The role of fructose 2,6-bisphosphate in glycolytic oscillations in extracts and cells of Saccharomyces cerevisiae

Glycolytic reprogramming in cancer cells: PKM2 dimer predominance induced by pulsatile PFK-1 activity

The glycolytic enzyme pyruvate kinase M2 (PKM2) exists in both catalytically inactive dimeric and active tetrameric forms. In cancer cells, PKM2 dimer predominance contributes to tumor growth by triggering glycolytic reprogramming. However, the mechanism that promotes PKM2 dimer predominance over tetramer in cancer cells remains elusive. Here, we show that pulsatile phosphofructokinase (PFK-1) activity results in PKM2 dimer predominance. Mathematical simulations predict that pulsatile PFK-1 activity prevents the formation of PKM2 tetramer even under high levels of fructose-1,6-bisphosphate (FBP), a PKM2 tetramer-promoting metabolite produced by PFK-1. We experimentally confirm these predictions at the single-molecule level by providing evidence for pulsatile PFK-1 activity-induced synchronized dissociation of PKM2 tetramers and the subsequent accumulation of PKM2 dimers under high levels of FBP in HeLa cells. Moreover, we show that pulsatile PFK-1 activity-induced PKM2 dimer predominance also controls cell proliferation. Thus, our study reveals the significance of pulsatile PFK-1 activity in cancer cell metabolism.

Redox regulation in respiring Saccharomyces cerevisiae

BACKGROUND

In biological systems, redox reactions are central to most cellular processes and the redox potential of the intracellular compartment dictates whether a particular reaction can or cannot occur. Indeed the widespread use of redox reactions in biological systems makes their detailed description outside the scope of one review.

SCOPE OF THE REVIEW

Here we will focus on how system-wide redox changes can alter the reaction and transcriptional landscape of Saccharomyces cerevisiae. To understand this we explore the major determinants of cellular redox potential, how these are sensed by the cell and the dynamic responses elicited.

MAJOR CONCLUSIONS

Redox regulation is a large and complex system that has the potential to rapidly and globally alter both the reaction and transcription landscapes. Although we have a basic understanding of many of the sub-systems and a partial understanding of the transcriptional control, we are far from understanding how these systems integrate to produce coherent responses. We argue that this non-linear system self-organises, and that the output in many cases is temperature-compensated oscillations that may temporally partition incompatible reactions in vivo.

GENERAL SIGNIFICANCE

Redox biochemistry impinges on most of cellular processes and has been shown to underpin ageing and many human diseases. Integrating the complexity of redox signalling and regulation is perhaps one of the most challenging areas of biology. This article is part of a Special Issue entitled Systems Biology of Microorganisms.

Ethanol fermentation technologies from sugar and starch feedstocks

This article critically reviews some ethanol fermentation technologies from sugar and starch feedstocks, particularly those key aspects that have been neglected or misunderstood. Compared with Saccharomyces cerevisiae, the ethanol yield and productivity of Zymomonas mobilis are higher, because less biomass is produced and a higher metabolic rate of glucose is maintained through its special Entner-Doudoroff pathway. However, due to its specific substrate spectrum as well as the undesirability of its biomass to be used as animal feed, this species cannot readily replace S. cerevisiae in ethanol production. The steady state kinetic models developed for continuous ethanol fermentations show some discrepancies, making them unsuitable for predicting and optimizing the industrial processes. The dynamic behavior of the continuous ethanol fermentation under high gravity or very high gravity conditions has been neglected, which needs to be addressed in order to further increase the final ethanol concentration and save the energy consumption. Ethanol is a typical primary metabolite whose production is tightly coupled with the growth of yeast cells, indicating yeast must be produced as a co-product. Technically, the immobilization of yeast cells by supporting materials, particularly by gel entrapments, is not desirable for ethanol production, because not only is the growth of the yeast cells restrained, but also the slowly growing yeast cells are difficult to be removed from the systems. Moreover, the additional cost from the consumption of the supporting materials, the potential contamination of some supporting materials to the quality of the co-product animal feed, and the difficulty in the microbial contamination control all make the immobilized yeast cells economically unacceptable. In contrast, the self-immobilization of yeast cells through their flocculation can effectively overcome these drawbacks.

Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation inSaccharomyces cerevisiae

In the present work LC-MS/MS was applied to measure the concentrations of intermediates of glycolysis and TCA cycle during autonomous, cell-cycle synchronized oscillations in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. This study complements previously reported oscillations in carbon dioxide production rate, intracellular concentrations of trehalose and various free amino acids, and extracellular acetate and pyruvate in the same culture. Of the glycolytic intermediates, fructose 1,6-bisphosphate, 2- and 3-phosphoglycerate, and phosphoenolpyruvate show the most pronounced oscillatory behavior, the latter three compounds oscillating out of phase with the former. This agrees with previously observed metabolic control by phosphofructokinase and pyruvate kinase. Although individually not clearly oscillating, several intermediates of the TCA cycle, i.e., alpha-ketoglutarate, succinate, fumarate, and malate, exhibited increasing concentration during the cell cycle phase with high carbon flux through glycolysis and TCA cycle. The average mass action ratios of beta-phosphoglucomutase and fumarase agreed well with previously determined in vitro equilibrium constants. Minor differences resulted for phosphoglucose isomerase and enolase. Together with the observed close correlation of the pool sizes of the involved metabolites, this might indicate that, in vivo, these reactions are operating close to equilibrium, whereby care must be taken due to possible differences between in vivo and in vitro conditions. Combining the data with previously determined intracellular amino acid levels from the same culture, a few clear correlations between catabolism and anabolism could be identified: phosphoglycerate/serine and alpha-ketoglutarate/lysine exhibited correlated oscillatory behavior, albeit with different phase shifts. Oscillations in intracellular amino acids might therefore be, at least partly, following oscillations of their anabolic precursors.

The rhythm of yeast

Although yeast are unicellular and comparatively simple organisms, they have a sense of time which is not related to reproduction cycles. The glycolytic pathway exhibits oscillatory behaviour, i.e. the metabolite concentrations oscillate around phosphofructokinase. The frequency of these oscillations is about 1 min when using intact cells. Also a yeast cell extract can oscillate, though with a lower frequency. With intact cells the macroscopic oscillations can only be observed when most of the cells oscillate in concert. Transient oscillations can be observed upon simultaneous induction; sustained oscillations require an active synchronisation mechanism. Such an active synchronisation mechanism, which involves acetaldehyde as a signalling compound, operates under certain conditions. How common these oscillations are in the absence of a synchronisation mechanism is an open question. Under aerobic conditions an oscillatory metabolism can also be observed, but with a much lower frequency than the glycolytic oscillations. The frequency is between one and several hours. These oscillations are partly related to the reproductive cycle, i.e. the budding index also oscillates; however, under some conditions they are unrelated to the reproductive cycle, i.e. the budding index is constant. These oscillations also have an active synchronisation mechanism, which involves hydrogen sulfide as a synchronising agent. Oscillations with a frequency of days can be observed with yeast colonies on plates. Here the oscillations have a synchronisation mechanism which uses ammonia as a synchronising agent.

Cellular information transfer regarded from a stoichiometry and control analysis perspective

Metabolic control analysis (MCA) allows one to formalize important aspects of information processing in living cells. For example, information processing via multi-level enzyme cascades can be quantified in terms of the response coefficient of a cellular target to a signal. In many situations, control and response coefficients cannot be determined exactly for all enzymes involved, owing to difficulties in 'observing' all enzymes experimentally. Here, we review a number of qualitative approaches that were developed to cope with such situations. The usefulness of the concept of null-space of the stoichiometry matrix for analysing the structure of intracellular signaling networks is discussed. It is shown that signal transduction operates very efficiently when the network structure is such that the null-space matrix can be block-diagonalized (which may or may not imply that the network consists of several disconnected parts) and some enzymes have low elasticities to their substrates.

Diversity of temporal self-organized behaviors in a biochemical system

The numerical study of a glycolytic model formed by a system of three delay-differential equations revealed a notable richness of temporal structures which included the three main routes to chaos, as well as a multiplicity of stable coexisting states. The Feigenbaum, intermitency and quasiperiodicity routes to chaos can emerge in the biochemical oscillator. Moreover, different types of birhythmicity, trirhythmicity and hard excitation emerge in the phase space. For a single range of the control parameter it can be observed the coexistence of two quasiperiodicity routes to chaos, the coexistence of a stable steady state with a stable torus, and the coexistence of a strange attractor with different stable regimes such as chaos with different periodic regimes, chaos with bursting behavior, and chaos with torus. In most of the numerical studies, the biochemical oscillator has been considered under periodic input flux being the mean input flux rate 6 mM/h. On the other hand, several investigators have observed quasiperiodic time patterns and chaotic oscillations by monitoring the fluorescence of NADH in glycolyzing yeast under sinusoidal glucose input flux. Our numerical results match well with these experimental studies.

Further studies on the coupling of mitochondrially bound hexokinase to intramitochondrially compartmented ATP, generated by oxidative phosphorylation

Hexokinase, bound to nonphosphorylating rat brain mitochondria, exhibits Michaelis-Menten kinetic behavior, with an apparent K(m) for ATP of 0.44 +/- 0.08 mM. After initiation of oxidative phosphorylation, a steady-state rate of Glc phosphorylation is maintained despite the fact that extramitochondrial [ATP] continues to increase but remains well below saturating levels (i.e., < 0.4 mM). This independence from extramitochondrial [ATP] is taken to indicate that hexokinase is not utilizing extramitochondrial ATP as substrate, but rather draws substrate ATP from an intramitochondrial compartment supplied by oxidative phosphorylation. The steady-state rate of Glc phosphorylation by hexokinase bound to phosphorylating mitochondria is not altered by increase in total rate of ATP production resulting from addition of hexokinase-depleted mitochondria to the system. In contrast, the steady-state rate of Glc phosphorylation by yeast hexokinase, which does not bind to mitochondria, is directly related to the total rate of ATP production in the system. These results are also consistent with the view that, during oxidative phosphorylation, mitochondrially bound hexokinase is selectively using intramitochondrially compartmented ATP; such substrate selectivity would be expected to require physical association of hexokinase with the mitochondria and be dependent solely on the oxidative phosphorylation activity of the hexokinase-bearing organelles. The K(m) for Glc is only modestly affected by the binding of hexokinase to mitochondria and not further altered upon induction of active oxidative phosphorylation, suggesting that neither binding nor oxidative phosphorylation greatly affects the conformation of the Glc binding site. The reliance on intramitochondrial ATP is suggested to result from oxidative phosphorylation-dependent changes in the interaction between the mitochondrial surface and the regions of the hexokinase molecule involved in binding ATP.

Fructose 2,6-bisphosphate induces irreversible transitions in cell-free extracts of rat liver

The effect of fructose 2,6-bisphosphate on the dynamics of the 6-phosphofructo-1-kinase/fructose-1,6-bisphosphatase cycle is investigated in a cell-free extract of rat liver under steady-state conditions. Bistability emerges on the basis of the reciprocal allosteric modulation of 6-phosphofructo-1-kinase and fructose-1,6-bisphosphatase. Under conditions of bistability fructose 2,6-bisphosphate may cause transitions between alternative steady states. However, in contrast to what is frequently observed in bistable systems, within a broad range of experimental conditions these transitions proceed irreversibly from states with high ATP to states characterized by low ATP.

Sustained oscillations in free-energy state and hexose phosphates in yeast

In a population of intact cells of the yeast Saccharomyces cerevisiae the dynamics of glycolytic metabolism were investigated under the condition of sustained oscillations. At 5-s intervals cells were quenched in -40 degrees C methanol, extracted and the intracellular concentrations of glycolytic metabolites, adenine nucleotides and phosphate were analysed. Oscillations were found for the glycolytic intermediates glucose 6-phosphate, fructose 6-phosphate and fructose 1,6-bisphosphate. At variance with earlier reports on transient glycolytic oscillations, some intermediates further down the glycolytic pathway did not oscillate significantly, even though NADH did. In addition, the adenylate energy charge and the free energy of ATP hydrolysis oscillated significantly. Dynamic coupling through the latter may be responsible for this effective compartmentation of glycolytic dynamics.

Caffeine-induced calcium oscillations in heavy-sarcoplasmic-reticulum vesicles from rabbit skeletal muscle

Heavy-sarcoplasmic-reticulum vesicles from rabbit skeletal muscle show not only caffeine-induced calcium release in a medium allowing active calcium loading, but also oscillations in calcium concentration under appropriate conditions. The xanthine derivatives 7-isobutyl-1-methylxanthine and theophylline also induce oscillations under the same conditions. Calcium-releasing substances with other chemical structures such as adenosine nucleotides or calmodulin antagonists do not induce this effect. With the help of specific inhibitors such as ruthenium red, neomycin or magnesium it was demonstrated that the oscillation mechanism involves the ryanodine receptor/calcium channel. When ATP was substituted by GTP or ITP no oscillations occurred after caffeine application. The subsequent application of ATP, but not of adenosine 5'-[gamma-thio]triphosphate or adenosine 5'-[beta,gamma-methylene]triphosphate activated the oscillating mechanism, showing ATP to be an essential component of the oscillating system. We investigated the influence of the experimental conditions by altering the caffeine and ATP concentrations, calcium load, pH and ionic strength amongst other parameters. Potassium and anion channels are not involved in calcium oscillations of heavy sarcoplasmic reticulum, nor are the oscillations dependent on membrane potential.