Control of glycolytic oscillations by temperature

External control of oscillatory glycolysis in yeast extract has been performed by application of either homogeneous temperature oscillations or stationary, spatial temperature gradients. Entrainment of the glycolytic oscillations by the 1/2- and 1/3-harmonic, as well as the fundamental input frequency, could be observed. From the phase response curve to a single temperature pulse, a distinct sensitivity of NADH-oxidizing processes, compared with NAD-reducing processes, is visible. Determination of glycolytic intermediates shows that the feedback-regulated phosphofructokinase as well as the glyceraldehyde-3-phosphate dehydrogenase are the most temperature-sensitive steps of glycolysis. We also find strong concentration changes in ATP and AMP at varying temperatures and, accordingly, in the energy charge. Construction of a feedback loop for spatial control of temperature by means of a Peltier element allowed us to apply a temperature gradient to the yeast extract. With this setup it is possible to initiate traveling waves and to control the wave velocity.     

How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment

Of all the lifeforms that obtain their energy from glycolysis, yeast cells are among the most basic. Under certain conditions the concentrations of the glycolytic intermediates in yeast cells can oscillate. Individual yeast cells in a suspension can synchronize their oscillations to get in phase with each other. Although the glycolytic oscillations originate in the upper part of the glycolytic chain, the signaling agent in this synchronization appears to be acetaldehyde, a membrane-permeating metabolite at the bottom of the anaerobic part of the glycolytic chain. Here we address the issue of how a metabolite remote from the pacemaking origin of the oscillation may nevertheless control the synchronization. We present a quantitative model for glycolytic oscillations and their synchronization in terms of chemical kinetics. We show that, in essence, the common acetaldehyde concentration can be modeled as a small perturbation on the "pacemaker" whose effect on the period of the oscillations of cells in the same suspension is indeed such that a synchronization develops.     

Induction of the activity of glycolytic enzymes correlates with enhanced hydrolysis of sucrose in the cytosol of transgenic potato tubers

The aim of this work was to define the metabolic factors which regulate the respiratory pathways in trangenic potato tubers. We previously found that respiration is enhanced in transgenic tubers which express a yeast invertase and a glucokinase from Zymomonas mobilis . In this study we investigated glycolysis in three further transgenic potato lines with profound changes in the mobilization of sucrose. We studied antisense ADPglucose pyrophosphorylase lines which are characterized by a reduction in starch accumulation and a significant build up of sucrose and related metabolic intermediates. We also report the generation of two novel double transgenic lines where the yeast invertase is expressed specifically in tubers of the ADPglucose pyrophosphorylase antisense line, targeted to either the cytosol or apopolast. We evaluated whether the localization of sucrose cleavage had an impact on the glycolytic induction, and assessed if invertase expression in the high-sucrose background had any further effects on glycolysis. We found that induction of the glycolytic enzymes only occurs when the invertase is targeted to the cytosol, and that the extent of this induction was comparable in the wild type and antisenseADPglucose pyrophosphorylase backgrounds. We conclude that the signal regulating glycolysis is directly linked to cytosolic sucrose hydrolysis.     

Triosephosphates as intermediates of the Crabtree effect

An increase in glucose concentration in the medium rapidly decreases respiration rate in many cell types, including tumor cells. The molecular mechanism of this phenomenon, the Crabtree effect, is still unclear. It was shown earlier that adding the intermediate product of glycolysis fructose-1,6-bisphosphate to isolated mitochondria suppresses their respiration. To study possible roles of glycolytic intermediates in the Crabtree effect, we used a model organism, the yeast Saccharomyces cerevisiae. To have the option to rapidly increase intracellular concentrations of certain glycolytic intermediates, we used mutant cells with glycolysis blocked at different stages. We studied fast effects of glucose addition on the respiration rate in such cells. We found that addition of glucose affected cells with deleted phosphoglycerate mutase (strain gpm1-delta) more strongly than ones with inactivated aldolase or phosphofructokinase. In the case of preincubation of gpm1-delta cells with 2-deoxyglucose, which blocks glycolysis at the stage of 2-deoxyglucosephosphate formation, the effect of glucose addition was absent. This suggests that triosephosphates are intermediates of the Crabtree effect. Apart from this, the incubation of gpm1-delta cells in galactose-containing medium appeared to cause a large increase in their size. It was previously shown that galactose addition did not have any short-term effect on respiration rate of gpm1-delta cells and, at the same time, strongly suppressed their growth rate. Apparently, the influence of increasing triosephosphate concentration on yeast physiology is not limited to the activation of the Crabtree effect.     

Inhibition of glycolysis induced by diethylstilbestrol in anaerobically grown yeast

In anaerobically grown yeast cells which lack functional mitochondria, the presence of diethylstilbestrol (DES) depressed glycolysis. The addition of the inhibitor markedly increased the cellular concentration of glycolytic intermediates which are formed prior to the pyruvate kinase step as well as to bring about an increase in the [ATP]/[ADP] ratio. Under these conditions an 18 fold decrease in the mass action ratio for pyruvate kinase [( pyruvate] [ATP]/[phosphoenolpyruvate] [ADP]) was noted, however, there was little if any effect on the other glycolytic enzymes. These results suggest that the depression of anaerobic glycolysis caused by DES results from a blockage at the level of the regulatory enzyme pyruvate kinase through a modification of its intracellular environment.     

Glycolytic enzymes associate dynamically with mitochondria in response to respiratory demand and support substrate channeling

In Arabidopsis thaliana, enzymes of glycolysis are present on the surface of mitochondria and free in the cytosol. The functional significance of this dual localization has now been established by demonstrating that the extent of mitochondrial association is dependent on respiration rate in both Arabidopsis cells and potato (Solanum tuberosum) tubers. Thus, inhibition of respiration with KCN led to a proportional decrease in the degree of association, whereas stimulation of respiration by uncoupling, tissue ageing, or overexpression of invertase led to increased mitochondrial association. In all treatments, the total activity of the glycolytic enzymes in the cell was unaltered, indicating that the existing pools of each enzyme repartitioned between the cytosol and the mitochondria. Isotope dilution experiments on isolated mitochondria, using (13)C nuclear magnetic resonance spectroscopy to monitor the impact of unlabeled glycolytic intermediates on the production of downstream intermediates derived from (13)C-labeled precursors, provided direct evidence for the occurrence of variable levels of substrate channeling. Pull-down experiments suggest that interaction with the outer mitochondrial membrane protein, VDAC, anchors glycolytic enzymes to the mitochondrial surface. It appears that glycolytic enzymes associate dynamically with mitochondria to support respiration and that substrate channeling restricts the use of intermediates by competing metabolic pathways.     

Modeling of glycolytic wave propagation in an open spatial reactor with inhomogeneous substrate influx

The spatio-temporal dynamics of traveling waves in glycolysis as it occurs in yeast extract have been studied, both theoretically and experimentally. We describe this phenomenon with the distributed Selkov model that accounts for the reactions of phosphofructokinase, which is a key enzyme of the glycolytic reaction cascade. To describe the experimentally observed phase waves in an open spatial reactor we introduce a non-homogeneous flux of substrate in the model. The experimental observation that waves can change their direction of propagation during the experiment is considered in the model. The mechanism for such a change in wave direction is discussed.     

Stimulation of glycolysis by imidazole

Imidazole stimulated glycolysis by rat diaphragm homogenates; this effect increased as the concentration of imidazole was raised. The simultaneous changes in concentration of some of the glycolytic intermediates suggested an action of imidazole at a step between triose phosphate and pyruvate. Addition of glyceraldehyde phosphate dehydrogenase increased glycolysis and abolished the stimulating effect of imidazole, thus leading to the conclusion that in the homogenate the activity of this enzyme was rate-limiting for glycolysis and was increased by imidazole.     

Oscillations in Yeast Observed Electrically

It has previously been demonstrated that oscillations occur in actively growing yeast cultures. These oscillations occur because yeast cells synchronize their glycolytic pathway following a saturation period. Periodic changes in the levels of intermediate metabolites in glycolysis as well as changes in pH ofthe media have been measured, that demonstrate this phenomenon. Here we observe that the conductivity of the media also changes periodically when yeast cells are cultured under similar conditions. As conductivity is easily measured, this provides a simple, more quantitative method to study these changes than those currently used. An electrical biosensor referred to as ECIS (electrical cell surface impedance sensing) was used to study the small conductivity changes (in the order of 0.1%). No significant differences in the observed periods were found in the two yeast strains or the commercially purchased yeast extract studied.     

Oscillations in Yeast Observed Electrically

It has previously been demonstrated that oscillations occur in actively growing yeast cultures. These oscillations occur because yeast cells synchronize their glycolytic pathway following a saturation period. Periodic changes in the levels of intermediate metabolites in glycolysis as well as changes in pH ofthe media have been measured, that demonstrate this phenomenon. Here we observe that the conductivity of the media also changes periodically when yeast cells are cultured under similar conditions. As conductivity is easily measured, this provides a simple, more quantitative method to study these changes than those currently used. An electrical biosensor referred to as ECIS (electrical cell surface impedance sensing) was used to study the small conductivity changes (in the order of 0.1%). No significant differences in the observed periods were found in the two yeast strains or the commercially purchased yeast extract studied.     

The role of ATPase in glycolysis of Ehrlich ascites tumor cells

Glycolysis in Ehrlich ascites tumor cells suspended in buffer containing 5 mM Pi was 50% inhibited by ouabain. In the absence of Pi the inhibition was less striking. Permeabilization of the cells with filipin abolished glycolysis, but glycolysis was restored by addition of Pi and AMP. Neither ouabain nor quercetin inhibited glycolysis in these permeabilized cells. We conclude that quercetin did not inhibit hexokinase sufficiently to affect glycolysis. An extract of Ehrlich ascites tumor cells glycolyzed weakly unless either Pi or an ATPase (e.g. (Na+K+)-ATPase) was added. The low rate of glycolysis of the extract was even further reduced when an endogenous ATPase was removed by precipitation with CaATP. The glycolytic activity of this ATPase-deficient extract was restored by addition of purified (Na+K+)-ATPase or of CaATP-precipitable ATPase. Addition of hexokinase without Pi did not restore glycolytic activity to the extract. An explanation for the contradictory conclusions by Bustamante, E., Morris, H.P., and Pedersen, P.L. (J. Biol. Chem. (1981) 265, 8699-8704) is presented.     

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics

A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was later applied to different experimental steady-state conditions, it often exhibited unrestrained metabolite accumulation.Here we resolve this issue by showing that the results of such ab initio modeling are improved substantially by (i) including appropriate allosteric regulation and (ii) measuring the enzyme kinetic parameters under conditions that resemble the intracellular environment. The following modifications proved crucial: (i) implementation of allosteric regulation of hexokinase and pyruvate kinase, (ii) implementation of V(max) values measured under conditions that resembled the yeast cytosol, and (iii) redetermination of the kinetic parameters of glyceraldehyde-3-phosphate dehydrogenase under physiological conditions.Model predictions and experiments were compared under five different conditions of yeast growth and starvation. When either the original model was used (which lacked important allosteric regulation), or the enzyme parameters were measured under conditions that were, as usual, optimal for high enzyme activity, fructose 1,6-bisphosphate and some other glycolytic intermediates tended to accumulate to unrealistically high concentrations. Combining all adjustments yielded an accurate correspondence between model and experiments for all five steady-state and dynamic conditions. This enhances our understanding of in vivo metabolism in terms of in vitro biochemistry.     

Electrical stimulation of the energy metabolism in yeast cells using a planar Ti-Au-Electrode interface

We report on the influence of dielectric pulse injection on the energy metabolism of yeast cells with a planar interdigitated electrode interface. The energy metabolism was measured via NADH fluorescence. The application of dielectric pulses results in a distinct decrease of the fluorescence, indicating a response of the energy metabolism of the yeast cells. The reduction of the NADH signal significantly depends on the pulse parameters, i.e., amplitude and width. Furthermore, the interface is used to detect electrical changes in the cell-electrolyte system, arising from glucose-induced oscillations in yeast cells and yeast extract, by dielectric spectroscopy at 10 kHz. These dielectric investigations revealed a β₁-dispersion for the system electrolyte/yeast cells as well as for the system electrolyte/yeast extract. In agreement with control measurements we obtained a glycolytic period of 45s for yeast cells and of 11min for yeast extract.     

Glycolytic regulation during an aerobic rest-to-work transition in dog gracilis muscle

Glycogen phosphorylase activity and several glycolytic intermediates were measured at rest and after 5, 10, 15, 30, 60, and 180 s of twitch stimulation at 4 Hz in fast-frozen samples of gracilis muscle. During an initial burst of glycolysis (0-5 s) only 3-phosphoglycerate and lactate accumulate. These changes are reversed during the period of low glycolytic flux (5-30 s). During a second burst of glycolysis (30-60 s) most glycolytic intermediates increase. The levels of glycogen phosphorylase a changes in parallel with the initial burst of glycolysis but remain at resting levels throughout the second burst. The phosphoglycerate mutase-enolase steps deviate from equilibrium during the initial burst of glycolysis, suggesting a transiently rate-limiting role. Analysis using a model of phosphofructokinase kinetics indicates that combined changes in cytosolic pH (R. J. Connett, J. Appl. Physiol. 63: 2360-2365, 1987) and free [ADP] and [AMP] can account for the initial burst of glycolysis. The second burst of glycolysis requires other regulatory factors. It is concluded that an initial alkalization is a major regulatory factor in the early burst of glycolysis during a rest-to-work transition in red muscle.     

Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance

Glycolysis is a conserved central pathway in energy metabolism that converts glucose to pyruvate with net production of two ATP molecules. Because ATP is produced only in the lower part of glycolysis (LG), preceded by an initial investment of ATP in the upper glycolysis (UG), achieving robust start-up of the pathway upon activation presents a challenge: a sudden increase in glucose concentration can throw a cell into a self-sustaining imbalanced state in which UG outpaces LG, glycolytic intermediates accumulate and the cell is unable to maintain high ATP concentration needed to support cellular functions. Such metabolic imbalance can result in “substrate-accelerated death”, a phenomenon observed in prokaryotes and eukaryotes when cells are exposed to an excess of substrate that previously limited growth. Here, we address why evolution has apparently not eliminated such a costly vulnerability and propose that it is a manifestation of an evolutionary trade-off, whereby the glycolysis pathway is adapted to quickly secure scarce or fluctuating resource at the expense of vulnerability in an environment with ample resource. To corroborate this idea, we perform individual-based eco-evolutionary simulations of a simplified yeast glycolysis pathway consisting of UG, LG, phosphate transport between a vacuole and a cytosol, and a general ATP demand reaction. The pathway is evolved in constant or fluctuating resource environments by allowing mutations that affect the (maximum) reaction rate constants, reflecting changing expression levels of different glycolytic enzymes. We demonstrate that under limited constant resource, populations evolve to a genotype that exhibits balanced dynamics in the environment it evolved in, but strongly imbalanced dynamics under ample resource conditions. Furthermore, when resource availability is fluctuating, imbalanced dynamics confers a fitness advantage over balanced dynamics: when glucose is abundant, imbalanced pathways can quickly accumulate the glycolytic intermediate FBP as intracellular storage that is used during periods of starvation to maintain high ATP concentration needed for growth. Our model further predicts that in fluctuating environments, competition for glucose can result in stable coexistence of balanced and imbalanced cells, as well as repeated cycles of population crashes and recoveries that depend on such polymorphism. Overall, we demonstrate the importance of ecological and evolutionary arguments for understanding seemingly maladaptive aspects of cellular metabolism.     

Flux regulation in glycogen-induced oscillatory glycolysis in cell-free extracts of Saccharomyces carlsbergensis

To localise the controlling point of the glycolytic system, the temporal changes of concentrations of glycolytic intermediates have been analysed after addition of glycogen to a substrate-depleted yeast extract. Three sequential metabolic states are clearly observable: a transition state at which there is continuous accumulation of the intermediates before the glyceraldehydephosphate dehydrogenase (GAPDH, EC 1.2.1.12) step; a stationary state with all glycolytic intermediates having concentrations oscillating at nearly stationary mean values; and a depletion state at which the intermediates before the GAPDH step are being depleted due to the exhaustion of glycogen. In all these states, the mean ethanol production rate and the concentration of ATP and the intermediates beyond the GAPDH-step are maintained fairly constant, while the glycogen consumption rate and intermediate concentrations of the upper part of the glycolytic system change considerably: the glycogen consumption rate varies 4-fold and fructose-bis-phosphate concentration more than 10-fold. Doubling of the initial glycogen concentration and the addition of a great excess of fructose-bis-phosphate do not affect the ethanol production rate and the mean glycerate-3-phosphate (3-PGA) and pyruvate levels. By contrast, ethanol production was accelerated by an increase of the net ATP consumption rate resulting from either the addition of apyrase or by substitution of trehalose for glycogen. Neither the mean absolute ATP level nor the adenylate energy charge were measurably affected, however all this data can be interpreted in terms of a very strong stoichiometric regulation and stabilization of the lower part of the glycolytic system.     

Riboneogenesis in yeast

Glucose is catabolized in yeast via two fundamental routes, glycolysis and the oxidative pentose phosphate pathway, which produces NADPH and the essential nucleotide component ribose-5-phosphate. Here, we describe riboneogenesis, a thermodynamically driven pathway that converts glycolytic intermediates into ribose-5-phosphate without production of NADPH. Riboneogenesis begins with synthesis, by the combined action of transketolase and aldolase, of the seven-carbon bisphosphorylated sugar sedoheptulose-1,7-bisphosphate. In the pathway's committed step, sedoheptulose bisphosphate is hydrolyzed to sedoheptulose-7-phosphate by the enzyme sedoheptulose-1,7-bisphosphatase (SHB17), whose activity we identified based on metabolomic analysis of the corresponding knockout strain. The crystal structure of Shb17 in complex with sedoheptulose-1,7-bisphosphate reveals that the substrate binds in the closed furan form in the active site. Sedoheptulose-7-phosphate is ultimately converted by known enzymes of the nonoxidative pentose phosphate pathway to ribose-5-phosphate. Flux through SHB17 increases when ribose demand is high relative to demand for NADPH, including during ribosome biogenesis in metabolically synchronized yeast cells.