Changes in carbohydrate composition and trehalase-activity during the budding cycle of Saccharomyces cerevisiae

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

A Nonlinear Delay Model for Metabolic Oscillations in Yeast Cells

We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We initially explore a single-protein model with a constraint equation governing the total resource available to the cell. The model is then extended to include three proteins that share a resource pool. Three approaches are considered at constant delay to numerically detect oscillations. First, we use a spectral element method to approximate the system as a discrete map and evaluate the stability of the linearized system about its equilibria by examining its eigenvalues. For the second method, we plot amplitudes of the simulation trajectories in 2D projections of the parameter space. We use a history function that is consistent with published experimental results to obtain metabolic oscillations. Finally, the spectral element method is used to convert the system to a boundary value problem whose solutions correspond to approximate periodic solutions of the system. Our results show that certain combinations of total resource available and the time delay, lead to oscillations. We observe that an oscillation region in the parameter space is between regions admitting steady states that correspond to zero and constant production. Similar behavior is found with the three-protein model where all proteins require the same production time. However, a shift in the protein production rates peaks occurs for low available resource suggesting that our model captures the shared resource pool dynamics.

Allosteric activation of yeast enzyme neutral trehalase by calcium and 14-3-3 protein

Neutral trehalase 1 (Nth1) from Saccharomyces cerevisiae catalyzes disaccharide trehalose hydrolysis and helps yeast to survive adverse conditions, such as heat shock, starvation or oxidative stress. 14-3-3 proteins, master regulators of hundreds of partner proteins, participate in many key cellular processes. Nth1 is activated by phosphorylation followed by 14-3-3 protein (Bmh) binding. The activation mechanism is also potentiated by Ca(2+) binding within the EF-hand-like motif. This review summarizes the current knowledge about trehalases and the molecular and structural basis of Nth1 activation. The crystal structure of fully active Nth1 bound to 14-3-3 protein provided the first high-resolution view of a trehalase from a eukaryotic organism and showed 14-3-3 proteins as structural modulators and allosteric effectors of multi-domain binding partners.

Flavin-based metabolic cycles are integral features of growth and division in single yeast cells

The yeast metabolic cycle (YMC) is a fascinating example of biological organization, in which cells constrain the function of specific genetic, protein and metabolic networks to precise temporal windows as they grow and divide. However, understanding the intracellular origins of the YMC remains a challenging goal, as measuring the oxygen oscillations traditionally associated with it requires the use of synchronized cultures growing in nutrient-limited chemostat environments. To address these limitations, we used custom-built microfluidic devices and time-lapse fluorescence microscopy to search for metabolic cycling in the form of endogenous flavin fluorescence in unsynchronized single yeast cells. We uncovered robust and pervasive metabolic cycles that were synchronized with the cell division cycle (CDC) and oscillated across four different nutrient conditions. We then studied the response of these metabolic cycles to chemical and genetic perturbations, showing that their phase synchronization with the CDC can be altered through treatment with rapamycin, and that metabolic cycles continue even in respiratory deficient strains. These results provide a foundation for future studies of the physiological importance of metabolic cycles in processes such as CDC control, metabolic regulation and cell aging.

Instability of the steady state solution in cell cycle population structure models with feedback

We show that when cell-cell feedback is added to a model of the cell cycle for a large population of cells, then instability of the steady state solution occurs in many cases. We show this in the context of a generic agent-based ODE model. If the feedback is positive, then instability of the steady state solution is proved for all parameter values except for a small set on the boundary of parameter space. For negative feedback we prove instability for half the parameter space. We also show by example that instability in the other half may be proved on a case by case basis.

A minimal "push-pull" bistability model explains oscillations between quiescent and proliferative cell states

A minimal model for oscillating between quiescent and growth/proliferation states, dependent on the availability of a central metabolic resource, is presented. From the yeast metabolic cycles, metabolic oscillations in oxygen consumption are represented as transitions between quiescent and growth states. We consider metabolic resource availability, growth rates, and switching rates (between states) to model a relaxation oscillator explaining transitions between these states. This frustrated bistability model reveals a required communication between the metabolic resource that determines oscillations and the quiescent and growth state cells. Cells in each state reflect memory, or hysteresis of their current state, and “push–pull” cells from the other state. Finally, a parsimonious argument is made for a specific central metabolite as the controller of switching between quiescence and growth states. We discuss how an oscillator built around the availability of such a metabolic resource is sufficient to generally regulate oscillations between growth and quiescence through committed transitions.

How yeast coordinates metabolism, growth and division

All cells, especially single cell organisms, need to adapt their metabolism, growth and division coordinately to the available nutrients. This coordination is mediated by extensive cross-talk between nutrient signaling, metabolism, growth, and the cell division cycle, which is only gradually being uncovered: Nutrient signaling not only controls entry into the cell cycle at the G1/S transition, but all phases of the cell cycle. Metabolites are even sensed directly by cell cycle regulators to prevent cell cycle progression in absence of sufficient metabolic fluxes. In turn, cell cycle regulators such as the cyclin-dependent kinase directly control metabolic fluxes during cell cycle progression. In this review, I highlight some recent advances in our understanding of how metabolism and the cell division cycle are coordinated in the model organism Saccharomyces cerevisiae.

Cyclin-Dependent Kinase Co-Ordinates Carbohydrate Metabolism and Cell Cycle in S. cerevisiae

Cyclin-dependent kinases (CDKs) control cell division in eukaryotes by phosphorylating proteins involved in division. But successful proliferation requires co-ordination between division and cellular growth in mass. Previous proteomic studies suggested that metabolic proteins, as well as cell division proteins, could potentially be substrates of cyclin-dependent kinases. Here we focus on two metabolic enzymes of the yeast S. cerevisiae, neutral trehalase (Nth1) and glycogen phosphorylase (Gph1), and show that their activities are likely directly controlled by CDK activity, thus allowing co-ordinate regulation of carbohydrate metabolism with cell division processes. In this case, co-ordinate regulation may optimize the decision to undertake a final cell division as nutrients are being exhausted. Co-regulation of cell division processes and metabolic processes by CDK activity may be a general phenomenon important for co-ordinating the cell cycle with growth.

The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression

Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation.

Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy

The functional basis of genetic robustness, the ability of organisms to suppress the effects of mutations, remains incompletely understood. We exposed a set of 15 strains of Saccharomyces cerevisiae form diverse environments to increasing doses of the chemical mutagen EMS. The number of the resulting random mutations was similar for all tested strains. However, there were differences in immediate mortality after the mutagenic treatment and in defective growth of survivors. An analysis of gene expression revealed that immediate mortality was lowest in strains with lowest expression of transmembrane proteins, which are rich in thiol groups and thus vulnerable to EMS. A signal of genuine genetic robustness was detected for the other trait, the ability to grow well despite bearing non-lethal mutations. Increased tolerance of such mutations correlated with high expression of genes responsible for the oxidative energy metabolism, suggesting that the negative effect of mutations can be buffered if enough energy is available. We confirmed this finding in three additional tests of the ability to grow on (i) fermentable or non-fermentable sources of carbon, (ii) under chemical inhibition of the electron transport chain and (iii) during overexpression of its key component, cytochrome c. Our results add the capacity to generate energy as a general mechanism of genetic robustness.

The ability to suppress phenotypic effects of mutations is termed genetic robustness. Its functional basis and evolutionary origin remain insufficiently understood despite decades of research. In fact, it is still largely untested whether genetic robustness is a trait of substantial, within-species variation. We used a model organism, Saccharomyces cerevisiae, to study both phenotypic signs and functional underpinnings of genetic robustness. We introduced random mutations into a set of well-characterized yeast strain. There was considerable variation in the growth rate among clones recovered after mutagenesis, which is an indication of genetic robustness. Using available data on gene expression for our strains, we found that genetic robustness was strongest among strains with enhanced expression of genes related to the energy metabolism. We reasoned that, regardless of the specific mutations, the capacity to generate metabolic energy may be a general underlying mechanism for buffering the effects of random mutations across the genome. We confirmed this hypothesis in further experiments in which we showed that genetic robustness decreases when the energy metabolism is compromised and increases when it is boosted.

Cell cycle Start is coupled to entry into the yeast metabolic cycle across diverse strains and growth rates

Cells have evolved oscillators with different frequencies to coordinate periodic processes. Here we studied the interaction of two oscillators, the cell division cycle (CDC) and the yeast metabolic cycle (YMC), in budding yeast. Previous work suggested that the CDC and YMC interact to separate high oxygen consumption (HOC) from DNA replication to prevent genetic damage. To test this hypothesis, we grew diverse strains in chemostat and measured DNA replication and oxygen consumption with high temporal resolution at different growth rates. Our data showed that HOC is not strictly separated from DNA replication; rather, cell cycle Start is coupled with the initiation of HOC and catabolism of storage carbohydrates. The logic of this YMC-CDC coupling may be to ensure that DNA replication and cell division occur only when sufficient cellular energy reserves have accumulated. Our results also uncovered a quantitative relationship between CDC period and YMC period across different strains. More generally, our approach shows how studies in genetically diverse strains efficiently identify robust phenotypes and steer the experimentalist away from strain-specific idiosyncrasies.

Cell cycle dynamics: clustering is universal in negative feedback systems

We study a model of cell cycle ensemble dynamics with cell-cell feedback in which cells in one fixed phase of the cycle S (Signaling) produce chemical agents that affect the growth and development rate of cells that are in another phase R (Responsive). For this type of system there are special periodic solutions that we call k-cyclic or clustered. Biologically, a k-cyclic solution represents k cohorts of synchronized cells spaced nearly evenly around the cell cycle. We show, under very general nonlinear feedback, that for a fixed k the stability of the k-cyclic solutions can be characterized completely in parameter space, a 2 dimensional triangle T. We show that T is naturally partitioned into k(2) sub-triangles on each of which the k-cyclic solutions all have the same stability type. For negative feedback we observe that while the synchronous solution (k = 1) is unstable, regions of stability of k ≥ 2 clustered solutions seem to occupy all of T. We also observe bi-stability or multi-stability for many parameter values in negative feedback systems. Thus in systems with negative feedback we should expect to observe cyclic solutions for some k. This is in contrast to the case of positive feedback, where we observe that the only asymptotically stable periodic orbit is the synchronous solution.

Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis

Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. During this course, the cells support a constant biomass-production rate with decreasing rates of respiration and ATP production but also decrease their stress resistance. As the respiration rate decreases, so do the levels of enzymes catalyzing rate-determining reactions of the tricarboxylic-acid cycle (providing NADH for respiration) and of mitochondrial folate-mediated NADPH production (required for oxidative defense). The findings demonstrate that exponential growth can represent not a single metabolic/physiological state but a continuum of changing states and that aerobic glycolysis can reduce the energy demands associated with respiratory metabolism and stress survival.

Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations

BACKGROUND

Resistance to stress is often heterogeneous among individuals within a population, which helps protect against intermittent stress (bet hedging). This is also the case for heat shock resistance in the budding yeast Saccharomyces cerevisiae. Interestingly, the resistance appears to be continuously distributed (vs. binary, switch-like) and correlated with replicative age (vs. random). Older, slower-growing cells are more resistant than younger, faster-growing ones. Is there a fitness benefit to age-correlated stress resistance?

RESULTS

Here this hypothesis is explored using a simple agent-based model, which simulates a population of individual cells that grow and replicate. Cells age by accumulating damage, which lowers their growth rate. They synthesize trehalose at a metabolic cost, which helps protect against heat shock. Proteins Tsl1 and Tps3 (trehalose synthase complex regulatory subunit TSL1 and TPS3) represent the trehalose synthesis complex and they are expressed using constant, age-dependent and stochastic terms. The model was constrained by calibration and comparison to data from the literature, including individual-based observations obtained using high-throughput microscopy and flow cytometry. A heterogeneity network was developed, which highlights the predominant sources and pathways of resistance heterogeneity. To determine the best trehalose synthesis strategy, model strains with different Tsl1/Tps3 expression parameters were placed in competition in an environment with intermittent heat shocks.

CONCLUSIONS

For high severities and low frequencies of heat shock, the winning strain used an age-dependent bet hedging strategy, which shows that there can be a benefit to age-correlated stress resistance. The study also illustrates the utility of combining individual-based observations and modeling to understand mechanisms underlying population heterogeneity, and the effect on fitness.

Application of statistical techniques for elucidating flow cytometric data of batch and fed-batch cultures

The objective of this work is to develop structured, segregated stochastic models for bioprocesses using time-series flow cytometric (FC) data. To this end, mammalian CHO cells were grown in both batch and fed-batch cultures, and their viable cell numbers (VCDs), monoclonal antibody (MAb), cell cycle phases, mitochondria membrane potential/mitochondria mass, Golgi apparatus, and endoplasmic reticulum (ER) were analyzed. For the fed-batch mode, soy hydrolysate was introduced at 24-H intervals. The cytometric data were analyzed for early indicators of growth and productivity by multiple linear regression analysis, which involved taking into account multicollinearity diagnostics, Durbin-Watson statistics, and Houston tests to determine and refine statistically significant correlations between categorical variables (FC parameters) and response variables (yield parameters). The results indicate that the percentage of G1 cells and ER was significantly correlated with VCD and MAb in the case of batch culture, whereas for fed-batch culture, the percentage of G2 cells and ER was correlated significantly. There was a significant difference between cells in the batch and fed-batch cultures in their ER content, suggesting that the increase in protein synthesis as reflected by the ER content and consequent increase in growth rate and MAb productivity both can be monitored at the cellular level by FC analysis of ER content.

A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

Transitions between the two phases of the cell growth cycle can account for the environmental stress response, the growth-rate response, and the cross-protection between slow growth and various types of stress factors. It is suggested that this mechanism is conserved across budding and fission yeast and normal human cells.

The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases that are most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is associated with the periodic expression of thousands of genes, producing oscillating patterns of gene expression found in synchronized cultures and in single cells of slowly growing unsynchronized cultures. Systematic variation in the durations of the HOC and LOC phases can account quantitatively for well-studied transcriptional responses to growth rate differences. Here we show that a similar mechanism—transitions from the HOC phase to the LOC phase—can account for much of the common environmental stress response (ESR) and for the cross-protection by a preliminary heat stress (or slow growth rate) to subsequent lethal heat stress. Similar to the budding yeast metabolic cycle, we suggest that a metabolic cycle, coupled in a similar way to the ESR, in the distantly related fission yeast, Schizosaccharomyces pombe, and in humans can explain gene expression and respiratory patterns observed in these eukaryotes. Although metabolic cycling is associated with the G0/G1 phase of the cell division cycle of slowly growing budding yeast, transcriptional cycling was detected in the G2 phase of the division cycle in fission yeast, consistent with the idea that respiratory metabolic cycling occurs during the phases of the cell division cycle associated with mass accumulation in these divergent eukaryotes.

Identification of informative metabolic responses using a minibioreactor: a small step change in the glucose supply rate creates a large metabolic response in Saccharomyces cerevisiae

In this study, a previously developed mini-bioreactor, the Biocurve, was used to identify an informative stimulus-response experiment. The identified stimulus-response experiment was a modest 50% shift-up in glucose uptake rate (qGLC) that unexpectedly resulted in a disproportionate transient metabolic response. The 50% shift-up in qGLC in the Biocurve resulted in a near tripling of the online measured oxygen uptake (qO2) and carbon dioxide production (qCO2) rates, suggesting a considerable mobilization of glycogen and trehalose. The 50% shift-up in qGLC was subsequently studied in detail in a conventional bioreactor (4 l working volume), which confirmed the results obtained with the Biocurve. Especially relevant is the observation that the 50% increase in glucose uptake rate led to a three-fold increase in glycolytic flux, due to mobilization of storage materials. This explains the unexpected ethanol and acetate secretion after the shift-up, in spite of the fact that after the shift-up the qGLC was far less than the critical value. Moreover, these results show that the correct in vivo fluxes in glucose pulse experiments cannot be obtained from the uptake and secretion rates only. Instead, the storage fluxes must also be accurately quantified. Finally, we speculate on the possible role that the transient increase in dissolved CO2 immediately after the 50% shift-up in qGLC could have played a part in triggering glycogen and trehalose mobilization.

Metabolic cycling without cell division cycling in respiring yeast

Despite rapid progress in characterizing the yeast metabolic cycle, its connection to the cell division cycle (CDC) has remained unclear. We discovered that a prototrophic batch culture of budding yeast, growing in a phosphate-limited ethanol medium, synchronizes spontaneously and goes through multiple metabolic cycles, whereas the fraction of cells in the G1/G0 phase of the CDC increases monotonically from 90 to 99%. This demonstrates that metabolic cycling does not require cell division cycling and that metabolic synchrony does not require carbon-source limitation. More than 3,000 genes, including most genes annotated to the CDC, were expressed periodically in our batch culture, albeit a mere 10% of the cells divided asynchronously; only a smaller subset of CDC genes correlated with cell division. These results suggest that the yeast metabolic cycle reflects a growth cycle during G1/G0 and explains our previous puzzling observation that genes annotated to the CDC increase in expression at slow growth.

Clustering in cell cycle dynamics with general response/signaling feedback

Motivated by experimental and theoretical work on autonomous oscillations in yeast, we analyze ordinary differential equations models of large populations of cells with cell-cycle dependent feedback. We assume a particular type of feedback that we call responsive/signaling (RS), but do not specify a functional form of the feedback. We study the dynamics and emergent behavior of solutions, particularly temporal clustering and stability of clustered solutions. We establish the existence of certain periodic clustered solutions as well as "uniform" solutions and add to the evidence that cell-cycle dependent feedback robustly leads to cell-cycle clustering. We highlight the fundamental differences in dynamics between systems with negative and positive feedback. For positive feedback systems the most important mechanism seems to be the stability of individual isolated clusters. On the other hand we find that in negative feedback systems, clusters must interact with each other to reinforce coherence. We conclude from various details of the mathematical analysis that negative feedback is most consistent with observations in yeast experiments.

Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate

Oscillations in patterns of expression of a large fraction of yeast genes are associated with the "metabolic cycle," usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells. Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations. We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.

Ultradian metabolic cycles in yeast

Budding yeast are capable of displaying various modes of oscillatory behavior. Such cycles can occur with a period ranging from 1 min up to many hours, depending on the growth and culturing conditions used to observe them. This chapter discusses the robust oscillations in oxygen consumption exhibited by high-density yeast cell populations during continuous, glucose-limited growth in a chemostat. These ultradian metabolic cycles offer a view of the life of yeast cells under a challenging, nutrient-poor growth environment and might represent useful systems to interrogate a variety of fundamental metabolic and regulatory processes.

Involvement of a cell size control mechanism in the induction and maintenance of oscillations in continuous cultures of budding yeast

Spontaneous oscillations occur in glucose-limited continuous cultures of Saccharomyces cerevisiae under aerobic conditions. The oscillatory behavior is detectable as a periodic change of many bioparameters such as dissolved oxygen, ethanol production, biomass concentration, as well as cellular content of storage carbohydrates and is associated to a marked synchronization of the yeast population. These oscillations may be related to a periodic accumulation of ethanol produced by yeast in the culture medium.The addition of ethanol to oscillating yeast cultures supports this hypothesis: indeed, no effect was observed if ethanol was added when already present in the medium, while a marked phase oscillation shift was obtained when ethanol was added at any other time. Moreover, the addition of ethanol to a nonoscillating culture triggers new oscillations. An accurate analysis performed at the level of nonoscillating yeast populations perturbed by addition of ethanol showed that both the growth rate and the protein content required for cell division increased in the presence of mixed substrate (i.e., ethanol plus limiting glucose). A marked synchronization of the yeast population occurred when the added ethanol was exhausted and the culture resumed growth only on limiting glucose. A decrease of protein content required for cell division was also apparent. These experimental findings support a new model for spontaneous oscillations in yeast cultures in which the alternative growth on limiting glucose and limiting glucose plus ethanol modifies the critical protein content required for cell division.

Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations

Microbes tailor their growth rate to nutrient availability. Here, we measured, using liquid chromatography-mass spectrometry, >100 intracellular metabolites in steady-state cultures of Saccharomyces cerevisiae growing at five different rates and in each of five different limiting nutrients. In contrast to gene transcripts, where approximately 25% correlated with growth rate irrespective of the nature of the limiting nutrient, metabolite concentrations were highly sensitive to the limiting nutrient's identity. Nitrogen (ammonium) and carbon (glucose) limitation were characterized by low intracellular amino acid and high nucleotide levels, whereas phosphorus (phosphate) limitation resulted in the converse. Low adenylate energy charge was found selectively in phosphorus limitation, suggesting the energy charge may actually measure phosphorus availability. Particularly strong concentration responses occurred in metabolites closely linked to the limiting nutrient, e.g., glutamine in nitrogen limitation, ATP in phosphorus limitation, and pyruvate in carbon limitation. A simple but physically realistic model involving the availability of these metabolites was adequate to account for cellular growth rate. The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome.

Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae

Accumulation of glycogen and trehalose in nutrient-limited cultures of Saccharomyces cerevisiae is negatively correlated with the specific growth rate. Additionally, glucose-excess conditions (i.e., growth limitation by nutrients other than glucose) are often implicated in high-level accumulation of these storage carbohydrates. The present study investigates how the identity of the growth-limiting nutrient affects accumulation of storage carbohydrates in cultures grown at a fixed specific growth rate. In anaerobic chemostat cultures (dilution rate, 0.10 h(-1)) of S. cerevisiae, the identity of the growth-limiting nutrient (glucose, ammonia, sulfate, phosphate, or zinc) strongly affected storage carbohydrate accumulation. The glycogen contents of the biomass from glucose- and ammonia-limited cultures were 10- to 14-fold higher than those of the biomass from cultures grown under the other three glucose-excess regimens. Trehalose levels were specifically higher under nitrogen-limited conditions. These results demonstrate that storage carbohydrate accumulation in nutrient-limited cultures of S. cerevisiae is not a generic response to excess glucose but instead is strongly dependent on the identity of the growth-limiting nutrient. While transcriptome analysis of wild-type and msn2Delta msn4Delta strains confirmed that transcriptional upregulation of glycogen and trehalose biosynthesis genes is mediated by Msn2p/Msn4p, transcriptional regulation could not quantitatively account for the drastic changes in storage carbohydrate accumulation. The results of assays of glycogen synthase and glycogen phosphorylase activities supported involvement of posttranscriptional regulation. Consistent with the high glycogen levels in ammonia-limited cultures, the ratio of glycogen synthase to glycogen phosphorylase in these cultures was up to eightfold higher than the ratio in the other glucose-excess cultures.

Respiratory oscillations in yeasts

Respiratory oscillations in yeasts have been studied in three time domains with periods of (a) about a minute, (b) about 40 min, and (c) about a day. Reactive responses (damped oscillations), rhythms and temperature-compensated clocks have been described for (b) and (c), but a timekeeping clock has not yet been shown for (a). Synchronous populations reveal the time-structure that can only otherwise be studied in single organisms; this is because time-averaging through an asynchronous population conceals its fine structure. Early studies with synchronous cultures made by size selection methods indicated ultradian-clock driven oscillations in respiration, pools of adenylates, total protein, RNA synthesis and many enzyme activities (tau = 40 min in Schizosaccharomyces pombe, 30 min in Candida utilis), and more recently in self-synchronised continuous cultures of Saccharomyces cerevisiae (tau = 48 min). Most detailed understanding comes from the latter system, where continuous, noninvasive real-time monitoring (of 02 uptake, CO2 production, and NAD(P)H redox state) is combined with frequent discrete time samples (for other redox components, including H2S, GSH and cytochromes, metabolites, and mRNA levels). A redox switch lies at the heart of this ultradian clock and a plethora of outputs is optimized to a time-base that is genetically-determined and differs in different organisms. It is suggested that the entire temporal landscape of all eukaryotic organisms and the cells of higher plants and animals is constructed on this basis. A time frame for the coordination and coherence of all intracellular processes and the construction and assembly of cellular structures is provided by the ultradian clock The circadian clock matches these functions to the daily cycle of the external environment.

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast

We studied the relationship between growth rate and genome-wide gene expression, cell cycle progression, and glucose metabolism in 36 steady-state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil, or leucine). The expression of more than one quarter of all yeast genes is linearly correlated with growth rate, independent of the limiting nutrient. The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions. Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling. We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient. Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate, or ammonia did not; this phenomenon (reminiscent of the "Warburg effect" in cancer cells) was confirmed in batch cultures. Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an "instantaneous growth rate." This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle.

Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture

We monitored a continuous culture of the yeast Saccharomyces cerevisiae by membrane-inlet mass spectrometry. This technique allows very rapid simultaneous measurements (one point every 12 s) of several dissolved gases. During our experiment, the culture exhibited a multioscillatory mode in which the dissolved oxygen and carbon dioxide records displayed periodicities of 13 h, 36 min and 4 min. The 36- and 4-min modes were not visible at all times, but returned at regular intervals during the 13-h cycle. The 4-min mode, which has not previously been described in continuous culture, can also be seen when the culture displays simpler oscillatory behavior. The data can be used to visualize a metabolic attractor of this system, i.e. the set of dissolved gas concentrations which are consistent with the multioscillatory state. Computation of the leading Lyapunov exponent reveals the dynamics on this attractor to be chaotic.

Metabolic control of glucose degradation in yeast and tumor cells

Regulation of glucose degradation in both yeasts and tumor cells is very similar in many respects. In both cases it leads to excretion of intermediary metabolites (e.g., ethanol, lactate) in those cell types where uptake of glucose is unrestricted (Saccharomyces cerevisiae, Bowes melanoma cells). The similarities between glucose metabolism observed in yeast and tumor cells is explained by the fact that cell transformation of animal cells leads to inadequate expression of (proto-)oncogenes, which force the cell to enter the cell cycle. These events are accompanied by alterations at the signal transduction level, a marked increase of glucose transporter synthesis, enhancement of glycolytic key enzyme activities, and slightly reduced respiration of the tumor cell. In relation to homologous glucose degradation found in yeast and tumor cells there exist strong similarities on the level of cell division cycle genes, signal transduction and regulation of glycolytic key enzymes. It has been demonstrated that ethanol and lactate excretion in yeast and tumor cells, respectively, result from an overflow reaction at the point of pyruvate that is due to a carbon flux exceeding the capacity of oxidative breakdown. Therefore, the respiratory capacity of a cell determines the amount of glycolytic breakdown products if ample glucose is available. This restricted flux is also referred to as the respiratory bottleneck. The expression "catabolite repression", which is often used in textbooks to explain ethanol and acid excretion, should be abandoned, unless specific mechanisms can be demonstrated. Furthermore, it was shown that maximum respiration and growth rates are only obtained under optimum culture conditions, where the carbon source is limiting.

Metabolic cycle, cell cycle, and the finishing kick to Start

Slowly growing budding yeast store carbohydrate, then liquidate it in late G1 phase of the cell cycle, superimposing a metabolic cycle on the cell cycle. This metabolic cycle may separate biochemically incompatible processes. Alternatively it may provide a burst of energy and material for commitment to the cell cycle. Stored carbohydrate could explain the size requirement for cells passing the Start point.

Growth during the cell cycle

During the cell cycle, major bulk parameters such as volume, dry mass, total protein, and total RNA double and such growth is a fundamental property of the cell cycle. The patterns of growth in volume and total protein or RNA provide an "envelope" that contains and may restrict the gear wheels. The main parameters of cell cycle growth were established in the earlier work when people moved from this field to the reductionist approaches of molecular biology, but very little is known on the patterns of metabolism. Most of the bulk properties of cells show a continuous increase during the cell cycle, although the exact pattern of this increase may vary. Since the earliest days, there have been two popular models, based on an exponential increase and linear increase. In the first, there is no sharp change in the rate of increase through the cycle but a smooth increase by a factor of two. In the second, the rate of increase stays constant through much of the cycle but it doubles sharply at a rate change point (RCP). It is thought that the exponential increase is caused by the steady growth of ribosome numbers and the linear pattern is caused by a doubling of the structural genes during the S period giving an RCP--a "gene dosage" effect. In budding yeast, there are experiments fitting both models but on balance slightly favoring "gene dosage." In fission yeast, there is no good evidence of exponential increase. All the bulk properties, except O2 consumption, appear to follow linear patterns with an RCP during the short S period. In addition, there is in wild-type cells a minor RCP in G2 where the rate increases by 70%. In mammalian cells, there is good but not extensive evidence of exponential increase. In Escherichia coli, exponential increase appears to be the pattern. There are two important points: First, some proteins do not show peaks of periodic synthesis. If they show patterns of exponential increase both they and the total protein pattern will not be cell cycle regulated. However, if the total protein pattern is not exponential, then a majority of the individual proteins will be so regulated. If this majority pattern is linear, then it can be detected from rate measurements on total protein. However, it would be much harder at the level of individual proteins where the methods are at present not sensitive enough to detect a rate change by a factor of two. At a simple level, it is only the exponential increase that is not cell cycle regulated in a synchronous culture. The existence of a "size control" is well known and the control has been studied for a long time, but it has been remarkably resistant to molecular analysis. The attainment of a critical size triggers the periodic events of the cycle such as the S period and mitosis. This control acts as a homeostatic effector that maintains a constant "average" cell size at division through successive cycles in a growing culture. It is a vital link coordinating cell growth with periodic events of the cycle. A size control is present in all the systems and appears to operate near the start of S or of mitosis when the cell has reached a critical size, but the molecular mechanism by which size is measured remains both obscure and a challenge. A simple version might be for the cell to detect a critical concentration of a gene product.

Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae

We have investigated the role of 3',5'-cyclic-adenosine-monophosphate (cAMP) in mediating the coupling between energy metabolism and cell cycle progression in both synchronous cultures and oscillating continuous cultures of Saccharomyces cerevisiae. For the first time, a peak in intracellular cAMP was shown to precede the observed breakdown of trehalose and glycogen during cell cycle-related oscillations. Measurements in synchronous cultures demonstrated that this peak can be associated with the cell cycle dynamics of cAMP under conditions of glucose-limited growth, which was found to differ significantly from that observed in synchronous glucose-repressed cultures. Our results support the notion that cAMP plays a major role in mediating the integration of energy metabolism and cell cycle progression, both in the single cell and during cell cycle-related oscillations in continuous culture, respectively. Evidence is presented that the dynamic behaviour of intracellular cAMP during the cell cycle is modulated depending on nutrient supply. The implications of these findings regarding the role of cAMP in regulating cell cycle progression and energy metabolism are discussed.

Characterization of cell population growth by cell cycle parameters

The quantitative description of the relationships between global properties, defined at the cellular population level, and individual properties, defined at the single cell level, is considered in this communication along with the analysis of some segregated models of yeast and hybridoma cell cultures.

Cybernetic model of the growth dynamics of Saccharomyces cerevisiae in batch and continuous cultures

Growth of Saccharomyces cerevisiae on glucose in aerobic batch culture follows the well-documented diauxic pattern of completely fermenting glucose to ethanol during the first exponential growth phase, followed by an intermediate lag phase and a second exponential growth phase consuming ethanol. In continuous cultures over a range of intermediate dilution rates, the yeast bioreactor exhibits sustained oscillations in all the measured concentrations, such as cell mass, glucose, ethanol, and dissolved oxygen, the amounts of intracellular storage carbohydrates, such as glycogen and trehalose, the fraction of budded cells as well as the culture pH. We present here a structured, unsegregated model for the yeast growth dynamics developed from the 'cybernetic' modeling framework, to simulate the dynamic competition between all the available metabolic pathways. This cybernetic model accurately predicts all the key experimentally observed aspects: (i) in batch cultures, duration of the intermediate lag phase, sequential production and consumption of ethanol, and the dynamics of the gaseous exchange rates of oxygen and carbon dioxide; and (ii) in continuous cultures, the spontaneous generation of oscillations as well as the variations in period and amplitude of oscillations when the dilution rate or agitatin rate are changed.

Function of trehalose and glycogen in cell cycle progression and cell viability in Saccharomyces cerevisiae

Trehalose and glycogen accumulate in Saccharomyces cerevisiae when growth conditions deteriorate. It has been suggested that aside from functioning as storage factors and stress protectants, these carbohydrates may be required for cell cycle progression at low growth rates under carbon limitation. By using a mutant unable to synthesize trehalose and glycogen, we have investigated this requirement of trehalose and glycogen under carbon-limited conditions in continuous cultures. Trehalose and glycogen levels increased with decreasing growth rates in the wild-type strain, whereas no trehalose or glycogen was detected in the mutant. However, the mutant was still able to grow and divide at low growth rates with doubling times similar to those for the wild-type strain, indicating that trehalose and glycogen are not essential for cell cycle progression. Nevertheless, upon a slight increase of extracellular carbohydrates, the wild-type strain degraded its reserve carbohydrates and was able to enter a cell division cycle faster than the mutant. In addition, wild-type cells survived much longer than the mutant cells when extracellular carbon was exhausted. Thus, trehalose and glycogen have a dual role under these conditions, serving as storage factors during carbon starvation and providing quickly a higher carbon and ATP flux when conditions improve. Interestingly, the CO2 production rate and hence the ATP flux were higher in the mutant than in the wild-type strain at low growth rates. The possibility that the mutant strain requires this steady higher glycolytic flux at low growth rates for passage through Start is discussed.

Effects of different carbon fluxes on G1 phase duration, cyclin expression, and reserve carbohydrate metabolism in Saccharomyces cerevisiae

By controlled addition of galactose to synchronized galactose-limited Saccharomyces cerevisiae cultures, the growth rate could be regulated while external conditions were kept constant. By using this method, the G1 phase duration was modulated and expression of cell cycle-regulated genes was investigated. The expression of the cyclin genes CLN1 and CLN2 was always induced just before bud emergence, indicating that this event marks the decision to pass Start. Thus, G1 phase elongation was not due to a slower accumulation of the CLN1 and CLN2 mRNA levels. Only small differences in CLN3 expression levels were observed. The maximal SWI4 expression preceded maximal CLN1 and CLN2 expression under all conditions, as expected for a transcriptional activator. But whereas SWI4 was expressed at about 10 to 20 min, before CLN1 and CLN2 expression at high growth rates, this time increased to about 300 min below a particular consumption rate at which the G1 phase strongly elongated. In the slower-growing cultures, also an increase in SWI6 expression was observed in the G1 phase. The increase in G1 phase duration below a particular consumption rate was accompanied by a strong increase in the reserve carbohydrate levels. These carbohydrates were metabolized again before bud emergence, indicating that below this consumption rate, a transient increase in ATP flux is required for progression through the cell cycle. Since Start occurred at different cell sizes under different growth conditions, it is not just a certain cell size that triggers passage through Start.

Molecular biology of trehalose and the trehalases in the yeast Saccharomyces cerevisiae

The present state of knowledge of the role of trehalose and trehalose hydrolysis catalyzed by trehalase (EC 3.2.1.28) in the yeast Saccharomyces cerevisiae is reviewed. Trehalose is believed to function as a storage carbohydrate because its concentration is high during nutrient limitations and in resting cells. It is also believed to function as a stress metabolite because its concentration increases during certain adverse environmental conditions, such as heat and toxic chemicals. The exact way trehalose may perform the stress function is not understood, and conditions exist under which trehalose accumulation and tolerance to certain stress situations cannot be correlated. Three trehalases have been described in S. cerevisiae: 1) the cytosolic neutral trehalase encoded by the NTH1 gene, and regulated by cAMP-dependent phosphorylation process, nutrients, and temperature; 2) the vacuolar acid trehalase encoded by the ATH1 gene, and regulated by nutrients; and 3) a putative trehalase Nth1p encoded by the NTH2 gene (homolog of the NTH1 gene) and regulated by nutrients and temperature. The neutral trehalase is responsible for intracellular hydrolysis of trehalose, in contrast to the acid trehalase, which is responsible for utilization of extracellular trehalose. The role of the putative trehalase Nth2p in trehalose metabolism is not known. The NTH1 and NTH2 genes are required for recovery of cells after heat shock at 50 degrees C, consistent with their heat inducibility and sequence similarity. Other stressors, such as toxic chemicals, also induce the expression of these genes. We therefore propose that the NTH1 and NTH2 genes have stress-related function and the gene products may be called stress proteins. Whether the stress function of the trehalase genes is linked to trehalose is not clear, and possible mechanisms of stress protective function of the trehalases are discussed.

Continuous cultivation of the yeast Saccharomyces cerevisiae at different dilution rates and glucose concentrations in nutrient media

The influence of glucose concentration in nutrient media on the specific growth rate and biomass yield in the course of continuous fermentation of Saccharomyces cerevisiae was investigated. An increase of glucose content in media decreased the specific growth rate and the biomass yield. Glucose concentration had significant effects on protein and phosphate contents of cells. However, an increased glucose concentration increased the fermentative power of S. cerevisiae (SJA-method). An increase of the dilution rate decreased the cell concentration in the fermentor. Specific growth rate approach the values of the dilution rate. The best agreement has been obtained at a dilution rate of 0.20/h. This dilution rate proved to be most convenient for the investigated microorganism and cultivation conditions (media composition, pH, aeration intensity and temperature). Biomass yield proved to be decreased by an increase of the dilution rate.

Analysis of oscillations in yeast continuous cultures by a new simplified model

The autonomous oscillations in yeast continuous cultures are investigated analytically and related to the behaviour of the single cell by means of a suitable modified version of Monod's classical chemostat model. Two main cell phases or states are considered to account for the experimentally observed changes occurring in the cell growth course: the budded phase and the unbudded one. Thus, a sort of two compartment structure is given to the total biomass. The model so far obtained allows one to analyse the local properties of the predicted steady states under various assumptions, both on the yield coefficients and the specific growth rates. Necessary conditions for the local instability are derived and the existence of stable limit cycles is shown by computer simulation. With respect to the qualitative changes in the metabolic parameters, this analysis agrees with the results obtained by simulation of complex structured and segregated models. However, the oscillation period is too long compared with the experimental one and this fact may be mainly due to the strong simplifying assumptions on the dynamic evolution of the transfer rates between the two compartments. The model's usefulness seems until now restricted to the identification of the relationships between the cell cycle regulation and the oscillation triggering.

Fermentable sugars and intracellular acidification as specific activators of the RAS-adenylate cyclase signalling pathway in yeast: the relationship to nutrient-induced cell cycle control

The RAS proteins of the yeast Saccharomyces cerevisiae fulfil a similar control function on yeast adenylate cyclase as the mammalian Gs proteins on mammalian adenylate cyclase. The discovery that glucose and other fermentable sugars act as specific activators of the RAS-adenylate cyclase pathway in yeast appeared to offer a mechanism for the way in which at least one nutrient would control progression over the start point in the G1 phase of the yeast cell cycle by means of this pathway. Recently, however, evidence has been obtained to show that the glucose-activation pathway of adenylate cyclase is a glucose-repressible pathway and therefore not operative during growth on glucose. In addition, mutant strains were obtained which lack the glucose-activation pathway and show normal exponential growth on glucose. This appears to confine the physiological role of this pathway to control of the transition from the derepressed state (growth on respirative carbon sources) to the repressed state (growth on fermentative carbon sources) by means of an already well-documented cAMP-triggered protein phosphorylation cascade. Intracellular acidification also stimulates the RAS-adenylate cyclase pathway, which might constitute a rescue mechanism for cells suffering from stress conditions. The presence of a nitrogen source does not stimulate the RAS-adenylate cyclase pathway. Although other nutrient signals for the pathway might still be discovered, it appears more and more likely that the well-known requirement of cAMP for progression over the start point of the yeast cell cycle is limited to providing a basal cAMP level rather than acting as a second messenger for an extracellular signal.(ABSTRACT TRUNCATED AT 250 WORDS)

Production and localization of beta-fructosidase in asynchronous and synchronous chemostat cultures of yeasts

In synchronized continuous cultures of Saccharomyces cerevisiae CBS 8066, the production of the extracellular invertase (EC 3.2.1.26) showed a cyclic behavior that coincided with the budding cycle. The invertase activity increased during bud development and ceased at bud maturation and cell scission. The cyclic changes in invertase production resulted in cyclic changes in amounts of invertase localized in the cell wall. However, the amount of enzyme invertase present in the culture liquid remained constant throughout the budding cycle. Also, in asynchronous continuous cultures of S. cerevisiae, the production and localization of invertase showed significant fluctuation. The overall invertase production in an asynchronous culture was two to three times higher than in synchronous cultures. This could be due to more-severe invertase-repressive conditions in a synchronous chemostat culture. Both the intracellular glucose-6-phosphate concentration and residual glucose concentration were significantly higher in synchronous chemostat cultures than in asynchronous chemostat cultures. In the asynchronous and synchronous continuous cultures of S. cerevisiae, about 40% of the invertase was released into the culture liquid; it has generally been believed that S. cerevisiae releases only about 5% of its invertase. In contrast to invertase production and localization in the chemostat cultures of S. cerevisiae, no significant changes in inulinase (EC 3.2.1.7) production and localization were observed in chemostat cultures of Kluyveromyces maxianus CBS 6556. In cultures of K. marxianus about 50% of the inulinase was present in the culture liquid.

Changes in activities of several enzymes involved in carbohydrate metabolism during the cell cycle of Saccharomyces cerevisiae

Activity changes of a number of enzymes involved in carbohydrate metabolism were determined in cell extracts of fractionated exponential-phase populations of Saccharomyces cerevisiae grown under excess glucose. Cell-size fractionation was achieved by an improved centrifugal elutriation procedure. Evidence that the yeast populations had been fractionated according to age in the cell cycle was obtained by examining the various cell fractions for their volume distribution and their microscopic appearance and by flow cytometric analysis of the distribution patterns of cellular DNA and protein contents. Trehalase, hexokinase, pyruvate kinase, phosphofructokinase 1, and fructose-1,6-diphosphatase showed changes in specific activities throughout the cell cycle, whereas the specific activities of alcohol dehydrogenase and glucose-6-phosphate dehydrogenase remained constant. The basal trehalase activity increased substantially (about 20-fold) with bud emergence and decreased again in binucleated cells. However, when the enzyme was activated by pretreatment of the cell extracts with cyclic AMP-dependent protein kinase, no significant fluctuations in activity were seen. These observations strongly favor posttranslational modification through phosphorylation-dephosphorylation as the mechanism underlying the periodic changes in trehalase activity during the cell cycle. As observed for trehalase, the specific activities of hexokinase and phosphofructokinase 1 rose from the beginning of bud formation onward, finally leading to more than eightfold higher values at the end of the S phase. Subsequently, the enzyme activities dropped markedly at later stages of the cycle. Pyruvate kinase activity was relatively low during the G1 phase and the S phase, but increased dramatically (more than 50-fold) during G2. In contrast to the three glycolytic enzymes investigated, the highest specific activity of the gluconeogenic enzyme fructose-1, 6-diphosphatase 1 was found in fractions enriched in either unbudded cells with a single nucleus or binucleated cells. The observed changes in enzyme activities most likely underlie pronounced alterations in carbohydrate metabolism during the cell cycle.

Heat-induced accumulation and futile cycling of trehalose in Saccharomyces cerevisiae

Heat shock resulted in rapid accumulation of large amounts of trehalose in Saccharomyces cerevisiae. In cultures growing exponentially on glucose, the trehalose content of the cells increased from 0.01 to 1 g/g of protein within 1 h after the incubation temperature was shifted from 27 to 40 degrees C. When the temperature was readjusted to 27 degrees C, the accumulated trehalose was rapidly degraded. In parallel, the activity of the trehalose-phosphate synthase, the key enzyme of trehalose biosynthesis, increased about sixfold during the heat shock and declined to the normal level after readjustment of the temperature. Surprisingly, the activity of neutral trehalase, the key enzyme of trehalose degradation, also increased about threefold during the heat shock and remained almost constant during recovery of the cells at 27 degrees C. In pulse-labeling experiments with [14C]glucose, trehalose was found to be turned over rapidly in heat-shocked cells, indicating that both anabolic and catabolic enzymes of trehalose metabolism were active in vivo. Possible functions of the heat-induced accumulation of trehalose and its rapid turnover in an apparently futile cycle during heat shock are discussed.