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Metabolic Fluxes (metabolic + flux)
Terms modified by Metabolic Fluxes Selected AbstractsError propagation from prime variables into specific rates and metabolic fluxes for mammalian cells in perfusion cultureBIOTECHNOLOGY PROGRESS, Issue 4 2009Chetan T. Goudar Abstract Error propagation from prime variables into specific rates and metabolic fluxes was quantified for high-concentration CHO cell perfusion cultivation. Prime variable errors were first determined from repeated measurements and ranged from 4.8 to 12.2%. Errors in nutrient uptake and metabolite/product formation rates for 5,15% error in prime variables ranged from 8,22%. The specific growth rate, however, was characterized by higher uncertainty as 15% errors in the bioreactor and harvest cell concentration resulted in 37.8% error. Metabolic fluxes were estimated for 12 experimental conditions, each of 10 day duration, during 120-day perfusion cultivation and were used to determine error propagation from specific rates into metabolic fluxes. Errors of the greater metabolic fluxes (those related to glycolysis, lactate production, TCA cycle and oxidative phosphorylation) were similar in magnitude to those of the related greater specific rates (glucose, lactate, oxygen and CO2 rates) and were insensitive to errors of the lesser specific rates (amino acid catabolism and biosynthesis rates). Errors of the lesser metabolic fluxes (those related to amino acid metabolism), however, were extremely sensitive to errors of the greater specific rates to the extent that they were no longer representative of cellular metabolism and were much less affected by errors in the lesser specific rates. We show that the relationship between specific rate and metabolic flux error could be accurately described by normalized sensitivity coefficients, which were readily calculated once metabolic fluxes were estimated. Their ease of calculation, along with their ability to accurately describe the specific rate-metabolic flux error relationship, makes them a necessary component of metabolic flux analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] PERSPECTIVE: EVOLUTION AND DETECTION OF GENETIC ROBUSTNESSEVOLUTION, Issue 9 2003J. Arjan G. M. de Visser Abstract Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding, metabolic flux, physiological homeostasis, development, and even organismal fitness. The mechanisms underlying robustness are diverse, ranging from thermodynamic stability at the RNA and protein level to behavior at the organismal level. Phenotypes can be robust either against heritable perturbations (e.g., mutations) or nonheritable perturbations (e.g., the weather). Here we primarily focus on the first kind of robustness,genetic robustness,and survey three growing avenues of research: (1) measuring genetic robustness in nature and in the laboratory; (2) understanding the evolution of genetic robustness; and (3) exploring the implications of genetic robustness for future evolution. [source] Are UV-induced nonculturable Escherichia coli K-12 cells alive or dead?FEBS JOURNAL, Issue 12 2003Andrea Villarino Cells that have lost the ability to grow in culture could be defined operationally as either alive or dead depending on the method used to determine cell viability. As a consequence, the interpretation of the state of ,nonculturable' cells is often ambiguous. Escherichia coli K12 cells inactivated by UV-irradiation with a low (UV1) and a high (UV2) dose were used as a model of nonculturable cells. Cells inactivated by the UV1 dose lost ,culturability' but they were not lysed and maintained the capacity to respond to nutrient addition by protein synthesis and cell wall synthesis. The cells also retained both a high level of glucose transport and the capacity for metabolizing glucose. Moreover, during glucose incorporation, UV1-treated cells showed the capacity to respond to aeration conditions modifying their metabolic flux through the Embden,Meyerhof and pentose-phosphate pathways. However, nonculturable cells obtained by irradiation with the high UV2 dose showed several levels of metabolic imbalance and retained only residual metabolic activities. Nonculturable cells obtained by irradiation with UV1 and UV2 doses were diagnosed as active and inactive (dying) cells, respectively. [source] Two phenotypically compensating isocitrate dehydrogenases in Ralstonia eutrophaFEMS MICROBIOLOGY LETTERS, Issue 1 2003Zheng-Xiang Wang Abstract The tricarboxylic acid (TCA) cycle enzyme isocitrate dehydrogenase (IDH) and the glyoxylate bypass enzyme isocitrate lyase are involved in catabolism of isocitrate and play a key role in controlling the metabolic flux between the TCA cycle and the glyoxylate shunt. Two IDH genes icd1 and icd2 of Ralstonia eutropha HF39, encoding isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2), were identified and characterized. Icd1 was functionally expressed in Escherichia coli, whereas icd2 was expressed in E. coli but no activity was obtained. Interposon-mutants of icd1 (HF39,icd1) and icd2 (HF39,icd2) of R. eutropha HF39 were constructed and their phenotypes were investigated. HF39,icd1 retained 43% of IDH activity, which was not induced by acetate, and HF39,icd2 expressed 74% of acetate-induced IDH activity. Both HF39,icd1and HF39,icd2 kept the same growth rate on acetate as the wild-type. These data suggested that IDH1 is induced by acetate. The interposon-mutants HF39,icd1 and HF39,icd2 accumulated the same amount of poly(3-hydroxybutyric acid) as the wild-type. [source] Mechanistic understanding of the fermentative L -glutamic acid overproduction by Corynebacterium glutamicum through combined metabolic flux profiling and transmembrane transport characteristicsJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 12 2004Theodora Tryfona Abstract Since the 1950s when Micrococcus glutamicus later renamed Corynebacterium glutamicum was discovered, the production of amino acids by fermentative methods has become an important aspect of industrial microbiology. Numerous studies to understand and improve the metabolic conditions leading to amino acid overproduction have been carried out. Most amino acids are currently produced by use of mutants that contain combinations of auxotrophic and regulatory mutations. L -Glutamic acid is the amino acid produced in the greatest quantities (106 tonnes per year) and Corynebacteria are central to its industrial production. However, further improvements to strain performance are difficult to obtain by empirical optimization and a more rational approach is required. The use of metabolic flux analysis provides valuable information regarding bottlenecks in the formation of desired metabolites. Such techniques have found application in elucidating flux control, provided insight into metabolic network function and developed methods to amplify or redirect fluxes in engineered bioprocesses. Hence, branch points in biosynthesis, precursor supply in fuelling reactions and export of metabolites can be manipulated, resulting in high glutamic acid overproduction by Corynebacterium glutamicum fermentations. In this review, in addition to reviewing the state of play in metabolic flux analysis for glutamate overproduction, the metabolic pathways involved in the production of L -glutamic acid, the mechanisms mediating its efflux and secretion as well as their manipulation to achieve higher glutamate production, are discussed. The link between metabolic flux and transmembrane transport of glutamic acid are also considered. Copyright © 2004 Society of Chemical Industry [source] Effects of exogenous glucose on carotenoid accumulation in tomato leavesPHYSIOLOGIA PLANTARUM, Issue 2 2008Anne Mortain-Bertrand To investigate the effect of carbohydrate on carotenoid accumulation in leaves, excised plants of tomato (Lycopersicum esculentum var. cerasiformae, wva 106) were supplied with glucose through the transpiration stream for 48 h. We report here that sugar accumulation in leaves led to a decrease of carotenoid content, which was related to the reduction of Chl. The decrease in carotenoid amount correlated with a sugar-induced repression of genes encoding enzymes of the carotenoid and of the Rohmer pathways. The lower 1-deoxy- d -xylulose-5-phosphate synthase transcript level probably leads to a decreased metabolic flux through the methylerythritol pathway and subsequently to a lower amount of substrate available for plastidic isoprenoid synthesis. Differences between responses of young (sink) and mature (source) leaves to carbohydrate accumulation are discussed. [source] Ageing in Plants: Conserved Strategies and Novel PathwaysPLANT BIOLOGY, Issue 5 2003H.-C. Jing Abstract: Ageing increases chaos and entropy and ultimately leads to the death of living organisms. Nevertheless, single gene mutations substantially alter lifespan, revealing that ageing is subject to genetic control. In higher plants, ageing is most obviously manifested by the senescence of leaves, and recent molecular genetic studies, in particular the isolation of Arabidopsis mutants with altered leaf senescence, have greatly advanced our understanding of ageing regulation in plants. This paper provides an overview of the identified genes and their respective molecular pathways. Hormones, metabolic flux, reactive oxygen species and protein degradation are prominent strategies employed by plants to control leaf senescence. Plants predominantly use similar ageing-regulating strategies as yeast and animals but have evolved different molecular pathways. The senescence window concept is proposed to describe the age-dependent actions of the regulatory genes. It is concluded that the similarities and differences in ageing between plants and other organisms are deeply rooted in the evolution of ageing and we hope to stimulate discussion and research in the fascinating field of leaf senescence. [source] Tobacco Mg protoporphyrin IX methyltransferase is involved in inverse activation of Mg porphyrin and protoheme synthesisTHE PLANT JOURNAL, Issue 2 2005Ali E. Alawady Summary Protoporphyrin, a metabolic intermediate of tetrapyrrole biosynthesis, is metabolized by Mg chelatase and ferrochelatase and is directed into the Mg-branch for chlorophyll synthesis and in the Fe-branch for protoheme synthesis respectively. Regulation of the enzyme activities at the beginning of this branchpoint ensures accurate partition of protoporphyrin, but is still not entirely understood. Transgenic tobacco plants were generated that express antisense or sense RNA for inhibited and excessive expression of Mg protoporphyrin methyltransferase (MgPMT) respectively. This enzyme accepts Mg protoporphyrin from Mg chelatase and catalyses the transfer of a methyl group to the carboxyl group of the C13-propionate side chain. Low MgPMT activity is correlated with reduced Mg chelatase activity and a low synthesis rate of 5-aminolevulinate, but with enhanced ferrochelatase activity. In contrast, high MgPMT activity leads to inverse activity profiles: high activities of Mg chelatase and for 5-aminolevulinate synthesis, but reduced activity of ferrochelatase, indicating a direct influence of MgPMT in combination with Mg chelatase on the metabolic flux of ALA and the distribution of protoporphyrin into the branched pathway. The modified enzyme activities in tetrapyrrole biosynthesis in the transgenic plants can be explained with changes of certain corresponding mRNA contents: increased 5-aminolevulinate synthesis and Mg chelatase activity correlate with enhanced transcript levels of the HemA, Gsa, and CHLH gene encoding glutamyl-tRNA reductase, glutamate-1-semialdehyde aminotransferase and a Mg chelatase subunit respectively. It is proposed that reduced and increased MgPMT activity in chloroplasts is communicated to the cytoplasm for modulating transcriptional activities of regulatory enzymes of the pathway. [source] Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated proteinBIOTECHNOLOGY PROGRESS, Issue 1 2010Afshan S. Shaikh Abstract Microbial production of many commercially important secondary metabolites occurs during stationary phase, and methods to measure metabolic flux during this growth phase would be valuable. Metabolic flux analysis is often based on isotopomer information from proteinogenic amino acids. As such, flux analysis primarily reflects the metabolism pertinent to the growth phase during which most proteins are synthesized. To investigate central metabolism and amino acids synthesis activity during stationary phase, addition of fully 13C-labeled glucose followed by induction of green fluorescent protein (GFP) expression during stationary phase was used. Our results indicate that Escherichia coli was able to produce new proteins (i.e., GFP) in the stationary phase, and the amino acids in GFP were mostly from degraded proteins synthesized during the exponential growth phase. Among amino acid biosynthetic pathways, only those for serine, alanine, glutamate/glutamine, and aspartate/asparagine had significant activity during the stationary phase. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] A novel three-stage light irradiation strategy in the submerged fermentation of medicinal Mushroom Ganoderma lucidum for the efficient production of ganoderic acid and Ganoderma polysaccharidesBIOTECHNOLOGY PROGRESS, Issue 6 2008Wei Zhang Abstract A novel three-stage light irradiation strategy in the submerged fermentation of medicinal mushroom Ganoderma lucidum for the efficient production of bioactive metabolites ganoderic acid (GA) and Ganoderma polysaccharides was developed. Significance of light quality, i.e., blue light (390,500 nm, ,max = 470 nm), red light (560,700 nm, ,max = 625 nm), and white light (400,740 nm, ,max = 550 nm), was studied at first. Interestingly, there was a gradual decrease trend of GA content after the culture of day 2 when the maximal GA content was obtained, while GA content decreased slowly under white light irradiation after day 6. The dark environment was favorable to the specific GA biosynthesis (i.e., GA content) before day 6, and after that the optimum was white light irradiation. A relatively lower irradiation density of white light (i.e., 0.94 and 2.82 W/m2) was beneficial for the specific GA biosynthesis before day 6, while GA content was higher under higher irradiation density of white light (i.e., 4.70 and 9.40 W/m2) at the later-stage of cultivation. 4.70 W/m2 white light irradiation culture was the best from the viewpoint of GA accumulation. Therefore, a two-stage light irradiation strategy by combing the first 2 days dark culture with the following 4.70 W/m2 white light irradiation culture was developed. The highest GA production in the two-stage culture was 276.0 ± 12.5 mg/L, which was increased by 19% compared to 4.70 W/m2 white light irradiation culture (i.e., 232.4 ± 15.8 mg/L) and by 178% compared to the dark culture (i.e., 99.4 ± 1.0 mg/L). Although there still existed a gradual decrease trend of GA content after day 2 when the maximal GA content was obtained in the two-stage culture. Following three-stage light irradiation strategy was further demonstrated in order to turn around the sharp decrease of GA content after day 2. The first-stage was the 2-day dark culture; the second-stage was the following six-day 0.94 W/m2 white light irradiation culture, and the third-stage was 4.70 W/m2 white light irradiation culture until the end of fermentation. During the three-stage culture of G. lucidum, the gradual decrease trend of GA content after day 2 was turned around, which suggested that 0.94 W/m2 white light irradiation was beneficial for the metabolic flux towards the GA biosynthesis. The maximal GA content of 3.1 ± 0.1 mg/100 mg DW was obtained, which was higher by 41% compared to the two-stage culture. The maximal GA production (i.e., 466.3 ± 24.1 mg/L) and productivity (i.e., 38.9 mg/L per day) in the three-stage culture were 69 and 101% higher than those obtained in the two-stage culture. This is the first report investigating the significance of light irradiation on the medicinal mushroom submerged fermentation. Such work is very helpful to other mushroom fermentations for useful metabolite production. [source] Developmental control of inositol phosphate biosynthesis is altered in the brain of both curly and phenotypically normal straight tail mutant mice,BIRTH DEFECTS RESEARCH, Issue 10 2009Hana Dawood Ali Alebous Abstract BACKGROUND: Altered levels of inositol phosphate in the central nervous system (CNS) are hypothesized to produce distorted brain signaling and lead to numerous neurologic maladies. Little is known of mechanisms controlling the complex metabolic flux of inositol phosphate. Less is known of controls that regulate inositol-phosphate biosynthesis in the mammalian brain. The expression of 1L-myo-inositol,1 phosphate synthase (MIP), the only enzyme known to synthesize inositol phosphate, was studied in the brain of normal (CBA) and curly tail (CT) mutant mice. The CT strain exhibits a neural tube defect, spina bifida, responsive to inositol supplementation, but not to folic acid treatment. METHODS: Utilizing enzyme assays to determine the specific activity of MIP, Western blotting to detect expression, gas chromatography/mass spectrometry to measure inositol concentration, and statistical analyses to evaluate quantitative data, MIP expression was analyzed in newborn, young, and adult brains of CBA and CT (curly tail [ct-CT] and straight tail [st-CT]) mutant mice. RESULTS: Data analyses suggest there is a significant difference in MIP activity in the brain of CBA mice as compared to that of CT mutant mice and that temporal and spatial control of MIP expression and inositol concentrations are altered in the brain of both the ct-CT and phenotypically normal st-CT mutant. Moreover, two differentially expressed forms of MIP were identified in the adult mouse brain. CONCLUSIONS: These findings implicate a role for MIP in the maturation of the CNS and evoke a hypothesis regarding the regulation of inositol phosphate biosynthesis in brain development. Birth Defects Research (Part A), 2009. © 2009 Wiley-Liss, Inc. [source] The role of metabolic memory in the ATP paradox and energy homeostasisFEBS JOURNAL, Issue 21 2008Juan C. Aledo In yeast, a sudden transition from glucose limitation to glucose excess leads to a new steady state at increased metabolic fluxes with a sustained decrease in the ATP concentration. Although this behaviour has been rationalized as an adaptive metabolic strategy, the mechanism behind it remains unclear. Nevertheless, it is thought that, on glucose addition, a metabolite derived from glycolysis may up-regulate ATP-consuming reactions. The adenine nucleotides themselves have been ruled out as the signals that mediate this regulation. This is mainly because, in that case, it would be expected that the new steady state at increased fluxes would be accompanied by an increased stationary ATP concentration. In this study, we present a core model consisting of a monocyclic interconvertible enzyme system. Using a supply,demand approach, we demonstrate that this system can account for the empirical observations without involving metabolites other than the adenine nucleotides as effectors. Moreover, memory is an emerging property of such a system, which may allow the cell to sense both the current energy status and the direction of the changes. [source] 13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiaeFEMS YEAST RESEARCH, Issue 4 2007Roeland Costenoble Abstract This study addresses the question of whether observable changes in fluxes in the primary carbon metabolism of Saccharomyces cerevisiae occur between the different phases of the cell division cycle. To detect such changes by metabolic flux analysis, a 13C-labeling experiment was performed with a fed-batch culture inoculated with a partially synchronized cell population obtained through centrifugal elutriation. Such a culture exhibits dynamic changes in the fractions of cells in different cell cycle phases over time. The mass isotopomer distributions of free intracellular metabolites in central carbon metabolism were measured by liquid chromatography,mass spectrometry. For four time points during the culture, these distributions were used to obtain the best estimates for the metabolic fluxes. The obtained flux fits suggested that the optimally fitted split ratio for the pentose phosphate pathway changed by almost a factor of 2 up and down around a value of 0.27 during the experiment. Statistical analysis revealed that some of the fitted flux distributions for different time points were significantly different from each other, indicating that cell cycle-dependent variations in cytosolic metabolic fluxes indeed occurred. [source] Effects of a hexokinase II deletion on the dynamics of glycolysis in continuous cultures of Saccharomyces cerevisiaeFEMS YEAST RESEARCH, Issue 2 2002Jasper A. Diderich Abstract In glucose-limited aerobic chemostat cultures of a wild-type Saccharomyces cerevisiae and a derived hxk2 null strain, metabolic fluxes were identical. However, the concentrations of intracellular metabolites, especially fructose 1,6-bisphosphate, and hexose-phosphorylating activities differed. Interestingly, the hxk2 null strain showed a higher maximal growth rate and higher Crabtree threshold dilution rate, revealing a higher oxidative capacity for this strain. After a pulse of glucose, aerobic glucose-limited cultures of wild-type S. cerevisiae displayed an overshoot in the intracellular concentrations of glucose 6-phosphate, fructose 6-phosphate, and fructose 1,6-bisphosphate before a new steady state was established, in contrast to the hxk2 null strain which reached a new steady state without overshoot of these metabolites. At low dilution rates the overshoot of intracellular metabolites in the wild-type strain coincided with the immediate production of ethanol after the glucose pulse. In contrast, in the hxk2 null strain the production of ethanol started gradually. However, in spite of the initial differences in ethanol production and dynamic behaviour of the intracellular metabolites, the steady-state fluxes after transition from glucose limitation to glucose excess were not significantly different in the wild-type strain and the hxk2 null strain at any dilution rate. [source] Profiling human gut bacterial metabolism and its kinetics using [U- 13C]glucose and NMRNMR IN BIOMEDICINE, Issue 1 2010Albert A. de Graaf Abstract This study introduces a stable-isotope metabolic approach employing [U- 13C]glucose that, as a novelty, allows selective profiling of the human intestinal microbial metabolic products of carbohydrate food components, as well as the measurement of the kinetics of their formation pathways, in a single experiment. A well-established, validated in vitro model of human intestinal fermentation was inoculated with standardized gastrointestinal microbiota from volunteers. After culture stabilization, [U- 13C]glucose was added as an isotopically labeled metabolic precursor. System lumen and dialysate samples were taken at regular intervals. Metabolite concentrations and isotopic labeling were determined by NMR, GC, and enzymatic methods. The main microbial metabolites were lactate, acetate, butyrate, formate, ethanol, and glycerol. They together accounted for a 13C recovery rate as high as 91.2%. Using an NMR chemical shift prediction approach, several minor products that showed 13C incorporation were identified as organic acids, amino acids, and various alcohols. Using computer modeling of the 12C contents and 13C labeling kinetics, the metabolic fluxes in the gut microbial pathways for synthesis of lactate, formate, acetate, and butyrate were determined separately for glucose and unlabeled background substrates. This novel approach enables the study of the modulation of human intestinal function by single nutrients, providing a new rational basis for achieving control of the short-chain fatty acids profile by manipulating substrate and microbiota composition in a purposeful manner. Copyright © 2009 John Wiley & Sons, Ltd. [source] Altered metabolic fluxes result from shifts in metabolite levels in sucrose phosphorylase-expressing potato tubersPLANT CELL & ENVIRONMENT, Issue 10 2002A. R. Fernie Abstract As reported in a previous paper (Plant, Cell and Environment 24, 357,365, 2001), introduction of sucrose phosphorylase into the cytosol of potato results in increased respiration, an inhibition of starch accumulation and decreased tuber yield. Herein a more detailed investigation into the effect of sucrose phosphorylase expression on tuber metabolism, in order to understand why storage and growth are impaired is described. (1) Although the activity of the introduced sucrose phosphorylase was low and accounted for less than 10% of that of sucrose synthase its expression led to a decrease in the activities of enzymes of starch synthesis relative to enzymes of glycolysis and relative to total amylolytic activity. (2) Incubation of tuber discs in [14C]glucose revealed that the transformants display a two-fold increase of the unidirectional rate of sucrose breakdown. However this was largely compensated by a large stimulation of sucrose re-synthesis and therefore the net rate of sucrose breakdown was not greatly affected. Despite this fact major shifts in tuber metabolism, including depletion of sucrose to very low levels, higher rates of glycolysis, and larger pools of amino acids were observed in these lines. (3) Expression of sucrose phosphorylase led to a decrease of the cellular ATP/ADP ratio and energy charge in intact growing tubers. It was estimated that at least 30% of the ATP formed during respiration is consumed as a result of the large acceleration of the cycle of sucrose breakdown and re-synthesis in the transformants. Although the absolute rate of starch synthesis in short-term labelling experiments with discs rose, starch synthesis fell relative to other fluxes including respiration, and the overall starch content of the tubers was lower than in wild-type tubers. (4) External supply of amino acids to replace sucrose as an osmoticum led to a feed-back inhibition of glycolysis, but did not restore allocation to starch. (5) However, an external supply of the non-metabolizable sucrose analogue palatinose , but not sucrose itself , stimulated flux to starch in the transformants. (6) The results indicate that the impaired performance of sucrose phosphorylase-expressing tubers is attributable to decreased levels of sucrose and increased energy consumption during sucrose futile cycling, and imply that sucrose degradation via sucrose synthase is important to maintain a relatively large sucrose pool and to minimize the ATP consumption required for normal metabolic function in the wild type. [source] Regulation of lactate production at the onset of ischaemia is independent of mitochondrial NADH/NAD+: insights from in silico studiesTHE JOURNAL OF PHYSIOLOGY, Issue 3 2005Lufang Zhou Ischaemia decreases mitochondrial NADH oxidation, activates glycolysis, increases the NADH/NAD+ ratio, and causes lactate production. The mechanisms that regulate anaerobic glycolysis and the NADH/NAD+ ratio during ischaemia are unclear. Although continuous measurements of metabolic fluxes and NADH/NAD+ in cytosol and mitochondria are not possible in vivo with current experimental techniques, computational models can be used to predict these variables by simulations with in silico experiments. Such predictions were obtained using a mathematical model of cellular metabolism in perfused myocardium. This model, which distinguishes cytosolic and mitochondrial domains, incorporates key metabolic species and processes associated with energy transfer. Simulation of metabolic responses to mild, moderate and severe ischaemia in large animals showed that mitochondrial NADH/NAD+ was rapidly reset to higher values in proportion to the reduced O2 delivery and myocardial oxygen consumption . Cytosolic NADH/NAD+, however, showed a biphasic response, with a sharp initial increase that was due to activation of glycogen breakdown and glycolysis, and corresponded with lactate production. Whereas the rate of glycolysis and the malate,aspartate shuttle had a significant effect on the cytosolic NADH/NAD+, their effects on the mitochondrial NADH/NAD+ were minimal. In summary, model simulations of the metabolic response to ischaemia showed that mitochondrial NADH/NAD+ is primarily determined by O2 consumption, while cytosolic NADH/NAD+ is largely a function of glycolytic flux during the initial phase, and is determined by mitochondrial NADH/NAD+ and the malate,aspartate shuttle during the steady state. [source] Plastidic metabolite transporters and their physiological functions in the inducible crassulacean acid metabolism plant Mesembryanthemum crystallinumTHE PLANT JOURNAL, Issue 3 2000Rainer E. Häusler Summary The inducible crassulacean acid metabolism (CAM) plant Mesembryanthemum crystallinum accumulates malic acid during the night and converts it to starch during the day via a pathway that, because it is located in different subcellular compartments, depends on specific metabolite transport across membranes. The chloroplast glucose transporter (pGlcT) and three members of the phosphate translocator (PT) family were isolated. After induction of CAM, transcript amounts of the phosphoenolpyruvate (PEP) phosphate translocator (PPT) and the glucose-6-phosphate (Glc6P) phosphate translocator (GPT) genes were increased drastically, while triose phosphate (TP) phosphate translocator (TPT) and the pGlcT transcripts remained unchanged. PPT- and GPT-specific transcripts and transporter activities exhibited a pronounced diurnal variation, displaying the highest amplitude in the light. pGlcT transcripts were elevated towards the end of the light period and at the beginning of the dark period. These findings, combined with diurnal variations of enzyme activities and metabolite contents, helped to elucidate the roles of the PPT, GPT, TPT and pGlcT in CAM. The main function of the PPT is the daytime export from the stroma of PEP generated by pyruvate orthophosphate:dikinase (PPDK). The increased transport activity of GPT in the light suggests a higher requirement for Glc6P import for starch synthesis rather than starch mobilization. Most likely, Glc6P rather than 3-phosphoglycerate or triose phosphates is the main substrate for daytime starch biosynthesis in M. crystallinum plants in which CAM has been induced (CAM-induced), similar to non-green plastids. In the dark, starch is mobilized both phosphorylytically and amylolytically and the products are exported by the GPT, TPT and pGlcT. The transport activities of all three phosphate translocators and the transcript amounts of the pGlcT adapt to changing transport requirements in order to maintain high metabolic fluxes during the diurnal CAM cycle. [source] Metabolic systems maintain stable non-equilibrium via thermodynamic bufferingBIOESSAYS, Issue 10 2009Abir U. Igamberdiev Abstract Here, we analyze how the set of nucleotides in the cell is equilibrated and how this generates simple rules that help the cell to organize itself via maintenance of a stable non-equilibrium state. A major mechanism operating to achieve this state is thermodynamic buffering via high activities of equilibrating enzymes such as adenylate kinase. Under stable non-equilibrium, the ratios of free and Mg-bound adenylates, Mg2+ and membrane potentials are interdependent and can be computed. The adenylate status is balanced with the levels of reduced and oxidized pyridine nucleotides through regulated uncoupling of the pyridine nucleotide pool from ATP production in mitochondria, and through oxidation of substrates non-coupled to NAD+ reduction in peroxisomes. The set of adenylates and pyridine nucleotides constitutes a generalized cell energy status and determines rates of major metabolic fluxes. As the result, fluxes of energy and information become organized spatially and temporally, providing conditions for self-maintenance of metabolism. [source] Cumulative bondomers: A new concept in flux analysis from 2D [13C,1H] COSY NMR dataBIOTECHNOLOGY & BIOENGINEERING, Issue 7 2002Wouter A. van Winden Abstract A well-established way of determining metabolic fluxes is to measure 2D [13C,1H] COSY NMR spectra of components of biomass grown on uniformly 13C-labeled carbon sources. When using the entire set of measured data to simultaneously determine all fluxes in a proposed metabolic network model, the 13C-labeling distribution in all measured compounds has to be simulated. This requires very large sets of isotopomer or cumomer balances. This article introduces the new concept of bondomers; entities that only vary in the numbers and positions of C,C bonds that have remained intact since the medium substrate molecule entered the metabolism. Bondomers are shown to have many analogies to isotopomers. One of these is that bondomers can be transformed to cumulative bondomers, just like isotopomers can be transformed to cumomers. Similarly to cumomers, cumulative bondomers allow an analytical solution of the entire set of balances describing a metabolic network. The main difference is that cumulative bondomer models are considerably smaller than corresponding cumomer models. This saves computational time, allows easier identifiability analysis, and yields new insights in the information content of 2D [13C,1H] COSY NMR data. We illustrate the theoretical concepts by means of a realistic example of the glycolytic and pentose phosphate pathways. The combinations of 2D [13C,1H] COSY NMR data that allow identification of all metabolic fluxes in these pathways are analyzed, and it is found that the NMR data contain less information than was previously expected. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 731,745, 2002. [source] Error propagation from prime variables into specific rates and metabolic fluxes for mammalian cells in perfusion cultureBIOTECHNOLOGY PROGRESS, Issue 4 2009Chetan T. Goudar Abstract Error propagation from prime variables into specific rates and metabolic fluxes was quantified for high-concentration CHO cell perfusion cultivation. Prime variable errors were first determined from repeated measurements and ranged from 4.8 to 12.2%. Errors in nutrient uptake and metabolite/product formation rates for 5,15% error in prime variables ranged from 8,22%. The specific growth rate, however, was characterized by higher uncertainty as 15% errors in the bioreactor and harvest cell concentration resulted in 37.8% error. Metabolic fluxes were estimated for 12 experimental conditions, each of 10 day duration, during 120-day perfusion cultivation and were used to determine error propagation from specific rates into metabolic fluxes. Errors of the greater metabolic fluxes (those related to glycolysis, lactate production, TCA cycle and oxidative phosphorylation) were similar in magnitude to those of the related greater specific rates (glucose, lactate, oxygen and CO2 rates) and were insensitive to errors of the lesser specific rates (amino acid catabolism and biosynthesis rates). Errors of the lesser metabolic fluxes (those related to amino acid metabolism), however, were extremely sensitive to errors of the greater specific rates to the extent that they were no longer representative of cellular metabolism and were much less affected by errors in the lesser specific rates. We show that the relationship between specific rate and metabolic flux error could be accurately described by normalized sensitivity coefficients, which were readily calculated once metabolic fluxes were estimated. Their ease of calculation, along with their ability to accurately describe the specific rate-metabolic flux error relationship, makes them a necessary component of metabolic flux analysis. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Insights into the Central Metabolism of Spodoptera frugiperda (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4(Tn -5) Insect Cells by Radiolabeling StudiesBIOTECHNOLOGY PROGRESS, Issue 1 2005Chouki Benslimane The insect cell baculovirus expression vector system (BEVS) is one of the most commonly used expression systems for recombinant protein production. This system is also widely used for the production of recombinant virus and virus-like particles. Although several published reports exist on recombinant protein expression using insect cells, information dealing with their metabolism in vitro is relatively scarce. In this work we have analyzed the metabolism of glucose and glutamine, the main carbon and/or energy compounds, of the two most commonly used insect cell lines, Spodoptera frugiperda (Sf-9) and the Trichoplusia niBTI-Tn-5B1 - 4 (Tn-5). Radiolabeled substrates have been used to determine the flux of glucose carbon entering the tricarboxylic acid cycle (TCA) and the pentose phosphate (PP) pathway by direct measurement of 14CO2 produced. The percentage of total glucose metabolized to CO2 via the TCA cycle was higher in the case of the Sf-9 (2.7%) compared to Tn-5 (0.6%) cells, while the percentage of glucose that is metabolized via the PP pathway was comparable at 14% and 16% for the two cell lines, respectively. For both cell lines, the remaining 83% of glucose is metabolized through other pathways generating, for example, lactate, alanine, etc. The percentage of glutamine oxidized in the TCA cycle was approximately 5-fold higher in the case of the Tn-5 (26.1%) as compared to the Sf-9 cells (4.6%). Furthermore, the changes in the metabolic fluxes of glucose and glutamine in Tn-5-PYC cells, which have been engineered to express a cytosolic pyruvate carboxylase, have been studied and compared to the unmodified cells Tn-5. As a result of this metabolic engineering, significant increase in the percentage of glucose oxidized in the TCA cycle (3.2%) as well as in the flux through the PP pathway (34%) of the Tn-5-PYC were observed. [source] | |||||||||||||||||||||||||||||||