Regulation of carbon metabolism in Saccharomyces cerevisiae and related yeasts

Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species

Environmental conditions can influence mutation rates, but the reasons are often unclear. Budding yeast can utilize many carbon sources, with variation in the degree of fermentation versus respiration. Since aerobic respiration produces mutagenic reactive oxygen species, we hypothesized that yeast grown in media promoting aerobic respiration would show higher mutation rates. We found significant differences across five media types, with the highest mutation rate in pyruvate and the lowest in glucose. However, mutation rates responded to respiration rate in a nonlinear fashion, suggesting that the degree of respiration in a given environment is only partly predictive of mutation rate.

Fueling the protein transition: Can waste-derived ethanol enable efficient and high-quality microbial protein production?

Meeting the protein needs of a growing population will require significant resources. In this context, microbial protein (MP) offers a nutritious and versatile protein source from recovered resources. This meta-analysis of over 100 studies examines the efficiency and nutritional quality of MP production using ethanol. Ethanol, a feedstock derived from CO2 and biological waste, is used by various microorganisms, and has an established role in the food sector. Results show that ethanol-based MP production is technically feasible for food applications, reaching biomass concentrations of 14-230 g/L and productivities of 11-13 g/L/h. The protein content of MP correlates with productivity, and the nutritional quality of ethanol-grown MP matches common sources like pork and tofu. Lastly, operational choices affect the techno-economic feasibility of using waste-derived ethanol and other recovered resources. This meta-analysis highlights the potential of ethanol-grown MP, though further research is needed to close existing knowledge gaps.

Investigation into struvite precipitation: A commonly encountered problem during fermentations on chemically defined media

Chemically defined mineral media are widely used in bioprocesses, as these show less batch to batch variation compared with complex media. Nonetheless, the recommended media formulations often lead to the formation of precipitants at elevated pH values. These precipitates are insoluble and reduce the availability of macronutrients to the cells, which can result in limiting growth rates and lower productivity. They can also damage equipment by clogging pipes, hoses, and spargers in stirred tank fermenters. In this study, the observed precipitate was analyzed via X-ray fluorescence spectroscopy and identified as the magnesium ammonium phosphate salt struvite (MgNH4 PO4  × 6H2 O). The solubility of struvite crystals is known to be extremely low, causing the macronutrients magnesium, phosphate, and ammonium to be bound in the struvite crystals. Here, it was shown that struvite precipitates can be redissolved under common fermentation conditions. Furthermore, it was found that the struvite particle size distribution has a significant effect on the dissolution kinetics, which directly affects macronutrient availability. At a certain particle size, struvite crystals rapidly dissolved and provided unlimiting growth conditions. Therefore, struvite formation should be considered during media and bioprocess development, to ensure that the dissolution kinetics of struvite are faster than the growth kinetics.

The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion

To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.

Comb spectroscopy of CO2 produced from microbial metabolism

We have developed a direct frequency comb spectroscopy instrument, which we have tested on Saccharomyces cerevisiae (baker's yeast) by measuring its CO2 output and production rate as we varied the environmental conditions, including the amount and type of feed sugar, the temperature, and the amount of yeast. By feeding isotopically-enhanced sugar to the yeast, we demonstrate the capability of our device to differentiate between two isotopologues of CO2, with a concentration measurement precision of 260 ppm for 12C16O2 and 175 ppm for 13C16O2. We also demonstrate the ability of our spectrometer to measure the proportion of carbon in the feed sugar converted to CO2, and estimate the amount incorporated into the yeast biomass.

Toward standardized solid medium cultivations: Online microbial monitoring based on respiration activity

Cultivating microorganisms on solid agar media is a fundamental technique in microbiology and other related disciplines. For the evaluation, most often, a subjective visual examination is performed. Crucial information, such as metabolic activity, is not assessed. Thus, time-resolved monitoring of the respiration activity in agar cultivations is presented to provide additional insightful data on the metabolism. A modified version of the Respiration Activity MOnitoring System (RAMOS) was used to determine area-specific oxygen and carbon dioxide transfer rates and the resulting respiratory quotients of agar cultivations. Therewith, information on growth, substrate consumption, and product formation was obtained. The validity of the presented method was tested for different prokaryotic and eukaryotic organisms on agar, such as Escherichia coli BL21, Pseudomonas putida KT2440, Streptomyces coelicolor A3(2), Saccharomyces cerevisiae WT, Pichia pastoris WT, and Trichoderma reesei RUT-C30. Furthermore, it is showcased that several potential applications, including the determination of colony forming units, antibiotic diffusion tests, quality control for spore production or for pre-cultures and media optimization, can be quantitatively evaluated by interpretation of the respiration activity.

Effects of a high-dose Saccharomyces cerevisiae inoculum alone or in combination with Lactobacillus plantarum on the nutritional composition and fermentation traits of maize silage

Context The inoculation of silage with Saccharomyces cerevisiae to deliver viable yeast cells is a novel concept. Aims The effects of a high-dose S. cerevisiae inoculum alone or combined with Lactobacillus plantarum on the nutritional composition, fermentation traits and aerobic stability of maize silage were studied after 30, 60 and 90 days of storage. Methods Whole-crop maize (309.3 g dry matter (DM)/kg as fed) was subjected to one of three treatments: deionised water (untreated control); S. cerevisiae at an estimated concentration of 108 CFU/g fresh forage (S); or S. cerevisiae at an estimated concentration of 108 CFU/g and L. plantarum at an estimated concentration of 105 CFU/g of fresh forage (SL). Key results Compared with the control, the S and SL groups showed increases (P < 0.001) in average pH (3.98 in S and 4.01 in SL vs 3.65 in the control), crude protein (85 g/kg DM in S and 80 g/kg DM in SL vs 63 g/kg DM in the control) and ammonia nitrogen/total nitrogen (122.2 g/kg in S and 163.9 g/kg in SL vs 52.9 g/kg in the control) but a lower (P < 0.001) average concentration of water-soluble carbohydrate (0.9 g/kg DM in S and 0.7 g/kg DM in SL vs 2.3 g/kg DM in the control). The levels of neutral detergent fibre and acid detergent fibre were greater (P < 0.001) in S silage than in the control and SL silages, and the hemicellulose level was lower (P = 0.004) in the SL group than the control and S groups. Starch and aerobic stability were unaffected by treatment, and the average lactate and ethanol concentrations were higher (P < 0.001) in the S (53.7 g lactate/kg DM and 28.7 g ethanol/kg DM) and SL (56.9 g lactate/kg DM and 21.4 g ethanol/kg DM) groups than the control (40.1 g lactate/kg DM and 5.3 g ethanol/kg DM) over 90 days of ensiling. Conclusions Overall, a high-dose inoculum of S. cerevisiae alone or combined with L. plantarum affected the nutritional composition and fermentation traits of maize silage. Implications The inoculation of maize silage with a high dose of S. cerevisiae needs to be performed with caution.

Pre-purification of Plantago lanceolata extracts with biologically active compounds using yeast cells

Leaves of the plant Plantago lanceolata contain many economically interesting bioactive compounds, among them aucubin and catalpol are the most attractive. However, soluble saccharides passing to water extracts during isolation complicate chromatographic purification of these compounds. Their degradation by microbial cells transforming, for example, glucose, fructose, or sucrose to ethanol could bring important production costs savings and improved final product quality. It has been shown that the best saccharide degradation in extracts is achieved with the Saccharomyces cerevisiae cells. The cells were very active also in their immobilized form and they were able to completely remove glucose from the extract within four hours in a packed bed reactor combined with a stirring system with infinite medium recirculation.

A simple mathematical model involving reaction kinetics and mass transfer limitations in the cell particles was proposed for the evaluation of cell effectiveness in their immobilized form in term of effectiveness factor. Values of the effectiveness factor calculated from the model were far below 1, indicating strong mass transfer limitations of the reaction. The model is suitable for optimization of preparation of immobilized cell particles, mainly from the point of view of cell charge in particles.

Simultaneous saccharification and bioethanol production from corn cobs: Process optimization and kinetic studies

This study investigates the simultaneous saccharification and fermentation (SSF) process for bioethanol production from corn cobs with prehydrolysis (PSSF) and without prehydrolysis (OSSF). Two response surface models were developed with high coefficients of determination (>0.90). Process optimization gave high bioethanol concentrations and bioethanol conversions for the PSSF (36.92 ± 1.34 g/L and 62.36 ± 2.27%) and OSSF (35.04 ± 0.170 g/L and 58.13 ± 0.283%) models respectively. Additionally, the logistic and modified Gompertz models were used to study the kinetics of microbial cell growth and ethanol formation under microaerophilic and anaerobic conditions. Cell growth in the OSSF_{microaerophilic} process gave the highest maximum specific growth rate (µ_max) of 0.274 h^-1. The PSSF_{microaerophilic} bioprocess gave the highest potential maximum bioethanol concentration (P_m) (42.24 g/L). This study demonstrated that microaerophilic rather than anaerobic culture conditions enhanced cell growth and bioethanol production, and that additional prehydrolysis steps do not significantly impact on the bioethanol concentration and conversion in SSF process.

A common mechanism explains the induction of aerobic fermentation and adaptive antioxidant response in Phaffia rhodozyma

Background

Growth conditions that bring about stress on Phaffia rhodozyma cells encourage the synthesis of astaxanthin, an antioxidant carotenoid, which protects cells against oxidative damage. Using P. rhodozyma cultures performed with and without copper limitation, we examined the kinetics of astaxanthin synthesis along with the expression of asy, the key astaxanthin synthesis gene, as well as aox, which encodes an alternative oxidase protein.

Results

Copper deficiency had a detrimental effect on the rates of oxygen consumption and ethanol reassimilation at the diauxic shift. In contrast, copper deficiency prompted alcoholic fermentation under aerobic conditions and had a favorable effect on the astaxanthin content of cells, as well as on aox expression. Both cultures exhibited strong aox expression while consuming ethanol, but particularly when copper was absent.

Conclusion

We show that the induction of either astaxanthin production, aox expression, or aerobic fermentation exemplifies the crucial role that redox imbalance plays in triggering any of these phenomena. Based on our own results and data from others, we propose a mechanism that rationalizes the central role played by changes of respiratory activity, which lead to redox imbalances, in triggering both the short-term antioxidant response as well as fermentation in yeasts and other cell types.

High-throughput FTIR-based bioprocess analysis of recombinant cyprosin production

To increase the knowledge of the recombinant cyprosin production process in Saccharomyces cerevisiae cultures, it is relevant to implement efficient bioprocess monitoring techniques. The present work focuses on the implementation of a mid-infrared (MIR) spectroscopy-based tool for monitoring the recombinant culture in a rapid, economic, and high-throughput (using a microplate system) mode. Multivariate data analysis on the MIR spectra of culture samples was conducted. Principal component analysis (PCA) enabled capturing the general metabolic status of the yeast cells, as replicated samples appear grouped together in the score plot and groups of culture samples according to the main growth phase can be clearly distinguished. The PCA-loading vectors also revealed spectral regions, and the corresponding chemical functional groups and biomolecules that mostly contributed for the cell biomolecular fingerprint associated with the culture growth phase. These data were corroborated by the analysis of the samples’ second derivative spectra. Partial least square (PLS) regression models built based on the MIR spectra showed high predictive ability for estimating the bioprocess critical variables: biomass (R2 = 0.99, RMSEP 2.8%); cyprosin activity (R2 = 0.98, RMSEP 3.9%); glucose (R2 = 0.93, RMSECV 7.2%); galactose (R2 = 0.97, RMSEP 4.6%); ethanol (R2 = 0.97, RMSEP 5.3%); and acetate (R2 = 0.95, RMSEP 7.0%). In conclusion, high-throughput MIR spectroscopy and multivariate data analysis were effective in identifying the main growth phases and specific cyprosin production phases along the yeast culture as well as in quantifying the critical variables of the process. This knowledge will promote future process optimization and control the recombinant cyprosin bioprocess according to Quality by Design framework.

Npr2 inhibits TORC1 to prevent inappropriate utilization of glutamine for biosynthesis of nitrogen-containing metabolites

Cells must be capable of switching between growth and autophagy in unpredictable nutrient environments. The conserved Npr2 protein complex (comprising Iml1, Npr2, and Npr3; also called SEACIT) inhibits target of rapamycin complex 1 (TORC1) kinase signaling, which inhibits autophagy in nutrient-rich conditions. In yeast cultured in media with nutrient limitations that promote autophagy and inhibit growth, loss of Npr2 enables cells to bypass autophagy and proliferate. We determined that Npr2-deficient yeast had a metabolic state distinct from that of wild-type yeast when grown in minimal media containing ammonium as a nitrogen source and a nonfermentable carbon source (lactate). Unlike wild-type yeast, which accumulated glutamine, Npr2-deficient yeast metabolized glutamine into nitrogen-containing metabolites and maintained a high concentration of S-adenosyl methionine (SAM). Moreover, in wild-type yeast grown in these nutrient-limited conditions, supplementation with methionine stimulated glutamine consumption for synthesis of nitrogenous metabolites, demonstrating integration of a sulfur-containing amino acid cue and nitrogen utilization. These data revealed the metabolic basis by which the Npr2 complex regulates cellular homeostasis and demonstrated a key function for TORC1 in regulating the synthesis and utilization of glutamine as a nitrogen source.

Yeast biomass production: a new approach in glucose-limited feeding strategy

The aim of this work was to implement experimentally a simple glucose-limited feeding strategy for yeast biomass production in a bubble column reactor based on a spreadsheet simulator suitable for industrial application. In biomass production process using Saccharomyces cerevisiae strains, one of the constraints is the strong tendency of these species to metabolize sugars anaerobically due to catabolite repression, leading to low values of biomass yield on substrate. The usual strategy to control this metabolic tendency is the use of a fed-batch process in which where the sugar source is fed incrementally and total sugar concentration in broth is maintained below a determined value. The simulator presented in this work was developed to control molasses feeding on the basis of a simple theoretical model in which has taken into account the nutritional growth needs of yeast cell and two input data: the theoretical specific growth rate and initial cell biomass. In experimental assay, a commercial baker’s yeast strain and molasses as sugar source were used. Experimental results showed an overall biomass yield on substrate of 0.33, a biomass increase of 6.4 fold and a specific growth rate of 0.165 h⁻¹ in contrast to the predicted value of 0.180 h-1 in the second stage simulation.

Fluxes of carbon, phosphorylation, and redox intermediates during growth of saccharomyces cerevisiae on different carbon sources

In the present work we develop a method for estimating anabolic fluxes when yeast are growing on various carbon substrates (glucose, glycerol, lactate, pyruvate, acetate, or ethanol) in minimal medium. Fluxes through the central amphibolic pathways were calculated from the product of the total required amount of a specified carbon intermediate times the growth rate. The required amount of each carbon intermediate was estimated from the experimentally determined macromolecular composition of cells grown in each carbon source and the monomer composition of macromolecules.Substrates sharing most metabolic pathways such as ethanol and acetate, despite changes in the macromolecular composition, namely carbohydrate content (34% +/- 1 and 21% +/- 3, respectively), did not show large variations in the overall fluxes through the main amphibolic pathways. For instance, in order to supply anabolic precursors to sustain growth rates in the range of 0.16/h to 0.205/h, similar large fluxes through Acetyl CoA synthase were required by acetate (4.2 mmol/hr g dw) or ethanol (5.2 mmol/h g dw).The V(max) activities of key enzymes of the main amphibolic pathways measured in permeabilized yeast cells allowed to confirm, qualitatively, the operation of those pathways for all substrates and were consistent on most substrates with the estimated fluxes required to sustain growth.When ATP produced from oxidation of the NADH synthesized along with the key intermediary metabolites was taken into account, higher Y(ATP) (max) values (36 with respect to 24 g dw/mol ATP) were obtained for glucose. The same result was obtained for glycerol, ethanol, and acetate. A yield index (YI) was defined as the ratio of the theoretically estimated substrate flux required to sustain a given growth rate over the experimentally measured flux of substrate consumption. Comparison of Yl between growth on various carbon sources led us to conclude that ethanol (Yl = 0.84), acetate (Yl = 0.77), and lactate (Yl = 0.77) displayed the most efficient use of substrate for biomass production. For the other substrates, the Yl decayed in the following order: pyruvate > glycerol > glucose.An improvement of the quantitative understanding of yeast metabolism, energetics, and physiology is provided by the present analysis. The methodology proposed can be applied to other eukaryotic organisms of known chemical composition. (c) 1995 John Wiley & Sons, Inc.

Effect of volatile compounds in grass silage on voluntary intake by growing cattle

Twenty-four low dry matter (DM) silages differing in fermentation quality were harvested at the same time from a crop that consisted mainly of timothy (Phleum pratense), and meadow fescue (Festuca pratensis). The silage samples were analysed by gas chromatography (GC) - mass spectrometry and gas chromatography - flame ionisation detection in order to determine and quantify volatiles present in silage. The voluntary intake of the 24 silages had been measured in a previous feeding trial with growing steers of Norwegian Red. Thirteen esters, five aldehydes, three alcohols, and one sulphide were identified and quantified. A total of 51 variables describing the chemical composition of the silages were included in a partial least-squares regression, and the relationship of silage fermentation quality to voluntary intake was elucidated. The importance of variables describing silage fermentation quality in relation to intake was judged from a best combination procedure, jack-knifing, and empirical correlations of the variables to intake. The GC-analysed compounds were mainly present in poorly fermented silages. However, compared with other explanatory chemical variables none of these compounds was of importance for the voluntary intake as evaluated by partial least-squares regression. A validated variance of 71% in silage DM intake was explained with the selected variables: total acids (TA), total volatile fatty acids (TVFA), lactic acid/total acid ratio and propionic acid. In this study extent (by the variable TA) and type of silage fermentation (by TVFA) influenced intake. Further, it is suggested that by restricting the fermentation in low DM grass silages the potential intake of silage DM is maximised.

Transient-state analysis of metabolic fluxes in crabtree-positive and crabtree-negative yeasts

In bakers' yeast, an immediate alcoholic fermentation begins when a glucose pulse is added to glucose-limited, aerobically grown cells. The mechanism of this short-term Crabtree effect was investigated via a comparative enzymic analysis of eight yeast species. It was established that the fermentation rate of the organisms upon transition from glucose limitation to glucose excess is positively correlated with the level of pyruvate decarboxylase (EC 4.1.1.1). In the Crabtree-negative yeasts, the pyruvate decarboxylase activity was low and did not increase when excess glucose was added. In contrast, in the Crabtree-positive yeasts, the activity of this enzyme was on the average sixfold higher and increased after exposure to glucose excess. In Crabtree-negative species, relatively high activities of acetaldehyde dehydrogenases (EC 1.2.1.4 and EC 1.2.1.5) and acetyl coenzyme A synthetase (EC 6.2.1.1), in addition to low pyruvate decarboxylase activities, were present. Thus, in these yeasts, acetaldehyde can be effectively oxidized via a bypass that circumvents the reduction of acetaldehyde to ethanol. Growth rates of most Crabtree-positive yeasts did not increase upon transition from glucose limitation to glucose excess. In contrast, the Crabtree-negative yeasts exhibited enhanced rates of biomass production which in most cases could be ascribed to the intracellular accumulation of reserve carbohydrates. Generally, the glucose consumption rate after a glucose pulse was higher in the Crabtree-positive yeasts than in the Crabtree-negative yeasts. However, the respiratory capacities of steady-state cultures of Crabtree-positive yeasts were not significantly different from those of Crabtree-negative yeasts. Thus, a limited respiratory capacity is not the primary cause of the Crabtree effect in yeasts. Instead, the difference between Crabtree-positive and Crabtree-negative yeasts is attributed to differences in the kinetics of glucose uptake, synthesis of reserve carbohydrates, and pyruvate metabolism.

Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

BACKGROUND

The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions.

RESULTS

We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition.

CONCLUSION

Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.

Growth rate and medium composition strongly affect folate content in Saccharomyces cerevisiae

Folate content in a Saccharomyces cerevisiae strain was monitored during aerobic batch fermentation in synthetic growth medium, yeast peptone dextrose medium, and a molasses based medium. During growth in the synthetic medium large differences in intracellular folate content was observed at different phases. Specific folate levels, expressed per unit biomass, were highest during respiro-fermentative growth (120 microg/g) and decreased during the respiratory and stationary phases. Thus, the physiological state of the cells clearly affects the folate content. This was confirmed in chemostat cultures where total intracellular folate content increased linearly with increasing growth rate (r(2)=0.998), indicating high growth rate i.e. respiro-fermentative growth to be most favourable to obtain high specific folate content. In complex media however, much lower folate content (15-40 microg/g) was found throughout the batch growth. Only minor growth-phase related differences were detected. This shows the impact of cultivation medium on folate content in yeast. To further investigate which components that influence folate content, batch experiments in synthetic medium with addition of specific components were performed. Adding a raw mixture of peptides and amino acids (peptone) decreased folate levels extensively (90%) whereas adding amino acids one-by-one only had minor effects on the intracellular folate content. Furthermore, supplementing synthetic medium with pABA, folate or nucleotides did not change the intracellular folate content. This work constitutes the first steps towards an optimised process for production of natural folates for fortification purposes, as well as an effort to gain fundamental understanding of folate requirements in yeast in relation to environmental conditions.

Oleic acid delays and modulates the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae after exposure to glucose excess

This work aimed to study the transition from respiratory to fermentative metabolism in Saccharomyces cerevisiae CEN.PK 113-7D and more specifically to evaluate the implication of the acetyl-coenzymeA-derived carbon transport from cytosol to mitochondria in the onset of the metabolic shift. The strategy consisted in introducing, during aerobic glucose-limited chemostat (D = 0.16 h(-1)), [corrected] a local perturbation around the step to be studied by the addition of cosubstrate and in analyzing the consequences of such a perturbation on the metabolic transition. Oleic acid and L: -carnitine were among the tested cosubstrates because they were known to stimulate enzymes implicated in the acetyl-coenzymeA transport between the different cell compartments, such as the carnitine acetyl transferases. The metabolic transition was then comparatively quantified in sole glucose and in glucose/oleic acid chemostats in presence/absence of L: -carnitine after a pulse of glucose. Feeding the culture with oleic acid (D (ole) = 0.0041 and 0.0073 h(-1)) [corrected] led to a delay in the onset of the metabolic shift (up to 15 min), a 33% decrease in the ethanol production and a redirection of the carbon flux toward biomass production. The data clearly showed a modulation of the carbon distribution among respiration and fermentation, in favor of a decrease in the "short-term" Crabtree effect by the oleic acid.

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

After whole-genome duplication (WGD), deletions return most loci to single copy. However, duplicate loci may survive through selection for increased dosage. Here, we show how the WGD increased copy number of some glycolytic genes could have conferred an almost immediate selective advantage to an ancestor of Saccharomyces cerevisiae, providing a rationale for the success of the WGD. We propose that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes. This increase gave post-WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose-rich environments. Our hypothesis is supported by data from enzyme kinetics and comparative genomics. Because changes in gene dosage follow directly from post-WGD deletions, dosage selection can confer an almost instantaneous benefit after WGD, unlike neofunctionalization or subfunctionalization, which require specific mutations. We also show theoretically that increased fermentative capacity is of greatest advantage when glucose resources are both large and dense, an observation potentially related to the appearance of angiosperms around the time of WGD.

Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae

Respiratory metabolism plays an important role in energy production in the form of ATP in all aerobically growing cells. However, a limitation in respiratory capacity results in overflow metabolism, leading to the formation of byproducts, a phenomenon known as "overflow metabolism" or "the Crabtree effect." The yeast Saccharomyces cerevisiae has served as an important model organism for studying the Crabtree effect. When subjected to increasing glycolytic fluxes under aerobic conditions, there is a threshold value of the glucose uptake rate at which the metabolism shifts from purely respiratory to mixed respiratory and fermentative. It is well known that glucose repression of respiratory pathways occurs at high glycolytic fluxes, resulting in a decrease in respiratory capacity. Despite many years of detailed studies on this subject, it is not known whether the onset of the Crabtree effect is due to limited respiratory capacity or is caused by glucose-mediated repression of respiration. When respiration in S. cerevisiae was increased by introducing a heterologous alternative oxidase, we observed reduced aerobic ethanol formation. In contrast, increasing nonrespiratory NADH oxidation by overexpression of a water-forming NADH oxidase reduced aerobic glycerol formation. The metabolic response to elevated alternative oxidase occurred predominantly in the mitochondria, whereas NADH oxidase affected genes that catalyze cytosolic reactions. Moreover, NADH oxidase restored the deficiency of cytosolic NADH dehydrogenases in S. cerevisiae. These results indicate that NADH oxidase localizes in the cytosol, whereas alternative oxidase is directed to the mitochondria.

Substrate inhibition kinetics of Saccharomyces cerevisiae in fed-batch cultures operated at constant glucose and maltose concentration levels

Fed-batch culture is the mode of operation of choice in industrial baker's yeast fermentation. The particular mode of culture, operated at stable glucose and maltose concentration levels, was employed in this work in order to estimate important kinetic parameters in a process mostly described in the literature as batch or continuous culture. This way, the effects of a continuously falling sugar level during a batch process were avoided and therefore the effects of various (stable) sugar levels on growth kinetics were evaluated. Comparing the kinetics of growth and the inhibition by the substrate in cultures grown on glucose, which is the preferential sugar source for Saccharomyces cerevisiae, and maltose, the most common sugar source in industrial media for baker's yeast production, a milder inhibition effect by the substrate in maltose-grown cells was observed, as well as a higher yield coefficient. The observed sugar inhibition effect in glucostat cultures was taken into account in modeling substrate inhibition kinetics. The inhibition coefficient Ki increased with increasing sugar concentration levels, but it appeared to be unaffected by the type of substrate and almost equal for both substrates at elevated concentration levels.

Factors involved in anaerobic growth ofSaccharomyces cerevisiae

Life in the absence of molecular oxygen requires several adaptations. Traditionally, the switch from respiratory metabolism to fermentation has attracted much attention in Saccharomyces cerevisiae, as this is the basis for the use of this yeast in the production of alcohol and in baking. It has also been clear that under anaerobic conditions the yeast is not able to synthesize sterols and unsaturated fatty acids and that for anaerobic growth these have to be added to the media. More recently it has been found that many more factors play a role. Several other biosynthetic reactions also require molecular oxygen and the yeast must have alternatives for these. In addition, the composition of the cell wall and cell membrane show major differences when aerobic and anaerobic cells are compared. All these changes are reflected by the observation that the transcription of more than 500 genes changes significantly between aerobically and anaerobically growing cultures. In this review we will give an overview of the factors that play a role in the survival in the absence of molecular oxygen.

Proof-of-concept of a novel micro-bioreactor for fast development of industrial bioprocesses

The experimental performance of a novel micro-bioreactor envisaged for parallel screening and development of industrial bioprocesses has been tested in this work. The micro-bioreactor with an internal volume of 4.5 mL is operated under oscillatory flow mixing (OFM), where a controllable mixing and mass transfer rates are achieved under batch or continuous laminar flow conditions. Several batch fermentations with a flocculent Saccharomyces cerevisiae strain were carried out at initial glucose concentrations (S(0)) range of approximately 5-20 g/L and compared to yeast growth kinetics in a stirred tank (ST) bioreactor. Aerobic fermentations were monitored ex situ in terms of pH, DO, glucose consumption, and biomass and ethanol production (wherever applicable). An average biomass production increase of 83% was obtained in the micro-bioreactor when compared with the ST, with less 93.6% air requirements. It also corresponded to a 214% increase on biomass production when compared with growth in a shaken flask (SF) at S(0) = 20 g/L. Further anaerobic fermentations at the same initial glucose concentration ranges gave the opportunity to use state-of-the-art fiber optics technology for on-line and real-time monitoring of this bioprocess. Time profiles of biomass concentration (measured as optical density (OD)) were very similar in the ST bioreactor and in the micro-bioreactor, with a highly reproducible yeast growth in these two scale-down platforms.

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.

Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the heme-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration. Thus, overexpression of HAP4 has been shown to result in a 10% increase in the respiratory capacity. Here the physiology of a HAP4-deleted S. cerevisiae strain was investigated, and we found that the hap4delta S. cerevisiae exhibited poor growth on ethanol, although the growth rate on glucose was indifferent from the wild type in aerobic as well as anaerobic cultures. Moreover, it exhibited a large (75%) reduction in the critical glucose uptake rate at which fermentative metabolism is onset, indicating a substantial reduction in respiratory capacity. We also performed whole genome transcription analysis for the hap4delta and the wild type, grown in carbon-limited chemostat cultures operated at a dilution rate of 0.05 h(-1). Although both strains exhibited respiratory metabolism, there was significant change in expression of many genes in the hap4delta strain. These genes are involved in several different parts of the metabolism, including oxidative stress response, peroxisomal functions, and energy generation. This study strongly indicates that Hap4 activation only occurs at intermediate specific growth rates, below which the transcription of genes responsible for respiration is dependent on the Hap2/3/5 complex and above which the Hap4 protein augments the transcription. Furthermore, statistical analysis of the transcription data and integration of the data with a genome scale metabolic network provided new insight and evidence for the role of Hap4 in transcriptional regulation of mitochondrial respiration.

Do mitochondria regulate the heat-shock response in Saccharomyces cerevisiae?

A mild heat shock induces the synthesis of heat-shock proteins (hsps), which protect cells from damage during more extreme heat exposure. The nature of the signals that induce transcription of heat shock-regulated genes remains conjectural. In this work we studied the role of mitochondria in regulating hsps synthesis in Saccharomyces cerevisiae. The results obtained clearly indicate that a mild heat shock elicits a hyperpolarization of the inner mitochondrial membrane and such an event is one of several signals triggering the chain of reactions that activates the expression of the HSP104 gene and probably the expression of other heat shock-regulated genes in S. cerevisiae. The uncouplers or mitochondrial inhibitors which are capable of dissipating the potential on the inner mitochondrial membrane under particular experimental conditions prevent the synthesis of Hsp104 induced by mild heat shock and thus inhibit the development of induced thermotolerance. It is suggested that cAMP-dependent protein kinase A is participating in the mitochondrial regulation of nuclear genes.

Manipulation of malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments

The yeast Saccharomyces cerevisiae is an attractive cell factory, but in many cases there are constraints related with balancing the formation and consumption of redox cofactors. In this work, we studied the effect of having an additional source of NADPH in the cell. In order to do this, two strains were engineered by overexpression of malic enzyme. In one of them, malic enzyme was overexpressed as its wild-type mitochondrial form, and in the other strain a short form lacking the mitochondrial targeting sequence was overexpressed. The recombinant strains were analyzed in aerobic batch and continuous cultivations, and the basic growth characteristics were generally not affected to a great extent, even though pleiotropic effects of the manipulations could be seen by the altered in vitro activities of selected enzymes of the central metabolism. Moreover, the decreased pentose-phosphate pathway flux and the ratios of redox cofactors showed that a net transhydrogenase effect was obtained, which can be directed to the cytosol or the mitochondria. This may find application in redirecting fluxes for improving specific biotechnological applications.

Glucose as a hormone: receptor-mediated glucose sensing in the yeast Saccharomyces cerevisiae

Because glucose is the principal carbon and energy source for most cells, most organisms have evolved numerous and sophisticated mechanisms for sensing glucose and responding to it appropriately. This is especially apparent in the yeast Saccharomyces cerevisiae, where these regulatory mechanisms determine the distinctive fermentative metabolism of yeast, a lifestyle it shares with many kinds of tumour cells. Because energy generation by fermentation of glucose is inefficient, yeast cells must vigorously metabolize glucose. They do this, in part, by carefully regulating the first, rate-limiting step of glucose utilization: its transport. Yeast cells have learned how to sense the amount of glucose that is available and respond by expressing the most appropriate of its 17 glucose transporters. They do this through a signal transduction pathway that begins at the cell surface with the Snf3 and Rgt2 glucose sensors and ends in the nucleus with the Rgt1 transcription factor that regulates expression of genes encoding glucose transporters. We explain this glucose signal transduction pathway, and describe how it fits into a highly interconnected regulatory network of glucose sensing pathways that probably evolved to ensure rapid and sensitive response of the cell to changing levels of glucose.

Aerobic physiology of redox-engineered Saccharomyces cerevisiae strains modified in the ammonium assimilation for increased NADPH availability

Recombinant strains altered in the ammonium assimilation pathways were constructed with the purpose of increasing NADPH availability. The NADPH-dependent glutamate dehydrogenase encoded by GDH1, which accounts for a major fraction of the NADPH consumption during growth on ammonium, was deleted, and alternative pathways for ammonium assimilation were overexpressed: GDH2 (NADH-consuming) or GLN1 and GLT1 (the GS-GOGAT system). The flux through the pentose phosphate pathway during aerobic growth on glucose decreased to about half that of the reference strain Saccharomyces cerevisiae CEN.PK113-7D, indicating a major redox alteration in the strains. The basic growth characteristics of the recombinant strains were not affected to a great extent, but the dilution rate at which the onset of aerobic fermentation occurred decreased, suggesting a relation between the onset of the Crabtree effect and the flux through the Embden-Meyerhof-Parnas pathway downstream of glucose 6-phosphate. No redox effect was observed in a strain containing a deletion of GLR1, encoding glutathione reductase, an enzyme that is NADPH-consuming.

Production of fungal α-amylase by Saccharomyces kluyveri in glucose-limited cultivations

Heterologous protein production by the yeast Saccharomyces kluyveri was investigated under aerobic glucose-limited conditions. Alpha-amylase from Aspergillus oryzae was used as model protein and the gene was expressed from a S. cerevisiae 2 micro plasmid. For comparison, strains of both S. kluyveri and S. cerevisiae were transformed with the same plasmid, which led to secretion of active alpha-amylase in both cases. The S. cerevisiae 2 micro plasmid was found to be stable in S. kluyveri as evaluated by a constant alpha-amylase productivity in a continuous cultivation for more than 40 generations. S. kluyveri and S. cerevisiae secreted alpha-amylase with similar yields during continuous cultivations at dilution rates of 0.1 and 0.2 h(-1) (4.8-5.7 mg (g dry weight)(-1)). At a dilution rate of 0.3 h(-1) the metabolism of S. kluyveri was fully respiratory, whereas S. cerevisiae produced significant amounts of ethanol. A fed-batch cultivation was carried out with S. kluyveri where the biomass concentration reached 85 g l(-1) and the alpha-amylase concentration reached 320 mg l(-1). Even though S. kluyveri could be grown to high cell density, it was also observed that it has a high maintenance coefficient, which resulted in low biomass yields at the low specific growth rates prevailing towards the end of the fed-batch cultivation.

Switching the mode of metabolism in the yeast Saccharomyces cerevisiae

The biochemistry of most metabolic pathways is conserved from bacteria to humans, although the control mechanisms are adapted to the needs of each cell type. Oxygen depletion commonly controls the switch from respiration to fermentation. However, Saccharomyces cerevisiae also controls that switch in response to the external glucose level. We have generated an S. cerevisiae strain in which glucose uptake is dependent on a chimeric hexose transporter mediating reduced sugar uptake. This strain shows a fully respiratory metabolism also at high glucose levels as seen for aerobic organisms, and switches to fermentation only when oxygen is lacking. These observations illustrate that manipulating a single step can alter the mode of metabolism. The novel yeast strain is an excellent tool to study the mechanisms underlying glucose-induced signal transduction.

HOCl-mediated cell death and metabolic dysfunction in the yeast Saccharomyces cerevisiae

The nature of oxidative damage to Saccharomyces cerevisiae caused by levels of HOCl that inhibit cell replication was explored with the intent of identifying the loci of lethal lesions. Functions of cytosolic enzymes and organelles that are highly sensitive to inactivation by HOCl, including aldolase, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and the mitochondrion, were only marginally affected by exposure of the yeast to levels of HOCl that completely inhibited colony formation. Loss of function in membrane-localized proteins, including the hexose transporters and PMA1 H(+)-ATPase, which is the primary proton pump located within the S. cerevisiae plasma membrane, was also marginal and K(+) leak rates to the extracellular medium increased only slowly with exposure to increasing amounts of HOCl, indicating that the plasma membrane retained its intrinsic impermeability to ions and metabolites. Adenylate phosphorylation levels in fermenting yeast declined in parallel with viability; however, yeast grown on respiratory substrates maintained near-normal phosphorylation levels at HOCl doses several-fold greater than that required for killing. This overall pattern of cellular response to HOCl differs markedly from that previously reported for bacteria, which appear to be killed by inhibition of plasma membrane proteins involved in energy transduction. The absence of significant loss of function in critical oxidant-sensitive cellular components and retention of ATP-synthesizing capabilities in respiring yeast cells exposed to lethal levels of HOCl suggests that toxicity in this case may arise by programmed cell death.

Bioprocess kinetics in a horizontal rotating tubular bioreactor

A horizontal rotating tubular bioreactor (HRTB) is a plug flow bioreactor whose interior is provided with O-ring-shaped partition walls that serve as carriers for microbial biomass. During this investigation, microbial biomass was grown in suspension and on the bioreactor inner surface as a microbial biofilm with average mass that was considerably higher than suspended biomass. The dynamics of bioprocess in HRTB was studied by different combinations of process parameters (bioreactor rotation speed and mean residence time) and it was monitored by withdrawing the samples from five positions along the bioreactor. During this investigation it was also observed that mean residence time had a more pronounced effect on the bioprocess dynamics than bioreactor rotation speed. For the description of bioprocess kinetics in HRTB an unstructured kinetic model was established that defines biomass growth, product formations and substrate consumption rate by using a modified Monod (Levenspiel) model. This kinetic model defines changes in suspension and in microbial biofilm, and it shows relatively good agreement with experimental data.

Oscillatory metabolism of Saccharomyces cerevisiae: an overview of mechanisms and models

The budding yeast Saccharomyces cerevisiae displays steady oscillations in continuous cultures under certain conditions. Oscillatory responses are important both metabolically and in process applications. Although much information has become available, a definitive theory to explain and model these oscillations is yet to be formulated. Models of oscillatory cultivation have focussed primarily either on intracellular reactions or on transport processes coupled to substantially lumped intracellular kinetics. This review discusses the development of the models and the directions they provide for a comprehensive model of oscillatory metabolism.

Meiotic differentiation during colony maturation in Saccharomyces cerevisiae

As yeast colonies ceased growth, cells at the edge of these colonies transited from the cell division cycle into meiosis at high efficiency. This transition occurred remarkably synchronously and only at late stages of colony maturation. The transition occurred on medium containing acetate or low concentrations of glucose, but not on medium containing high glucose. The repression by high glucose was overcome when IME1 was overexpressed from a plasmid. Experiments with different growth media imply that meiosis in colonies is triggered by changes in the nutrient environment as colonies mature. HAP2 is required to sporulate in any carbon source, whereas GRR1 is required for glucose repression of sporulation. CLN3 is required to repress meiosis in colonies but not in liquid cultures, indicating that the regulators that mediate the transition to meiosis in colonies are not identical to the regulators that mediate this transition in liquid cultures.

Steady-state and transient-state analyses of aerobic fermentation in Saccharomyces kluyveri

Some yeasts, such as Saccharomyces cerevisiae, produce ethanol at fully aerobic conditions, whereas other yeasts, such as Kluyveromyces lactis, do not. In this study we investigated the occurrence of aerobic alcoholic fermentation in the petite-negative yeast Saccharomyces kluyveri that is only distantly related to S. cerevisiae. In aerobic glucose-limited continuous cultures of S. kluyveri, two growth regimens were observed: at dilution rates below 0.5 h(-1) the metabolism was purely respiratory, and at dilution rates above 0.5 h(-1) the metabolism was respiro-fermentative. The dilution rate at which the switch in metabolism occurred, i.e. the critical dilution rate, was 66% higher than the typical critical dilution rate of S. cerevisiae. The maximum specific oxygen consumption rate around the critical dilution rate was found to 13.6 mmol (g dry weight)(-1) h(-1) and the capacity of the pyruvate dehydrogenase-bypass pathway was estimated to be high from in vitro enzyme activities; especially the specific activity of acetyl-CoA synthetase was much higher than in S. cerevisiae at all tested conditions. Addition of glucose to respiring cells of S. kluyveri led to ethanol formation after a delay of 20-50 min (depending on culture conditions prior to the pulse), which is in contrast to S. cerevisiae that ferments immediately after glucose addition.

Optimizing scale-up fermentation processes

There are many aims associated with the optimization of fermentation processes. Optimization is expected to increase the yield of the final product but the process must be compliant with good manufacturing practices, the available equipment and the expected final scale of operation. Dealing with genetically modified microorganisms that overproduce recombinant protein has the advantage that the vast majority of the processes use only three different species, namely Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris. Standard processes for each organism are described in textbooks and serve as a basis for the development of a tailored process. This article outlines the general philosophy that we have devised to ensure an efficient approach of scaling up fermentation processes for biopharmaceutical purposes, in a multidisciplinary environment.