by HPLC confirmed degradation. Enzymatic analysis showed twofold and fourfold increase in the activity of azoreductase and laccase enzymes, respectively, indicating involvement of both reductive and oxidative enzymes in biodegradation of Red HE7B. Degraded products which were identified by GC/MS analysis included various metabolites like 8-nitroso 1-naphthol, 2-diazonium naphthalene. Mono azo dye intermediate was initially generated from the parent molecule. This mono azo dye was further degraded by the organism, into additional products, depending on the site of cleavage of R–N=N–R molecule. Based on the degradation products identified, three different pathways have been proposed. The mechanism of degradation in two of these pathways is different from that of the previously reported pathway for azo dye degradation. This is the first report of a microbial isolate following multiple pathways for azo dye degradation. Azo dye Red HE7B was observed to be phytotoxic, leading to decrease in root development, shoot length and seedling fresh weight. However, after biotreatment the resulting degradation products were non-phytotoxic.