Metabolic flux analysis during the exponential growth phase of Saccharomyces cerevisiae in wine fermentations

Insights into intraspecific diversity of central carbon metabolites in Saccharomyces cerevisiae during wine fermentation

Saccharomyces cerevisiae is a major actor in winemaking that converts sugars from the grape must into ethanol and CO2 with outstanding efficiency. Primary metabolites produced during fermentation have a great importance in wine. While ethanol content contributes to the overall profile, other metabolites like glycerol, succinate, acetate or lactate also have significant impacts, even when present in lower concentrations. S. cerevisiae is known for its great genetic diversity that is related to its natural or technological environment. However, the variation range of metabolic diversity which can be exploited to enhance wine quality depends on the pathway considered. Our experiment assessed the diversity of primary metabolites production in a set of 51 S. cerevisiae strains from various genetic backgrounds. Results pointed out great yield differences depending on the metabolite considered, with ethanol having the lowest variation. A negative correlation between ethanol and glycerol was observed, confirming glycerol synthesis as a suitable lever to reduce ethanol yield. Genetic groups were linked to specific yields, such as the wine group and high α-ketoglutarate and low acetate yields. This research highlights the potential of using natural yeast diversity in winemaking. It also provides a detailed data set on production of well known (ethanol, glycerol, acetate) or little-known (lactate) primary metabolites.

Energy efficiency in winemaking industry: Challenges and opportunities

The United Nations has issued a warning over the limited time for climate disaster prevention. In the last two decades, several countries have set targets to reduce fossil fuel usage and greenhouse gas emissions. These goals are tracked through the adoption of energy systems that prioritise efficiency and low-carbon alternatives, in alignment with the Sustainable Development Goals outlined by the United Nations. In the winemaking sector, the wine produced in the European Union comprised 65 % of the worldwide total from 2014 to 2018, with vineyards making up 4.7 % of its farms in 2020. Electricity is the primary source of energy used in vineries, accounting for around 90 % of the total energy consumption. The energy consumption associated with winemaking is mostly attributed to two key processes: fermentation, which accounts for 45 % to 90 % of the entire energy consumption, and bottling and storage, which contribute around 18 % of the overall energy consumption. The aim of this article is to provide an integrated review of energy efficiency in wineries through examining 144 academic publications. The selected publications cover various aspects, including sustainable energy utilisation in the wine industry, thermal performance analysis of buildings, energy efficiency assessment of systems and technologies, and the integration of renewable energy sources. A link has been established between the geographic distribution of academic publications and wine-producing countries. In relation to European publications, it is observed that research funding is associated with the energy directives of the European Union. It can also be concluded that wine customers are pushing for environmentally friendly practices. However, not everyone in the winemaking sector is moving in the same direction or at the same pace. To identify areas for improvement, winemakers must have supporting tools to manage energy use. Systems optimisation, monitoring, and accounting can be used to decrease energy consumption in winemaking processes or equipment. Progresses on sustainable energy use through greater energy efficiency and share of renewable energies in the wineries can contribute to the reduction of greenhouse gas emissions, and consequently, brings the wine industry closer to climate neutrality.

Evaluation of Arabica Coffee Fermentation Using Machine Learning

This study explores the variances in the organic, chemical, and sensory attributes of fermented coffee beans, specifically examining how post-harvest processes influence cup quality. Coffee fruits from the Catuaí IAC-144 variety were processed using both natural coffee (NC) and pulped coffee (PC) methods. The fruits were then subjected to self-induced anaerobic fermentation (SIAF) using one of the following fermentation methods: solid-state fermentation (SSF) or submerged fermentation (SMF). Within these methods, either spontaneous fermentation (SPF) or starter culture fermentation (SCF) was applied. Each method was conducted over periods of 24, 48, and 72 h. For this purpose, two-hundred-liter bioreactors were used, along with two control treatments. Numerous parameters were monitored throughout the fermentation process. A comprehensive chemical profiling and sensory analysis, adhering to the guidelines of the Specialty Coffee Association, were conducted to evaluate the influence of these fermentation processes on the flavor, aroma, and body characteristics of the coffee beverage across multiple dimensions. Data analysis and predictive modeling were performed using machine learning techniques. This study found that NC exhibited a higher production of acids (citric, malic, succinic, and lactic) compared to PC, resulting in distinct chemical and sensory profiles. The decision tree showed that fructose and malic and succinic acids were identified as the main factors enhancing sensory notes during cupping. SMF promoted higher concentrations of lactic acid, while SSF led to increased ethanol content. Consequently, the SIAF process enhances the sensory quality of coffee, adding value to the product by generating diverse sensory profiles.

Distinguishing anaerobic digestion from electrochemical anaerobic digestion: Metabolic pathways and the role of the microbial community

In this study, we explored why electrochemical anaerobic digestion (EAD) results in higher methane conversion and lower CO₂ emissions than anaerobic digestion (AD). Single-chamber AD and EAD reactors were used in this experiment, and the temperature was set as the disturbance factor. Current, pH, electrode potential, gas content, and microbial community were used as indicators for our analysis. Flux balance analysis (FBA) and high-pass next-generation sequencing (NGS) were used to explore the relationships between AD and EAD methane-producing metabolic fluxes and microorganisms. The results showed that the average methane fluxes were 22.27 (AD) and 29.65 (EAD). Compared with AD, EAD had improved hydrogen-dependent CO₂ reduction pathway. Trichloromonas was the dominant electricity-producing microorganism on the EAD anode film, which was closely related to the H₂ flux at the cathode. Oscillibacter and Syntrophomonas were the dominant bacteria in the fermentation broth, specific to EAD. The abundance of Oscillibacter was positively correlated with the H₂ flux, and the presence of Oscillibacter enhanced CO₂ reduction by hydrogen. Methanosaeta was the only dominant methanogenic bacterium in AD and EAD, and its abundance was higher in the experimental group with a greater methane flux.

Metabolic Modeling of Wine Fermentation at Genome Scale

Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the metabolic and physiological phenomena taking place during this process can be now attained at a genome scale with the help of metabolic models. In this chapter, we present a detailed protocol for modeling wine fermentation using genome-scale metabolic models. In particular, we illustrate how metabolic fluxes can be computed, optimized and interpreted, for both yeast and bacteria under winemaking conditions. We also show how nutritional requirements can be determined and simulated using these models in relevant test cases. This chapter introduces fundamental concepts and practical steps for applying flux balance analysis in wine fermentation, and as such, it is intended for a broad microbiology audience as well as for practitioners in the metabolic modeling field.

FORMATION OF THE QUALITY OF UNFORTIFIED WINE MATERIALS OBTAINED FROM BLACK ELDERBERRIES

The use of local non-conventional raw materials will allow significantly enriching unfortified fruit wines with ascorbic acid and phenolic substances and make it possible to obtain products with increased biological value. The paper considers black elderberries grown in the forest steppe zone of Ukraine. It has been determined that they contain 12–13% of soluble solids, 6.9–8.1 of sugars, 0.93–1.2% of titratable acids, 33.4–53.1 mg/100 g of ascorbic acid, and 2331–3888 mg/100 g of phenolic substances. The pressing process and its dependence on the method of treating berries have been studied. It has been proved that juice extraction from black elderberries is the highest when they are pretreated with heat at 98±2°C for 3–5 minutes, with 15% of water added. Depending on the treatment method, juices retain ascorbic acid (15.8–33.4 mg/100 g) and phenolic substances (2538–3888 mg/100 g), which indicates their high biological value. Juices like these can be used to improve the biological composition of blended juices and wines. To ferment high-sugar black elderberry must, active dry yeast was used, namely the yeast races EC-1118 of the genus Saccharomyces bayanus (France) and ENSIS LE-1 or ENSIS LE-5 of the genus Saccharomyces cerevisiae (Spain). The musts were fermented for 36–62 days. The period of vigorous fermentation coincides with the period of initial fermentation and ends in 9–10 days, with accumulation of 12–14% of ethanol by volume. Unfortified wine materials obtained from black elderberries contain 22–38.3 mg/100 g of ascorbic acid (its content in wine materials is by 7.8–49.55% lower than in fresh berries) and 1750–3510 mg/100 g of phenolic substances (which is lower by 9.7–39.6%, as compared with fresh elderberries). The active acidity of black elderberry wine materials is 3.90–4.09 pH units, depending on the yeast race. A similar difference has been found for the redox potential (160–176 mV), which indicates that the wine materials from black elderberries are low-oxidised. The intensity of colour of the wine materials obtained from black elderberries (D420 + D520) varied from 3.08 to 3.20, and the colour shade from 0.88 to 0.92, which is typical of young red wines. These wine materials can be used to increase the quality and biological value of blended wines.

Monitoring Site-Specific Fermentation Outcomes via Oxidation Reduction Potential and UV-Vis Spectroscopy to Characterize "Hidden" Parameters of Pinot Noir Wine Fermentations

Real-time process metrics are standard for the majority of fermentation-based industries but have not been widely adopted by the wine industry. In this study, replicate fermentations were conducted with temperature as the main process parameter and assessed via in-line Oxidation Reduction Potential (ORP) probes and at-line profiling of phenolics compounds by UV-Vis spectroscopy. The California and Oregon vineyards used in this study displayed consistent vinification outcomes over five vintages and are representative of sites producing faster- and slower-fermenting musts. The selected sites have been previously characterized by fermentation kinetics, elemental profile, phenolics, and sensory analysis. ORP probes were integrated into individual fermentors to record how ORP changed throughout the fermentation process. The ORP profiles generally followed expected trends with deviations revealing previously undetectable process differences between sites and replicates. Site-specific differences were also observed in phenolic and anthocyanin extraction. Elemental composition was also analyzed for each vineyard, revealing distinctive profiles that correlated with the fermentation kinetics and may influence the redox status of these wines. The rapid ORP responses observed related to winemaking decisions and yeast activity suggest ORP is a useful process parameter that should be tracked in addition to Brix, temperature, and phenolics extraction for monitoring fermentations.

Curation and Analysis of a Saccharomyces cerevisiae Genome-Scale Metabolic Model for Predicting Production of Sensory Impact Molecules under Enological Conditions

One approach for elucidating strain-to-strain metabolic differences is the use of genome-scale metabolic models (GSMMs). To date GSMMs have not focused on the industrially important area of flavor production and, as such; do not cover all the pathways relevant to flavor formation in yeast. Moreover, current models for Saccharomyces cerevisiae generally focus on carbon-limited and/or aerobic systems, which is not pertinent to enological conditions. Here, we curate a GSMM (iWS902) to expand on the existing Ehrlich pathway and ester formation pathways central to aroma formation in industrial winemaking, in addition to the existing sulfur metabolism and medium-chain fatty acid (MCFA) pathways that also contribute to production of sensory impact molecules. After validating the model using experimental data, we predict key differences in metabolism for a strain (EC 1118) in two distinct growth conditions, including differences for aroma impact molecules such as acetic acid, tryptophol, and hydrogen sulfide. Additionally, we propose novel targets for metabolic engineering for aroma profile modifications employing flux variability analysis with the expanded GSMM. The model provides mechanistic insights into the key metabolic pathways underlying aroma formation during alcoholic fermentation and provides a potential framework to contribute to new strategies to optimize the aroma of wines.

QTL mapping of modelled metabolic fluxes reveals gene variants impacting yeast central carbon metabolism

The yeast Saccharomyces cerevisiae is an attractive industrial microorganism for the production of foods and beverages as well as for various bulk and fine chemicals, such as biofuels or fragrances. Building blocks for these biosyntheses are intermediates of yeast central carbon metabolism (CCM), whose intracellular availability depends on balanced single reactions that form metabolic fluxes. Therefore, efficient product biosynthesis is influenced by the distribution of these fluxes. We recently demonstrated great variations in CCM fluxes between yeast strains of different origins. However, we have limited understanding of flux modulation and the genetic basis of flux variations. In this study, we investigated the potential of quantitative trait locus (QTL) mapping to elucidate genetic variations responsible for differences in metabolic flux distributions (fQTL). Intracellular metabolic fluxes were estimated by constraint-based modelling and used as quantitative phenotypes, and differences in fluxes were linked to genomic variations. Using this approach, we detected four fQTLs that influence metabolic pathways. The molecular dissection of these QTLs revealed two allelic gene variants, PDB1 and VID30, contributing to flux distribution. The elucidation of genetic determinants influencing metabolic fluxes, as reported here for the first time, creates new opportunities for the development of strains with optimized metabolite profiles for various applications.

Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts

BACKGROUND

Efficient xylose fermentation still demands knowledge regarding xylose catabolism. In this study, metabolic flux analysis (MFA) and metabolomics were used to improve our understanding of xylose metabolism. Thus, a stoichiometric model was constructed to simulate the intracellular carbon flux and used to validate the metabolome data collected within xylose catabolic pathways of non-Saccharomyces xylose utilizing yeasts.

RESULTS

A metabolic flux model was constructed using xylose fermentation data from yeasts Scheffersomyces stipitis, Spathaspora arborariae, and Spathaspora passalidarum. In total, 39 intracellular metabolic reactions rates were utilized validating the measurements of 11 intracellular metabolites, acquired by mass spectrometry. Among them, 80% of total metabolites were confirmed with a correlation above 90% when compared to the stoichiometric model. Among the intracellular metabolites, fructose-6-phosphate, glucose-6-phosphate, ribulose-5-phosphate, and malate are validated in the three studied yeasts. However, the metabolites phosphoenolpyruvate and pyruvate could not be confirmed in any yeast. Finally, the three yeasts had the metabolic fluxes from xylose to ethanol compared. Xylose catabolism occurs at twice-higher flux rates in S. stipitis than S. passalidarum and S. arborariae. Besides, S. passalidarum present 1.5 times high flux rate in the xylose reductase reaction NADH-dependent than other two yeasts.

CONCLUSIONS

This study demonstrated a novel strategy for metabolome data validation and brought insights about naturally xylose-fermenting yeasts. S. stipitis and S. passalidarum showed respectively three and twice higher flux rates of XR with NADH cofactor, reducing the xylitol production when compared to S. arborariae. Besides then, the higher flux rates directed to pentose phosphate pathway (PPP) and glycolysis pathways resulted in better ethanol production in S. stipitis and S. passalidarum when compared to S. arborariae.

Saccharomyces cerevisiae and Torulaspora delbrueckii Intra- and Extra-Cellular Aromatic Amino Acids Metabolism

Tryptophan, phenylalanine, and tyrosine play an important role as nitrogen sources in yeast metabolism. They regulate biomass production and fermentation rate, and their catabolites contribute to wine health benefits and sensorial character through the yeast biotransformation of grape juice constitutes into biologically active and flavor-impacting components. A UHPLC-MS/MS method was applied to monitor 37 tryptophan/phenylalanine/tyrosine yeast metabolites both in extra- and intracellular extracts produced by the fermentation of two Saccharomyces cerevisiae strains and one Torulaspora delbrueckii. The results shed light on the intra- and extra-cellular metabolomic dynamics, by combining metabolic needs, stimuli, and signals. Among others, the results indicated (a) the production of 2-aminoacetophenone by yeasts, mainly by the two Saccharomyces cerevisiae; (b) the deactivation and/or detoxification of tryptophol via sulfonation reaction; and (c) the deacetylation of N-acetyl tryptophan ethyl ester and N-acetyl tyrosine ethyl ester by producing the corresponding ethyl esters.

Evaluation of the use of multiflora bee pollen on the volatile compounds and sensorial profile of Palomino fino and Riesling white young wines

This study investigates the impact of bee pollen on volatile compounds, odour activity values and sensory profiles in Palomino fino and Riesling young white wines. Commercial bee pollen was added to grape must using six different doses (0 (control), 0.1, 0.25, 1, 5, 10 and 20g/L) and fermented under controlled conditions. Volatile compounds were determined with GC and GC-MS chromatography and sensorial analysis using a qualified panel of tasters. Bee pollen produces an increase in volatile compounds depending on the grape variety and the dose applied. It also increases the synthesis of higher alcohols, methanol, esters, acetaldehyde and terpenes, reducing alcohols and fatty acids. Wines with low doses (0.1 and 0.25g/L) showed the higher OAV values (fruity and floral) and scores in overall judgment for the sensory evaluation. High pollen doses decrease fruity character and could result in deviations affecting the sensorial quality.

Correlation between Low Temperature Adaptation and Oxidative Stress in Saccharomyces cerevisiae

Many factors, such as must composition, juice clarification, fermentation temperature, or inoculated yeast strain, strongly affect the alcoholic fermentation and aromatic profile of wine. As fermentation temperature is effectively controlled by the wine industry, low-temperature fermentation (10–15°C) is becoming more prevalent in order to produce white and “rosé” wines with more pronounced aromatic profiles. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains. Previous research has shown the strong implication of oxidative stress response in adaptation to low temperature during the fermentation process. Here we aimed first to quantify the correlation between recovery after shock with different oxidants and cold, and then to detect the key genes involved in cold adaptation that belong to sulfur assimilation, peroxiredoxins, glutathione-glutaredoxins, and thioredoxins pathways. To do so, we analyzed the growth of knockouts from the EUROSCARF collection S. cerevisiae BY4743 strain at low and optimal temperatures. The growth rate of these knockouts, compared with the control, enabled us to identify the genes involved, which were also deleted and validated as key genes in the background of two commercial wine strains with a divergent phenotype in their low-temperature growth. We identified three genes, AHP1, MUP1, and URM1, whose deletion strongly impaired low-temperature growth.

Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments

Background

S. cerevisiae has attracted considerable interest in recent years as a model for ecology and evolutionary biology, revealing a substantial genetic and phenotypic diversity. However, there is a lack of knowledge on the diversity of metabolic networks within this species.

Results

To identify the metabolic and evolutionary constraints that shape metabolic fluxes in S. cerevisiae, we used a dedicated constraint-based model to predict the central carbon metabolism flux distribution of 43 strains from different ecological origins, grown in wine fermentation conditions. In analyzing these distributions, we observed a highly contrasted situation in flux variability, with quasi-constancy of the glycolysis and ethanol synthesis yield yet high flexibility of other fluxes, such as the pentose phosphate pathway and acetaldehyde production. Furthermore, these fluxes with large variability showed multimodal distributions that could be linked to strain origin, indicating a convergence between genetic origin and flux phenotype.

Conclusions

Flux variability is pathway-dependent and, for some flux, a strain origin effect can be found. These data highlight the constraints shaping the yeast operative central carbon network and provide clues for the design of strategies for strain improvement.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0456-0) contains supplementary material, which is available to authorized users.

Evolutionary engineering of a wine yeast strain revealed a key role of inositol and mannoprotein metabolism during low-temperature fermentation

BACKGROUND

Wine produced at low temperature is often considered to improve sensory qualities. However, there are certain drawbacks to low temperature fermentations: e.g. low growth rate, long lag phase, and sluggish or stuck fermentations. Selection and development of new Saccharomyces cerevisiae strains well adapted at low temperature is interesting for future biotechnological applications. This study aimed to select and develop wine yeast strains that well adapt to ferment at low temperature through evolutionary engineering, and to decipher the process underlying the obtained phenotypes.

RESULTS

We used a pool of 27 commercial yeast strains and set up batch serial dilution experiments to mimic wine fermentation conditions at 12 °C. Evolutionary engineering was accomplished by using the natural yeast mutation rate and mutagenesis procedures. One strain (P5) outcompeted the others under both experimental conditions and was able to impose after 200 generations. The evolved strains showed improved growth and low-temperature fermentation performance compared to the ancestral strain. This improvement was acquired only under inositol limitation. The transcriptomic comparison between the evolved and parental strains showed the greatest up-regulation in four mannoprotein coding genes, which belong to the DAN/TIR family (DAN1, TIR1, TIR4 and TIR3). Genome sequencing of the evolved strain revealed the presence of a SNP in the GAA1 gene and the construction of a site-directed mutant (GAA1 (Thr108)) in a derivative haploid of the ancestral strain resulted in improved fermentation performance. GAA1 encodes a GPI transamidase complex subunit that adds GPI, which is required for inositol synthesis, to newly synthesized proteins, including mannoproteins.

CONCLUSIONS

In this study we demonstrate the importance of inositol and mannoproteins in yeast adaptation at low temperature and the central role of the GAA1 gene by linking both metabolisms.

Increased resveratrol production in wines using engineered wine strains Saccharomyces cerevisiae EC1118 and relaxed antibiotic or auxotrophic selection

Resveratrol is a polyphenolic compound with diverse beneficial effects on human health. Red wine is the major dietary source of resveratrol but the amount that people can obtain from wines is limited. To increase the resveratrol production in wines, two expression vectors carrying 4-coumarate: coenzyme A ligase gene (4CL) from Arabidopsis thaliana and resveratrol synthase gene (RS) from Vitis vinifera were transformed into industrial wine strain Saccharomyces cerevisiae EC1118. When cultured with 1 mM p-coumaric acid, the engineered strains grown with and without the addition of antibiotics produced 8.249 and 3.317 mg/L of trans-resveratrol in the culture broth, respectively. Resveratrol content of the wine fermented with engineered strains was twice higher than that of the control, indicating that our engineered strains could increase the production of resveratrol during wine fermentation.

The impact of oxygen on the final alcohol content of wine fermented by a mixed starter culture

We have developed a wine fermentation procedure that takes advantage of the metabolic features of a previously characterized Metschnikowia pulcherrima strain in order to reduce ethanol production. It involves the use of M. pulcherrima/Saccharomyces cerevisiae mixed cultures, controlled oxygenation conditions during the first 48 h of fermentation, and anaerobic conditions thereafter. The influence of different oxygenation regimes and initial inoculum composition on yeast physiology and final ethanol content was studied. The impact of oxygenation on yeast physiology goes beyond the first aerated step and influences yields and survival rates during the anaerobic stage. The activity of M. pulcherrima in mixed oxygenated cultures resulted in a clear reduction in ethanol yield, as compared to S. cerevisiae. Despite relatively low initial cell numbers, S. cerevisiae always predominated in mixed cultures by the end of the fermentation process. Strain replacement was faster under low oxygenation levels. M. pulcherrima confers an additional advantage in terms of dissolved oxygen, which drops to zero after a few hours of culture, even under highly aerated conditions, and this holds true for mixed cultures. Alcohol reduction values about 3.7 % (v/v) were obtained for mixed cultures under high aeration, but they were associated to unacceptable volatile acidity levels. In contrast, under optimized conditions, only 0.35 g/L acetic acid was produced, for an alcohol reduction of 2.2 % (v/v), and almost null dissolved oxygen during the process.

Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations

BACKGROUND

The wine industry needs better-adapted yeasts to grow at low temperature because it is interested in fermenting at low temperature to improve wine aroma. Elucidating the response to cold in Saccharomyces cerevisiae is of paramount importance for the selection or genetic improvement of wine strains.

RESULTS

We followed a global approach by comparing transcriptomic, proteomic and genomic changes in two commercial wine strains, which showed clear differences in their growth and fermentation capacity at low temperature. These strains were selected according to the maximum growth rate in a synthetic grape must during miniaturized batch cultures at different temperatures. The fitness differences of the selected strains were corroborated by directly competing during fermentations at optimum and low temperatures. The up-regulation of the genes of the sulfur assimilation pathway and glutathione biosynthesis suggested a crucial role in better performance at low temperature. The presence of some metabolites of these pathways, such as S-Adenosilmethionine (SAM) and glutathione, counteracted the differences in growth rate at low temperature in both strains. Generally, the proteomic and genomic changes observed in both strains also supported the importance of these metabolic pathways in adaptation at low temperature.

CONCLUSIONS

This work reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature. We propose that a greater activation of this metabolic route enhances the synthesis of key metabolites, such as glutathione, whose protective effects can contribute to improve the fermentation process.

An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must

We used experimental evolution in order to identify genes involved in the adaptation of Saccharomyces cerevisiae to the early stages of alcoholic fermentation. Evolution experiments were run for about 200 generations, in continuous culture conditions emulating the initial stages of wine fermentation. We performed whole-genome sequencing of four adapted strains from three independent evolution experiments. Mutations identified in these strains pointed to the Rsp5p-Bul1/2p ubiquitin ligase complex as the preferred evolutionary target under these experimental conditions. Rsp5p is a multifunctional enzyme able to ubiquitinate target proteins participating in different cellular processes, while Bul1p is an Rsp5p substrate adaptor specifically involved in the ubiquitin-dependent internalization of Gap1p and other plasma membrane permeases. While a loss-of-function mutation in BUL1 seems to be enough to confer a selective advantage under these assay conditions, this did not seem to be the case for RSP5 mutated strains, which required additional mutations, probably compensating for the detrimental effect of altered Rsp5p activity on essential cellular functions. The power of this experimental approach is illustrated by the identification of four independent mutants, each with a limited number of SNPs, affected within the same pathway. However, in order to obtain information relevant for a specific biotechnological process, caution must be taken in the choice of the background yeast genotype (as shown in this case for auxotrophies). In addition, the use of very stable continuous fermentation conditions might lead to the selection of a rather limited number of adaptive responses that would mask other possible targets for genetic improvement.

Use of chemostat cultures mimicking different phases of wine fermentations as a tool for quantitative physiological analysis

Background

Saccharomyces cerevisiae is the most relevant yeast species conducting the alcoholic fermentation that takes place during winemaking. Although the physiology of this model organism has been extensively studied, systematic quantitative physiology studies of this yeast under winemaking conditions are still scarce, thus limiting the understanding of fermentative metabolism of wine yeast strains and the systematic description, modelling and prediction of fermentation processes. In this study, we implemented and validated the use of chemostat cultures as a tool to simulate different stages of a standard wine fermentation, thereby allowing to implement metabolic flux analyses describing the sequence of metabolic states of S. cerevisae along the wine fermentation.

Results

Chemostat cultures mimicking the different stages of standard wine fermentations of S. cerevisiae EC1118 were performed using a synthetic must and strict anaerobic conditions. The simulated stages corresponded to the onset of the exponential growth phase, late exponential growth phase and cells just entering stationary phase, at dilution rates of 0.27, 0.04, 0.007 h⁻¹, respectively. Notably, measured substrate uptake and product formation rates at each steady state condition were generally within the range of corresponding conversion rates estimated during the different batch fermentation stages.

Moreover, chemostat data were further used for metabolic flux analysis, where biomass composition data for each condition was considered in the stoichiometric model. Metabolic flux distributions were coherent with previous analyses based on batch cultivations data and the pseudo-steady state assumption.

Conclusions

Steady state conditions obtained in chemostat cultures reflect the environmental conditions and physiological states of S. cerevisiae corresponding to the different growth stages of a typical batch wine fermentation, thereby showing the potential of this experimental approach to systematically study the effect of environmental relevant factors such as temperature, sugar concentration, C/N ratio or (micro) oxygenation on the fermentative metabolism of wine yeast strains.