On the mechanisms of glycolytic oscillations in yeast

This work concerns the cause of glycolytic oscillations in yeast. We analyse experimental data as well as models in two distinct cases: the relaxation-like oscillations seen in yeast extracts, and the sinusoidal Hopf oscillations seen in intact yeast cells. In the case of yeast extracts, we use flux-change plots and model analyses to establish that the oscillations are driven by on/off switching of phosphofructokinase. In the case of intact yeast cells, we find that the instability leading to the appearance of oscillations is caused by the stoichiometry of the ATP-ADP-AMP system and the allosteric regulation of phosphofructokinase, whereas frequency control is distributed over the reaction network. Notably, the NAD+/NADH ratio modulates the frequency of the oscillations without affecting the instability. This is important for understanding the mutual synchronization of oscillations in the individual yeast cells, as synchronization is believed to occur via acetaldehyde, which in turn affects the frequency of oscillations by changing this ratio.     

On the mechanism of the glucose-induced ATP catabolism in ascites tumour cells and its reversal by pyruvate.

Addition of glucose to Ehrlich-Landschütz ascites tumour cells preincubated for 30-60 min in phosphate-buffered Krebs-Ringer salt solution ("starved cells") resulted within 1-2 min in an approx. 90% decline of their ATP content and a massive accumulation of fructose 1,6-bisphosphate. These alterations, which took place under both aerobic and anaerobic conditions, were followed by a gradual spontaneous recovery with restoration of normal ATP and fructose 1,6-bisphosphate values. The transient derangement of the energy metabolism after glucose addition to starved ascites tumour cells by preventable by simultaneous addition of pyruvate or 2-oxobutyrate, or by preincubating the cells in the presence of glucose. The protective effect of pyruvate was duplicated by addition of phenazine methosulphate or NAD+ to the incubation medium. The data seem to warrant the conclusion that the glucose-induced ATP depletion is determined by a blockade of glycolysis at the stage of glyceraldehyde phosphate dehydrogenase caused by the failure of the cells to oxidize the NADH produced in the same reaction. The continued unrestrained action of 6-phosphofructokinase results in accumulation of fructose 1,6-bisphosphate, which constitutes a trap for the high-energy phosphate bonds of ATP. The primary metabolic disturbance appears to consist of a transient inhibition of pyruvate kinase with the resultant inability of the cells to maintain an unimpaired supply of pyruvate, as required for the lactate dehydrogenase-mediated oxidation of NADH. The regulatory mechanism underlying this phenomenon is discussed.     

Single cell studies and simulation of cell-cell interactions using oscillating glycolysis in yeast cells

The observation of oscillations in the concentrations of NADH and other intermediates in glycolysis in dense yeast cell suspensions is generally believed to be the result of synchronization of such oscillations between individual cells. The synchrony is believed to be a property of cell density and the question is: does metabolism in each individual yeast cell continue to oscillate, but out of phase, in the absence of synchronization? Here we have used high-sensitivity fluorescence microscopy to measure NADH in single isolated yeast cells under conditions where we observe oscillations of glycolysis in dense cell suspensions. However, we have not been able to detect intracellular oscillations in NADH in these isolated cells, which cannot synchronize their metabolism with other cells. However, addition of acetaldehyde to a single cell as pulses with a frequency similar to the oscillations in dense cell suspensions will induce oscillations in that cell. Ethanol, another product of glycolysis, which has been proposed as a synchronizing agent of glycolysis in cells, was not able to induce oscillations when added as pulses. The experiments support the notion that the intracellular oscillations are associated with the cell density of the yeast cell suspension and mediated by acetaldehyde and perhaps also other substances.     

A comparison of lipid metabolism in hepatocytes isolated from fed and starved neonatal and adult rats.

1. The utilization of [1-14C]palmitate by hepatocytes prepared from fed and starved neonatal and adult rats has been examined by measuring isotopic incorporation into various products. 2. In cells from fed adult rats the principal products were esters (triglycerides and phospholipids) but ketone bodies were the main metabolic end products in cells from starved adult and fed and starved neonatal rats. Production of triglycerides exceeded that of phospholipids in fed adult cells whereas phospholipid formation always predominated in neonatal cells. 3. The high rate of fatty acid oxidation and hence NADH formation by neonatal cells is reflected by a lower acetoacetate--3-hydroxybutyrate ratio at the earlier stages of incubation of neonatal cells. 4. The addition of glycerol modified quantitatively the products of palmitate metabolism by adult hepatocytes but no such effects were observed with neonatal cells. 5. Compared with adult cells, neonatal hepatocytes showed very low rates of lipogenesis that were only enhanced a little by addition of lactate/pyruvate and did not show any effects of glucose concentration upon incorporation of tritium from 3H2O into lipids.     

Metabolic control in flow systems

Summary Continuous infusion of D-glucose, 10^-8–10^-6 mole/min/g fresh weight, to anaerobic Saccharomyces carlsbergensis cell suspensions induces sustained oscillations of intracellular NADH. Under these conditions the metabolic flux is 100 times less than that after singular addition of an excess of D-glucose. The infused D-glucose is being catabolized except for the periods of rising NADH, where an overshoot in D-glucose concentration occurs shortly before NADH peaks. The oscillatory characteristics under the two conditions are compared.Oscillatory fluctuations in metabolic concentrations are very useful tools in studies on metabolic control in flux systems. But unfortunately rapid damping is observed in yeast suspensions. The infusion technique, as proposed by Sel'Kov (personal communication) was found useful with glycolysing yeast extract (Hess and Boiteux, 1968). Since the cell-free extract of yeast cells varies from day to day with respect to its metabolic and control features, we decided to apply infusion technique to suspension of yeast cells.     

On the role of enzyme cooperativity in metabolic oscillations: analysis of the Hill coefficient in a model for glycolytic periodicities.

The role of enzyme cooperativity in the mechanism of metabolic oscillations is analyzed in a concerted allosteric model for the phosphofructokinase reaction. This model of a dimer enzyme activated by the reaction product accounts quantitatively for glycolytic periodicities observed in yeast and muscle. The Hill coefficient characteristic of enzyme-substrate interactions is determined in the model, both at the steady state and in the course of sustained oscillations. Positive cooperativity is a prerequisite for periodic behavior. A necessary condition for oscillation in a dimer K system is a Hill coefficient larger than 1.6 at the unstable stationary state. The analysis suggests that positive as well as negative effectors of phosphofructokinase inhibit glycolytic oscillations by inducing a decrease in enzyme cooperativity. The results are discussed with respect to glycolytic and other metabolic periodicities.     

A mathematical model of the pyruvate oxidation in liver mitochondria. 1. Regulation of the Krebs cycle by adenine and pyridine nucleotides]

A mathematical model is proposed to describe the behavior of the pyruvate metabolic reactions, Krebs cycle and oxidative phosphorylation over a wide range of changes in the pyruvate influx rate and the activities of ATPase and NADH-reoxidating dehydrogenase. The role of adenine and pyridine nucleotides in various allosteric regulations of the Krebs cycle enzymes is discussed. The accumulation of ATP and NADH has been shown to proceed in definite succession, which makes the allosteric regulation of the Krebs cycle enzymes successive too. First "works" the inhibition by ATP, then by NADH. It has been shown that the properties of the model are in qualitative agreement with the experimental data (Garber A., Hanson R. [1]) on pyruvate oxidation by mitochondria from guinea pig liver, when allosteric regulation of isocitrate dehydrogenase by adenine nucleotides is taken into account.     

Systems approaches for the study of metabolic cycles in yeast

Over four decades ago, the first oscillations in metabolism in yeast cells were reported. Since then, multiple forms of oscillatory behavior have been observed in yeast grown under a variety of continuous culturing environments. The remarkable synchrony of cells undergoing such oscillations has made them ideal subjects for investigation using systems-based approaches. Herein, we briefly summarize previous work on the characterization of such oscillations using systems approaches, and present the long-period, Yeast Metabolic Cycle as an excellent model system for deciphering the temporal organization of fundamental cellular and metabolic processes at unprecedented resolution.     

The effects of alpha-adrenergic stimulation on the regulation of the pyruvate dehydrogenase complex in the perfused rat liver

The regulation of the pyruvate dehydrogenase multienzyme complex was investigated during alpha-adrenergic stimulation with phenylephrine in the isolated perfused rat liver. The metabolic flux through the pyruvate dehydrogenase reaction was monitored by measuring the production of 14CO2 from infused [1-14C] pyruvate. In livers from fed animals perfused with a low concentration of pyruvate (0.05 mM), phenylephrine infusion significantly inhibited the rate of pyruvate decarboxylation without affecting the amount of pyruvate dehydrogenase in its active form. Also, phenylephrine caused no significant effect on tissue NADH/NAD+ and acetyl-CoA/CoASH ratios or on the kinetics of pyruvate decarboxylation in 14CO2 washout experiments. Phenylephrine inhibition of [1-14C]pyruvate decarboxylation was, however, closely associated with a decrease in the specific radioactivity of perfusate lactate, suggesting that the pyruvate decarboxylation response simply reflected dilution of the labeled pyruvate pool due to phenylephrine-stimulated glycogenolysis. This suggestion was confirmed in additional experiments which showed that the alpha-adrenergic-mediated inhibitory effect on pyruvate decarboxylation was reduced in livers perfused with a high concentration of pyruvate (1 mM) and was absent in livers from starved rats. Thus, alpha-adrenergic agonists do not exert short term regulatory effects on pyruvate dehydrogenase in the liver. Furthermore, the results suggest either that the rat liver pyruvate dehydrogenase complex is insensitive to changes in mitochondrial calcium or that changes in intramitochondrial calcium levels as a result of alpha-adrenergic stimulation are considerably less than suggested by others.     

Isolation and inactivation of the nuclear gene encoding the rotenone-insensitive internal NADH: ubiquinone oxidoreductase of mitochondria from Saccharomyces cerevisiae

We have recently described the isolation of a mitochondrial rotenone-insensitive NADH:ubiquinone oxidoreductase from Saccharomyces cerevisiae [de Vries, S. & Grivell, L. A. (1988) Eur. J. Biochem. 176, 377-384]. We now report the isolation of the nuclear gene encoding this single-subunit enzyme. Null mutants have been constructed by means of one-step gene disruption. Oxygen-uptake experiments, performed with mitochondria isolated from the mutant cells, showed that this NADH dehydrogenase catalyzes the oxidation of NADH generated inside the mitochondrion. Inactivation of this NADH dehydrogenase does not affect growth on glucose and ethanol, but growth on lactate, pyruvate and acetate is impaired or absent. This phenotype is discussed in terms of the interplay between different metabolic pathways in yeast.     

Quantitative NAD(P)H/flavoprotein autofluorescence imaging reveals metabolic mechanisms of pancreatic islet pyruvate response

Glucose-stimulated insulin secretion is a multistep process dependent on beta-cell metabolic flux. Our previous studies on intact pancreatic islets used two-photon NAD(P)H imaging as a quantitative measure of the combined redox signal from NADH and NADPH (referred to as NAD(P)H). These studies showed that pyruvate, a non-secretagogue, enters beta-cells and causes a transient rise in NAD(P)H. To further characterize the metabolic fate of pyruvate, we have now developed one-photon flavoprotein microscopy as a simultaneous assay of lipoamide dehydrogenase (LipDH) autofluorescence. This flavoprotein is in direct equilibrium with mitochondrial NADH. Hence, a comparison of LipDH and NAD(P)H autofluorescence provides a method to distinguish the production of NADH, NADPH, or both. Using this method, the glucose dose response is consistent with an increase in both NADH and NADPH. In contrast, the transient rise in NAD(P)H observed with pyruvate stimulation is not accompanied by a significant change in LipDH, which indicates that pyruvate raises cellular NADPH without raising NADH. In comparison, methyl pyruvate stimulated a robust NADH and NADPH response. These data provide new evidence that exogenous pyruvate does not induce a significant rise in mitochondrial NADH. This inability likely results in its failure to produce the ATP necessary for stimulated secretion of insulin. Overall, these data are consistent with either a restricted pyruvate dehydrogenase-dependent metabolism or a buffering of the NADH response by other metabolic mechanisms.     

Expression of α-amylases, carbohydrate metabolism, and autophagy in cultured rice cells is coordinately regulated by sugar nutrient

A rice suspension cell culture system has been established to study how sugar depletion regulates α-amylase expression, carbohydrate metabolism, and other physiological and cellular changes. It is shown here that a group of 44 kDa α-amylases are constitutively expressed whether or not the cells are starved of sucrose. However, expression of a new group of α-amylases of 46 kDa is dramatically induced when cells are starved of sucrose. Cellular sugar and starch were rapidly consumed and metabolic activity was decreased in the starved cells. Extensive autophagy also occurred in the starved cells, which caused an increase in vacuolar volume and degradation of cytoplasmic constituents including amyloplasts. Immunocytochemical studies revealed that α-amylases are localized in starch granules within amyloplasts, in cell walls, and in some of the vacuoles. The presence of putative signal sequences in the N-termini of nine rice α-amylases suggests hitherto unidentified pathways for import of α-amylases into amyloplasts. The studies show that differential α-amylase expression, carbohydrate metabolism, metabolic activity, and vacuolar autophagy are coordinately regulated by the sugar level in the medium. As the starved suspension cells exhibit some sugar-regulated characteristics of α-amylase expression in germinating rice embryos as well as physiological changes similar to those in senescing cells, this system represents an ideal tool for studying cellular, biochemical, and molecular biological aspects of α-amylase gene regulation, carbohydrate metabolism, senescence, and protein targeting in plants.     

Nonlinear dynamics of eucaryotic pyruvate dehydrogenase multienzyme complex: decarboxylation rate,oscillations, and multiplicity

Pyruvate conversion to acetyl-CoA by the pyruvate dehydrogenase (PDH) multienzyme complex is known as a key node in affecting the metabolic fluxes of animal cell culture. However, its possible role in causing possible nonlinear dynamic behavior such as oscillations and multiplicity of animal cells has received little attention. In this work, the kinetic and dynamic behavior of PDH of eucaryotic cells has been analyzed by using both in vitro and simplified in vivo models. With the in vitro model the overall reaction rate (nu(1)) of PDH is shown to be a nonlinear function of pyruvate concentration, leading to oscillations under certain conditions. All enzyme components affect nu(1) and the nonlinearity of PDH significantly, the protein X and the core enzyme dihydrolipoamide acyltransferase (E2) being mostly predominant. By considering the synthesis rates of pyruvate and PDH components the in vitro model is expanded to emulate in vivo conditions. Analysis using the in vivo model reveals another interesting kinetic feature of the PDH system, namely, multiple steady states. Depending on the pyruvate and enzyme levels or the operation mode, either a steady state with high pyruvate decarboxylation rate or a steady state with significantly lower decarboxylation rate can be achieved under otherwise identical conditions. In general, the more efficient steady state is associated with a lower pyruvate concentration. A possible time delay in the substrate supply and enzyme synthesis can also affect the steady state to be achieved and leads to oscillations under certain conditions. Overall, the predictions of multiplicity for the PDH system agree qualitatively well with recent experimental observations in animal cell cultures. The model analysis gives some hints for improving pyruvate metabolism in animal cell culture.     

Transient responses and adaptation to steady state in a eukaryotic gene regulation system

Understanding the structure and functionality of eukaryotic gene regulation systems is of fundamental importance in many areas of biology. While most recent studies focus on static or short-term properties, measuring the long-term dynamics of these networks under controlled conditions is necessary for their complete characterization. We demonstrate adaptive dynamics in a well-known system of metabolic regulation, the GAL system in the yeast S. cerevisiae. This is a classic model for a eukaryotic genetic switch, induced by galactose and repressed by glucose. We followed the expression of a reporter gfp under a GAL promoter at single-cell resolution in large population of yeast cells. Experiments were conducted for long time scales, several generations, while controlling the environment in continuous culture. This combination enabled us, for the first time, to distinguish between transient responses and steady state. We find that both galactose induction and glucose repression are only transient responses. Over several generations, the system converges to a single robust steady state, independent of external conditions. Thus, at steady state the GAL network loses its hallmark functionality as a sensitive carbon source rheostat. This result suggests that, while short-term dynamics are determined by specific modular responses, over long time scales inter-modular interactions take over and shape a robust steady state response of the regulatory system.     

A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic β cells

The construction and characterization of a core kinetic model of the glucose-stimulated insulin secretion system (GSIS) in pancreatic β cells is described. The model consists of 44 enzymatic reactions, 59 metabolic state variables, and 272 parameters. It integrates five subsystems: glycolysis, the TCA cycle, the respiratory chain, NADH shuttles, and the pyruvate cycle. It also takes into account compartmentalization of the reactions in the cytoplasm and mitochondrial matrix. The model shows expected behavior in its outputs, including the response of ATP production to starting glucose concentration and the induction of oscillations of metabolite concentrations in the glycolytic pathway and in ATP and ADP concentrations. Identification of choke points and parameter sensitivity analysis indicate that the glycolytic pathway, and to a lesser extent the TCA cycle, are critical to the proper behavior of the system, while parameters in other components such as the respiratory chain are less critical. Notably, however, sensitivity analysis identifies the first reactions of nonglycolytic pathways as being important for the behavior of the system. The model is robust to deletion of malic enzyme activity, which is absent in mouse pancreatic β cells. The model represents a step toward the construction of a model with species-specific parameters that can be used to understand mouse models of diabetes and the relationship of these mouse models to the human disease state. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mechanism of stimulation of endogenous fermentation in yeast by carbonyl cyanide m-chlorophenylhydrazone

Addition of the uncoupler and protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) to starved yeast cells starts endogenous alcoholic fermentation lasting about 20 min. Hexose 6-phosphates, fructose 2,6-bisphosphate, and pyruvate accumulate in less than 2 min after addition of CCCP from almost zero concentration to concentrations which correspond to 1/5-1/10 of the steady-state concentrations during fermentation of glucose. CCCP immediately causes a decrease of the intracellular cytosolic pH from 6.9 to 6.4. This change activates adenylate cyclase (Purwin, C., Nicolay, K., Scheffers, W.A., and Holzer, H. (1986) J. Biol. Chem. 261, 8744-8749) and leads to the previously observed transient increase of cyclic AMP. It is shown here that the following enzymes known from in vitro experiments to be activated by cyclic AMP-dependent phosphorylation are activated in the CCCP-treated starved yeast cells in vivo: glycogen phosphorylase, trehalase (pH 7), 6-phosphofructo-2-kinase. The activation of 6-phosphofructo-2-kinase leads to an accumulation of fructose 2,6-bisphosphate, which is known from in vitro experiments to activate 6-phosphofructo-1-kinase and to inhibit fructose-1,6-bisphosphatase. All effects observed in the intact yeast cells fit with the idea that the CCCP-initiated activation of adenylate cyclase leads to a sequence of events which by protein phosphorylation and allosteric effects initiates endogenous alcoholic fermentation.     

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations

Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of the oscillation propagates within and between cells. We here develop a method to establish by which route dynamics propagate through a biological reaction network. Application of the method to yeast demonstrates how the oscillations and the synchronization signal can be transduced. That transduction is not so much through the backbone of glycolysis, as via the Gibbs energy and redox coenzyme couples (ATP/ADP, and NADH/NAD), and via both intra- and intercellular acetaldehyde.     

Modeling the synchronization of yeast respiratory oscillations

The budding yeast Saccharomyces cerevisiae exhibits autonomous oscillations when grown aerobically in continuous culture with ethanol as the primary carbon source. A single cell model that includes the sulfate assimilation and ethanol degradation pathways recently has been developed to study these respiratory oscillations. We utilize an extended version of this single cell model to construct large cell ensembles for investigation of a proposed synchronization mechanism involving hydrogen sulfide. Ensembles with as many as 10,000 cells are used to simulate population synchronization and to compute transient number distributions from asynchronous initial cell states. Random perturbations in intracellular kinetic parameters are introduced to study the synchronization of single cells with small variations in their unsynchronized oscillation periods. The cell population model is shown to be consistent with available experimental data and to provide insights into the regulatory mechanisms responsible for the synchronization of yeast metabolic oscillations.