A mathematical model for the aerobic growth of Saccharomyces cerevisiae with a saturated respiratory capacity

A mathematical model for the aerobic growth of Saccharomyces cerevisiae in both batch and continuous culture is described. It was based on the experimental observation that the respiratory capacity of organism may become saturated and exhibit a maximum specific oxygen uptake rate after suitable adaptation. This experimental observation led to the possibility that transport into and out of the mitochondrion was of major importance in the overall metabolism of S. cerevisiae and was subject to long-term adaptation. Consistent with this observation a distributed model was proposed which. as its basis, assumed the control of repression or inhibition of the uptake rates of other substrates. No other regulation of fermentation and respiration was assumed. The model provided a suitable structure allowing precise quantification of the changes in rate and stoichiometry of energy production. The model clearly indicated that growth under the wide range of experimental conditions reported could not be predicted using constant values for the maximum specific respiratory rate of constant values of Y_ATP (g biomass/mol ATP) and PO ratio of (mol ATP/atom oxygen). The causes of the variation in the respiratory rate were not determined and it was concluded that a more detailed analysis (reported subsequently) was required. The variation of Y_ATP and PO ratio with specific growth rate implied that the efficiency of ATP generation or ATP utilization decreased with increasing specific growth rate. It was concluded that it was not possible to quantify the individual effect of Y_ATP and PO ratio until independent means for their reliable estimation is available.     

Characterization of the metabolic shift of Saccharomyces bayanus var. uvarum by continuous aerobic culture

Saccharomyces bayanus, being of interest for wine-making, is not as well known as S. cerevisiae and, due to many changes in the yeast classification, accurate data concerning its metabolic activity are difficult to find. In order to produce this yeast as an active dry yeast to be used as a starter in wine-making, its sensitivity to glucose was determined as the objective of our work. Using the pulse technique in continuous culture, it was found that growth in a synthetic medium was not limited by vitamins or mineral salts. We determined the critical dilution rate of a continuous culture and performed an aerobic continuous culture, measuring the respiratory quotient on-line in order to observe the metabolic shift from respiratory to fermentative metabolism. The S. bayanus var. uvarum strain studied was Crabtree-positive (glucose-sensitive) but had a weaker respiratory capacity than S. cerevisiae since the dilution rate of the metabolic shift was only 0.15 h(-1). These new data provide essential information for the biomass production of this yeast strain for wine-making.     

Increased aerobic metabolism is essential for the beneficial effects of caloric restriction on yeast life span

Calorie restriction is a dietary regimen capable of extending life span in a variety of multicellular organisms. A yeast model of calorie restriction has been developed in which limiting the concentration of glucose in the growth media of Saccharomyces cerevisiae leads to enhanced replicative and chronological longevity. Since S. cerevisiae are Crabtree-positive cells that present repression of aerobic catabolism when grown in high glucose concentrations, we investigated if this phenomenon participates in life span regulation in yeast. S. cerevisiae only exhibited an increase in chronological life span when incubated in limited concentrations of glucose. Limitation of galactose, raffinose or glycerol plus ethanol as substrates did not enhance life span. Furthermore, in Kluyveromyces lactis, a Crabtree-negative yeast, glucose limitation did not promote an enhancement of respiratory capacity nor a decrease in reactive oxygen species formation, as is characteristic of conditions of caloric restriction in S. cerevisiae. In addition, K. lactis did not present an increase in longevity when incubated in lower glucose concentrations. Altogether, our results indicate that release from repression of aerobic catabolism is essential for the beneficial effects of glucose limitation in the yeast calorie restriction model. Potential parallels between these changes in yeast and hormonal regulation of respiratory rates in animals are discussed. G. A. Oliveira and E. B. Tahara contributed equally to this work.     

Continuous culture study of transient behaviour of Saccharomyces cerevisiae growing on sucrose and fructose

During fully aerobic continuous growth of Saccharomyces cerevisiae on fructose- and sucrose-limited cultures, there exists the possibility of a number of distinct steady states at higher dilution rates. It is thus postulated that a number of discrete “states” exist for yeast cells under constant environmental conditions and that the particular “state” obtained is a function of the time spent under these conditions (adaptation) and the manner in which the steady state was approached. These observations are significant since they provide an insight into the large range of responses possible by yeasts in continuous cultures and may help to explain why unified views of sugar utilisation by yeasts have been so elusive.     

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

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

A general model for aerobic yeast growth: batch growth

A general model for aerobic yeast growth in batch culture is presented. It is based on the concept that the aerobic metabolism of all yeasts is determined by the relative sizes of the transport rate of sugar into the cell and the transport rate of respiratory intermediates into the mitochondrion. If the rate of sugar uptake rate exceeds the rate of transport of respiratory intermediates into the mitochondrion (as in Saccharomyces cerevisiae, S. uvarum, and S. pombe), the metabolism exhibits the features of ethanol excretion and limited specific oxygen uptake rate. If the rate of transport of respiratory intermediates into the mitochondrion is of the same order as the transport of sugar into the cell (as in Candida utilis), the metabolism is characterized by little or no ethanol excretion and a much higher specific oxygen uptake rate. Batch data from an extensive range of yeast and carbon sources is used to illustrate the use of this model. The ability of this model to fit such an extensive range of experimental data suggests that it can be used as a generalized model for aerobic yeast growth.     

Synthesis and regulation of extracellular beta (1-3) glucanase and protease by cytophaga sp. In batch and continuous culture

Lytic enzyme systems with the ability to break whole cells of yeast are a mixture of several enzymes and virtually all contain beta(1-3)glucanases and some protease. It appears that the presence of these two enzyme activities is necessary to break the two layers of the rigid cell wall. The enzyme system of Cytophaga NCIB 9497 has a high activity towards the walls of yeast and also of bacteria. This article describes the production of this extracellular lytic enzyme system in batch and continuous culture-it was found to be inducible. The synthesis and regulation of the two main constituent enzymes, beta(1-3)glucanase and protease, have been investigated. The synthesis of beta(1-3)glucanase is regulated by bothinduction (by an unknown inducer) and catabolite repression. Highbeta(1-3)glucanase activities were obtained in continuous culture at low dilution rates over a narrow range (0.05-0.10 h(-1)), and there is evidence of the presence of more than one glucanase enzyme. Proteolytic activity appears subject to catabolite repression and made up of the activities of more than one protease enzyme. Productivity and enzyme concentration were increased several fold in continuous culture when compared to batch culture.     

Control strategies of continuous bioprocesses based on biological activities

Based on the material balance principle applied to microbial reactions in continuous bioprocesses, the concept of reaction rate control has been developed theoretically. This concept provides a more direct way of controlling biological activities than the control of physical or chemical parameters in practice today. From an analysis of dynamic and steady-state experiments, two control systems for carbon dioxide production rate control during the continuous culture of baker's yeast have been designed and evaluated experimentally. In these control methods, intracellular NADH concentration is used as an immediate indication of the onset of glucose repression. A more sophisticated master controller based on the respiratory quotient can be combined with these control methods. The resulting control system provides a means to indirectly optimize biomass production while preventing ethanol formation in the continuous culture of baker's yeast.     

Continuous-culture studies of synthesis and regulation of extracellular beta(1-3) glucanase and protease enzymes from Oerskovia xanthineolytica

This article describes the synthesis and regulation of beta(1-3)glucanase and protease enzymes from the cell lytic system of Oerskovia xanthineolytica LL-G109 in continuous culture using different concentrations of carbon source (glucose) and inducer (glucan). These two enzyme activities are the main components of a lytic system capable of lysing and disrupting whole yeast cells; it is subject to catabolite repression by glucose and is induced by yeast glucan. Peaks of beta(1-3)glucanase and protease activity are obtained at dilution rates of between 0.05 and 0.15 h(-1). The glucanase-protease ratio is very high compared to other strains. At dilution rates above 0.15 h(-1) all activities are similar to those obtained in batch culture. The lytic enzyme system appears to contain several beta(1-3)glucanase enzymes. In continuous culture both productivity and enzyme concentrations are greatly in creased when compared to batch culture, 11- and 4.4-fold, respectively.     

Dynamics of growth in batch and continuous cultures of Saccharomyces cerevisiae during shifts from aerobiosis to anaerobiosis and reverse

Summary Saccharomyces cerevisiae H 1022 was cultivated in batch and continuous culture on a glucose substrate. The yeast was subjected to a sudden change from aerobic to anaerobic growth conditions by switching the inlet-gas stream from air to dinitrogen. The dynamics of growth and product formation during the periods of adaptation were studied. A structured growth model based on Monod-Blackman-kinetics was applied to simulate these shift-experiments. The immediate switch of the yeast to maximum anaerobic growth and ethanol production predicted by this model was confirmed very well in the chemostat-experiments. However, a slow adaptation was evident for the switch from anaerobiosis back to aerobiosis.Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-3300 Braunschweig-Stöckheim, Federal Republic of Germany     

What is the function of nitrogen catabolite repression in Saccharomyces cerevisiae?

In contrast to the previously held notion that nitrogen catabolite repression is primarily responsible for the ability of yeast cells to use good nitrogen sources in preference to poor ones, we demonstrate that this ability is probably the result of other control mechanisms, such as metabolite compartmentation. We suggest that nitrogen repression is functionally a long-term adaptation to changes in the nutritional environment of yeast cells.     

Disentangling genetic and epigenetic determinants of ultrafast adaptation

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical–experimental framework for disclosing the presence of such adaptation‐speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation–accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic‐adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data‐driven individual‐based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation‐speeding mechanisms in general.     

Effect of Amino Sugars on Catabolite Repression in Escherichia coli

N-acetylglucosamine was found to be a good repressor source for catabolite repression of the beta-galactosidase system in Escherichia coli. It was found capable of increasing the severity of repression by glucose or gluconate when included in the medium with either of these substrates. N-acetylglucosamine was shown to be assimilated under these conditions, but had no effect on culture growth rates. Its influence on catabolite repression was not altered by growth in the presence of inhibiting levels of penicillin. These findings indicated that catabolite repression may be associated with certain reactions of amino sugar metabolism. A working model has been formulated along these lines and will be used to explore this possible relationship further.     

Effet de l'accumulation de Zn-protoporphyrine par la cellule de levure sur la synthese et le fonctionnement de son systeme respiratoireEffect of Zn-protoporphyrin accumulation by yeast cells on synthesis and activity of their respiratory system

Yeast cells harvested from aerobic or anaerobic culture are able to synthesize considerable amounts of Zn-protoporphyrin, by aeration of resting cells in phosphate buffer (pH 8).

In yeast cells harvested from aerobic growth, Zn-protoporphyrin accumulation inhibits respiratory activity and produces some letality. In yeast cells harvested from anaerobic growth this accumulation produces both a strong inhibition of cytochrome biosynthesis and of respiratory adaptation, accompanied by an important letality.

Zn-protoporphyrin is accumulated into the mitochondrial fraction and causes a total inhibition of O₂ consumption by isolated mitochondria. The “in vitro” addition of purified Zn-protoporphyrin to intact mitochondria induces a lost of respiratory control.     

Induction and repression of arginase and ornithine transaminase in baker's yeast

The arginase and the ornithine transaminase of baker's yeast are induced byl-arginine. Both enzymes have been shown to be repressed by nitrogen compounds. This is evidenced primarily by the decrease in specific enzyme activities caused by the addition of readily assimilable nitrogen compounds to a yeast culture with arginine, secondly by the derepression of both enzymes during nitrogen starvation of the yeast grown in various arginine-free media. This derepression equals both in rate and in amount the enzyme synthesis during the adaptation of the yeast to a medium withl-arginine as the sole nitrogen source. It is inhibited by various assimilable and non-assimilable amino acids. The derepression is the result of the nitrogen deficiency itself, since during the starvation of the yeast for sulphate, phosphate or magnesium, neither of the two enzymes is derepressed, and since it is independent of the nature of the carbon source in the nitrogen starvation medium, provided the latter is immediately assimilable.The enzymes are not subject to catabolite repression by glucose metabolites.It is concluded that the synthesis of arginase and ornithine transaminase in yeast is regulated by induction and repression. Arginine induces the enzymes; they are repressed by nitrogen compounds, probably in cooperation with one or more vitamins.Thanks are due to Professor E. G. Mulder for his frequent encouragement, to the Heineken's Brouwerij, Rotterdam and to the Landbouwhogeschoolfonds for research grants, and to Miss H. P. M. Klinkers, to Mr. P. J. Buysman and to Mr. G. J. K. Pesch for their skilful technical assistance.     

Effects of growth conditions on mitochondrial morphology inSaccharomyces cerevisiae

Effects of growth conditions on mitochondrial morphology were studied in livingSaccharomyces cerevisiae cells by vital staining with the fluorescent dye dimethyl-aminostyryl-methylpyridinium iodine (DASPMI), fluorescence microscopy, and confocal-scanning laser microscopy. Cells from respiratory, ethanol-grown batch cultures contained a large number of small mitochondria. Conversely, cells from glucose-grown batch cultures, in which metabolism was respiro-fermentative, contained small numbers of large, branched mitochondria. These changes did not significantly affect the fraction of the cellular volume occupied by the mitochondria. Similar differences in mitochondrial morphology were observed in glucose-limited chemostat cultures. In aerobic chemostat cultures, glucose metabolism was strictly respiratory and cells contained a large number of small mitochondria. Anaerobic, fermentative chemostat cultivation resulted in the large, branched mitochondrial structures also seen in glucose-grown batch cultures. Upon aeration of a previously anaerobic chemostat culture, the maximum respiratory capacity increased from 10 to 70 µmole.min^–1.g weight^–1 within 10 h. This transition resulted in drastic changes of mitochondrial number, morphology and, consequently, mitochondrial surface area. These changes continued for several hours after the respiratory capacity had reached its maximum. Cyanide-insensitive oxygen consumption contributed ca. 50% of the total respiratory capacity in anaerobic cultures, but was virtually absent in aerobic cultures. The response of aerobic cultures to oxygen deprivation was qualitatively the reverse of the response of anaerobic cultures to aeration. The results indicate that mitochondrial morphology inS. cerevisiae is closely linked to the metabolic activity of this yeast: conditions that result in repression of respiratory enzymes generally lead to the mitochondrial morphology observed in anaerobically grown, fermenting cells.     

Use of malt extract as a nitrogen source for continuous cultivation of Candida utilis]

The effect of an aqueous extract from malt sprouts on the growth and development of fodder yeast was investigated during their continuous cultivation. The extract can be used as a nitrogen source during continuous cultivation of fodder yeast. It is supposed that the extract contains compounds capable to inhibit yeast growth. The extract should be added to the nutrient medium in the amount of 4 g/l of dry weight.     

The onset of fermentative metabolism in continuous cultures depends on the catabolite repression properties of saccharomyces cerevisiae

In glucose-limited continuous cultures, a Crabtree positive yeast such as Saccharomyces cerevisiae displays respiratory metabolism at low dilution rates (D) and respirofermentative metabolism at high D. We hypothesized that the onset of fermentative metabolism is related with the catabolite repression or glucose repression effect. To test this hypothesis, we have investigated the physiological behavior in glucose-limited continuous cultures of S. cerevisiae strain CEN.PK122 and isogenic mutants, snf1 (cat1) and snf4 (cat3), defective in proteins involved in the release from glucose repression and the mutant in glucose repression mig1. We analyzed the behavior of the wild type and mutant strains at steady state in chemostat cultures as a function of D. Wild-type cells displayed respiratory metabolism up to a D of 0.2 h⁻¹. snf1 and snf4 mutants started fermenting after a D of 0.1 and 0.15 h⁻¹, respectively. The latter behavior was not due to an impairment of respiration since their specific rate of oxygen consumption was similar or even higher than that shown by the wild type. The snf1 strain displayed much lower yields than the wild type and the other mutants in the whole range of D studied. We conclude that the onset of fermentative metabolism in yeast growing in chemostat cultures is related with glucose repression.