Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation

Machine Learning Techniques Disclose the Combined Effect of Fermentation Conditions on Yeast Mixed-Culture Dynamics and Wine Quality

The use of yeast starter cultures consisting of a blend of Saccharomyces cerevisiae and non-Saccharomyces yeasts has increased in recent years as a mean to address consumers’ demands for diversified wines. However, this strategy is currently limited by the lack of a comprehensive knowledge regarding the factors that determine the balance between the yeast-yeast interactions and their responses triggered in complex environments. Our previous studies demonstrated that the strain Hanseniaspora guilliermondii UTAD222 has potential to be used as an adjunct of S. cerevisiae in the wine industry due to its positive impact on the fruity and floral character of wines. To rationalize the use of this yeast consortium, this study aims to understand the influence of production factors such as sugar and nitrogen levels, fermentation temperature, and the level of co-inoculation of H. guilliermondii UTAD222 in shaping fermentation and wine composition. For that purpose, a Central Composite experimental Design was applied to investigate the combined effects of the four factors on fermentation parameters and metabolites produced. The patterns of variation of the response variables were analyzed using machine learning methods, to describe their clustered behavior and model the evolution of each cluster depending on the experimental conditions. The innovative data analysis methodology adopted goes beyond the traditional univariate approach, being able to incorporate the modularity, heterogeneity, and hierarchy inherent to metabolic systems. In this line, this study provides preliminary data and insights, enabling the development of innovative strategies to increase the aromatic and fermentative potential of H. guilliermondii UTAD222 by modulating temperature and the availability of nitrogen and/or sugars in the medium. Furthermore, the strategy followed gathered knowledge to guide the rational development of mixed blends that can be used to obtain a particular wine style, as a function of fermentation conditions.

Possible Role for Allelic Variation in Yeast MED15 in Ecological Adaptation

The propensity for Saccharomyces cerevisiae yeast to ferment sugars into ethanol and CO₂ has long been useful in the production of a wide range of food and drink. In the production of alcoholic beverages, the yeast strain selected for fermentation is crucial because not all strains are equally proficient in tolerating fermentation stresses. One potential mechanism by which domesticated yeast may have adapted to fermentation stresses is through changes in the expression of stress response genes. MED15 is a general transcriptional regulator and RNA Pol II Mediator complex subunit which modulates the expression of many metabolic and stress response genes. In this study, we explore the role of MED15 in alcoholic fermentation. In addition, we ask whether MED15 alleles from wine, sake or palm wine yeast improve fermentation activity and grape juice fermentation stress responses. And last, we investigate to what extent any differences in activity are due to allelic differences in the lengths of three polyglutamine tracts in MED15. We find that strains lacking MED15 are deficient in fermentation and fermentation stress responses and that MED15 alleles from alcoholic beverage yeast strains can improve both the fermentation capacity and the response to ethanol stresses when transplanted into a standard laboratory strain. Finally, we find that polyglutamine tract length in the Med15 protein is one determinant in the efficiency of the alcoholic fermentation process. These data lead to a working model in which polyglutamine tract length and other types of variability within transcriptional hubs like the Mediator subunit, Med15, may contribute to a reservoir of transcriptional profiles that may provide a fitness benefit in the face of environmental fluctuations.

Saccharomyces cerevisiae Gene Expression during Fermentation of Pinot Noir Wines at an Industrially Relevant Scale

This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms).

Saccharomyces cerevisiae metabolism produces ethanol and other compounds during the fermentation of grape must into wine. Thousands of genes change expression over the course of a wine fermentation, allowing S. cerevisiae to adapt to and dominate the fermentation environment. Investigations into these gene expression patterns previously revealed genes that underlie cellular adaptation to the grape must and wine environments, involving metabolic specialization and ethanol tolerance. However, the majority of studies detailing gene expression patterns have occurred in controlled environments that may not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, an analysis of the S. cerevisiae RC212 gene expression program is presented, drawing from 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. A core gene expression program was observed across all fermentations irrespective of vintage, similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomyces microorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight into Saccharomyces cerevisiae biology critical to fermentation outcomes under industry-relevant conditions.

IMPORTANCE This study characterized Saccharomyces cerevisiae RC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using industry-relevant conditions. The reported gene expression patterns of RC212 are generally similar to those observed under laboratory fermentation conditions but also contain gene expression signatures related to yeast-environment interactions found in a production setting (e.g., the presence of non-Saccharomyces microorganisms). Key genes and pathways highlighted by this work remain undercharacterized, indicating the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.

Phenotypic and transcriptional analysis of Saccharomyces cerevisiae during wine fermentation in response to nitrogen nutrition and co-inoculation with Torulaspora delbrueckii

Nitrogen content of grape musts strongly impacts on fermentation performance and wine metabolite production. As nitrogen is a limiting nutrient in most grape musts, nitrogen supplementation is a common practice that ensures yeast growth during fermentation. However, preferred nitrogen sources -as ammonium- repress the genes related to alternative nitrogen sources consumption, usually involved in aromatic compounds production. Here, we describe the effect of high ammonium doses in Saccharomyces cerevisiae fermentation performance and wine properties, and how it is affected by yeast co-inoculation in mixed (S. cerevisiae + Torulaspora delbrueckii) fermentations. In addition, an RNA-seq analysis allowed us to study the S. cerevisiae transcriptional response to ammonium nutrition and yeast interaction, demonstrating that T. delbrueckii presence affects the global S. cerevisiae transcriptional response, reducing ammonium effects at both phenotypic -fermentation kinetics and metabolite production- and transcriptional levels, under experimental conditions.

Differential Gene Expression and Allele Frequency Changes Favour Adaptation of a Heterogeneous Yeast Population to Nitrogen-Limited Fermentations

Alcoholic fermentation is fundamentally an adaptation process, in which the yeast Saccharomyces cerevisiae outperforms its competitors and takes over the fermentation process itself. Although wine yeast strains appear to be adapted to the stressful conditions of alcoholic fermentation, nitrogen limitations in grape must cause stuck or slow fermentations, generating significant economic losses for the wine industry. One way to discover the genetic bases that promote yeast adaptation to nitrogen-deficient environments are selection experiments, where a yeast population undergoes selection under conditions of nitrogen restriction for a number of generations, to then identify by sequencing the molecular characteristics that promote this adaptation. In this work, we carried out selection experiments in bioreactors imitating wine fermentation under nitrogen-limited fermentation conditions (SM60), using the heterogeneous SGRP-4X yeast population, to then sequence the transcriptome and the genome of the population at different time points of the selection process. The transcriptomic results showed an overexpression of genes from the NA strain (North American/YPS128), a wild, non-domesticated isolate. In addition, genome sequencing and allele frequency results allowed several QTLs to be mapped for adaptation to nitrogen-limited fermentation. Finally, we validated the ECM38 allele of NA strain as responsible for higher growth efficiency under nitrogen-limited conditions. Taken together, our results revealed a complex pattern of molecular signatures favouring adaptation of the yeast population to nitrogen-limited fermentations, including differential gene expression, allele frequency changes and loss of the mitochondrial genome. Finally, the results suggest that wild alleles from a non-domesticated isolate (NA) may have a relevant role in the adaptation to the assayed fermentation conditions, with the consequent potential of these alleles for the genetic improvement of wine yeast strains.

Disentangling the genetic bases of Saccharomyces cerevisiae nitrogen consumption and adaptation to low nitrogen environments in wine fermentation

The budding yeast Saccharomyces cerevisiae has been considered for more than 20 years as a premier model organism for biological sciences, also being the main microorganism used in wide industrial applications, like alcoholic fermentation in the winemaking process. Grape juice is a challenging environment for S. cerevisiae, with nitrogen deficiencies impairing fermentation rate and yeast biomass production, causing stuck or sluggish fermentations, thus generating sizeable economic losses for wine industry. In the present review, we summarize some recent efforts in the search of causative genes that account for yeast adaptation to low nitrogen environments, specially focused in wine fermentation conditions. We start presenting a brief perspective of yeast nitrogen utilization under wine fermentative conditions, highlighting yeast preference for some nitrogen sources above others. Then, we give an outlook of S. cerevisiae genetic diversity studies, paying special attention to efforts in genome sequencing for population structure determination and presenting QTL mapping as a powerful tool for phenotype-genotype correlations. Finally, we do a recapitulation of S. cerevisiae natural diversity related to low nitrogen adaptation, specially showing how different studies have left in evidence the central role of the TORC1 signalling pathway in nitrogen utilization and positioned wild S. cerevisiae strains as a reservoir of beneficial alleles with potential industrial applications (e.g. improvement of industrial yeasts for wine production). More studies focused in disentangling the genetic bases of S. cerevisiae adaptation in wine fermentation will be key to determine the domestication effects over low nitrogen adaptation, as well as to definitely proof that wild S. cerevisiae strains have potential genetic determinants for better adaptation to low nitrogen conditions.

Transcriptional Comparison Investigating the Influence of the Addition of Unsaturated Fatty Acids on Aroma Compounds During Alcoholic Fermentation

The levels of unsaturated fatty acids (UFAs) in grape must significantly influence yeast metabolism and the production of aroma compounds. In this work, cDNA microarray technology was applied to analyze the transcriptional discrepancies of wine yeast (commercial wine yeast Lalvin EC1118) fermenting in synthetic grape must supplemented with different concentrations of a mixture of UFAs (including linoleic acid, oleic acid, and α-linolenic acid). The results showed that the initial addition of a high level of UFAs can significantly enrich the intracellular UFAs when compared to a low addition of UFAs and further increase the cell population and most volatiles, including higher alcohols and esters, except for several fatty acids. Microarray analyses identified that 63 genes were upregulated, and 91 genes were downregulated during the different fermentation stages. The up-regulated genes were involved in yeast growth and proliferation, stress responses and amino acid transportation, while the repressed genes were associated with lipid and sterol biosynthesis, amino acid metabolism, TCA cycle regulation, mitochondrial respiration, and stress responses. Unexpectedly, the genes directly related to the biosynthesis of volatile compounds did not vary substantially between the fermentations with the high and low UFA additions. The beneficial aromatic function of the UFAs was ascribed to the increased biomass and amino acid transportation, considering that the incorporation of the additional UFAs in yeast cells maintains high membrane fluidity and increases the ability of the cells to resist deleterious conditions. Our results highlighted the importance of UFAs in the regulation of aroma biosynthesis during wine fermentation and suggested that the improvement of the resistance of yeast to extreme stresses during alcoholic fermentation is essential to effectively modulate and improve the production of aroma compounds. A potential way to achieve this goal could be the rational increase of the UFA contents in grape must.

Influence of nitrogen status in wine alcoholic fermentation

Nitrogen is an essential nutrient for yeast during alcoholic fermentation. Nitrogen is involved in the biosynthesis of protein, amino acids, nucleotides, and other metabolites, including volatile compounds. However, recent studies have called several mechanisms that regulate its role in biosynthesis into question. An initial focus on S. cerevisiae has highlighted that the concept of "preferred" versus "non-preferred" nitrogen sources is extremely variable and strain-dependent. Then, the direct involvement of amino acids consumed in the formation of proteins and volatile compounds has recently been reevaluated. Indeed, studies have highlighted the key role of lipids in nitrogen regulation in S. cerevisiae and their involvement in the mechanism of cell death. New winemaking strategies using non-Saccharomyces yeast strains in co- or sequential fermentation improve nitrogen management. Indeed, recent studies show that non-Saccharomyces yeasts have significant and specific needs for nitrogen. Moreover, sluggish fermentation can occur when they are associated with S. cerevisiae, necessitating nitrogen addition. In this context, we will present the consequences of nitrogen addition, discussing the sources, time of addition, transcriptome changes, and effect on volatile compound composition.

Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains

Metabolic engineering has been vital to the development of industrial microbes such as the yeast Saccharomyces cerevisiae. However, sequential rounds of modification are often needed to achieve particular industrial design targets. Systems biology approaches can aid in identifying genetic targets for modification through providing an integrated view of cellular physiology. Recently, research into the generation of commercial yeasts that can produce reduced-ethanol wines has resulted in metabolically-engineered strains of S. cerevisiae that are less efficient at producing ethanol from sugar. However, these modifications led to the concomitant production of off-flavour by-products. A combination of transcriptomics, proteomics and metabolomics was therefore used to investigate the physiological changes occurring in an engineered low-ethanol yeast strain during alcoholic fermentation. Integration of 'omics data identified several metabolic reactions, including those related to the pyruvate node and redox homeostasis, as being significantly affected by the low-ethanol engineering methodology, and highlighted acetaldehyde and 2,4,5-trimethyl-1,3-dioxolane as the main off-flavour compounds. Gene remediation strategies were then successfully applied to decrease the formation of these by-products, while maintaining the 'low-alcohol' phenotype. The data generated from this comprehensive systems-based study will inform wine yeast strain development programmes, which, in turn, could potentially play an important role in assisting winemakers in their endeavour to produce low-alcohol wines with desirable flavour profiles.

Sphingolipid accumulation causes mitochondrial dysregulation and cell death

Sphingolipids are structural components of cell membranes that have signaling roles to regulate many activities, including mitochondrial function and cell death. Sphingolipid metabolism is integrated with numerous metabolic networks, and dysregulated sphingolipid metabolism is associated with disease. Here, we describe a monogenic yeast model for sphingolipid accumulation. A csg2Δ mutant cannot readily metabolize and accumulates the complex sphingolipid inositol phosphorylceramide (IPC). In these cells, aberrant activation of Ras GTPase is IPC-dependent, and accompanied by increased mitochondrial reactive oxygen species (ROS) and reduced mitochondrial mass. Survival or death of csg2Δ cells depends on nutritional status. Abnormal Ras activation in csg2Δ cells is associated with impaired Snf1/AMPK protein kinase, a key regulator of energy homeostasis. csg2Δ cells are rescued from ROS production and death by overexpression of mitochondrial catalase Cta1, abrogation of Ras hyperactivity or genetic activation of Snf1/AMPK. These results suggest that sphingolipid dysregulation compromises metabolic integrity via Ras and Snf1/AMPK pathways.

Evolution of Volatile Sulfur Compounds during Wine Fermentation

Volatile sulfur compounds (VSCs) play a significant role in the aroma of foods and beverages. With very low sensory thresholds and strong unpleasant aromas, most VSCs are considered to have a negative impact on wine quality. In this study, headspace solid phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) was used to analyze the time course of the biosynthesis of 12 VSCs formed during wine fermentation. Two different strains of Saccharomyces cerevisiae, the laboratory strain BY4743 and a commercial strain, F15, were assessed using two media: synthetic grape media and Sauvignon Blanc juice. Seven VSCs were detected above background, with three rising above their sensory thresholds. The data revealed remarkable differences in the timing and evolution of production during fermentation, with a transient spike in methanethiol production early during anaerobic growth. Heavier VSCs such as benzothiazole and S-ethyl thioacetate were produced at a steady rate throughout grape juice fermentation, whereas others, such as diethyl sulfide, appear toward the very end of the winemaking process. The results also demonstrate significant differences between yeast strains and fermentation media.

Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii

Background

The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S.cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniasporaguilliermondii, this being the first time that this relevant yeast–yeast interaction is examined at a genomic scale.

Results

Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds.

Conclusions

By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0318-1) contains supplementary material, which is available to authorized users.

Response of yeast cells to high glucose involves molecular and physiological differences when compared to other osmostress conditions

Yeast cells can be affected by several causes of osmotic stress, such as high salt, sorbitol or glucose concentrations. The last condition is particularly interesting during natural processes where this microorganism participates. Response to osmostress requires the HOG (High Osmolarity Glycerol) pathway and several transcription factors, including Hot1, which plays a key role in high glucose concentrations. In this work, we describe how the yeast response to osmotic stress shows differences in accordance with the stress agent responsible for it. Compared with other conditions, under high glucose stress, delocalization of MAPK (Mitogen-Activated Protein Kinase) Hog1 is slower, induction of HOT1 expression is higher and Msn2/4 transcription factors are involved to a lesser extent. The transcriptomic analyses carried out with samples incubated for 30 min in the presence of high glucose or sorbitol reveal the presence of two functional categories with a differential expression between these conditions: glycogen biosynthesis and mobilization, and membrane-anchored proteins. We present data to demonstrate that the cells treated with 20% (w/v) (1.11 M) glucose contain higher chitin levels and are more sensitive to calcofluor white and ethanol.

Comparative transcriptomic analysis reveals similarities and dissimilarities in Saccharomyces cerevisiae wine strains response to nitrogen availability

Nitrogen levels in grape-juices are of major importance in winemaking ensuring adequate yeast growth and fermentation performance. Here we used a comparative transcriptome analysis to uncover wine yeasts responses to nitrogen availability during fermentation. Gene expression was assessed in three genetically and phenotypically divergent commercial wine strains (CEG, VL1 and QA23), under low (67 mg/L) and high nitrogen (670 mg/L) regimes, at three time points during fermentation (12 h, 24 h and 96 h). Two-way ANOVA analysis of each fermentation condition led to the identification of genes whose expression was dependent on strain, fermentation stage and on the interaction of both factors. The high fermenter yeast strain QA23 was more clearly distinct from the other two strains, by differential expression of genes involved in flocculation, mitochondrial functions, energy generation and protein folding and stabilization. For all strains, higher transcriptional variability due to fermentation stage was seen in the high nitrogen fermentations. A positive correlation between maximum fermentation rate and the expression of genes involved in stress response was observed. The finding of common genes correlated with both fermentation activity and nitrogen up-take underlies the role of nitrogen on yeast fermentative fitness. The comparative analysis of genes differentially expressed between both fermentation conditions at 12 h, where the main difference was the level of nitrogen available, showed the highest variability amongst strains revealing strain-specific responses. Nevertheless, we were able to identify a small set of genes whose expression profiles can quantitatively assess the common response of the yeast strains to varying nitrogen conditions. The use of three contrasting yeast strains in gene expression analysis prompts the identification of more reliable, accurate and reproducible biomarkers that will facilitate the diagnosis of deficiency of this nutrient in the grape-musts and the development of strategies to optimize yeast performance in industrial fermentations.

A genetic approach of wine yeast fermentation capacity in nitrogen-starvation reveals the key role of nitrogen signaling

Background

In conditions of nitrogen limitation, Saccharomyces cerevisiae strains differ in their fermentation capacities, due to differences in their nitrogen requirements. The mechanisms ensuring the maintenance of glycolytic flux in these conditions are unknown. We investigated the genetic basis of these differences, by studying quantitative trait loci (QTL) in a population of 133 individuals from the F2 segregant population generated from a cross between two strains with different nitrogen requirements for efficient fermentation.

Results

By comparing two bulks of segregants with low and high nitrogen requirements, we detected four regions making a quantitative contribution to these traits. We identified four polymorphic genes, in three of these four regions, for which involvement in the phenotype was validated by hemizygote comparison. The functions of the four validated genes, GCN1, MDS3, ARG81 and BIO3, relate to key roles in nitrogen metabolism and signaling, helping to maintain fermentation performance.

Conclusions

This study reveals that differences in nitrogen requirement between yeast strains results from a complex allelic combination. The identification of three genes involved in sensing and signaling nitrogen and specially one from the TOR pathway as affecting nitrogen requirements suggests a role for this pathway in regulating the fermentation rate in starvation through unknown mechanisms linking nitrogen signaling to glycolytic flux.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-495) contains supplementary material, which is available to authorized users.

Modeling acclimatization by hybrid systems: condition changes alter biological system behavior models

In order to describe the dynamic behavior of a complex biological system, it is useful to combine models integrating processes at different levels and with temporal dependencies. Such combinations are necessary for modeling acclimatization, a phenomenon where changes in environmental conditions can induce drastic changes in the behavior of a biological system. In this article we formalize the use of hybrid systems as a tool to model this kind of biological behavior. A modeling scheme called strong switches is proposed. It allows one to take into account both minor adjustments to the coefficients of a continuous model, and, more interestingly, large-scale changes to the structure of the model. We illustrate the proposed methodology with two applications: acclimatization in wine fermentation kinetics, and acclimatization of osteo-adipo differentiation system linking stimulus signals to bone mass.

Nitrogen regulation involved in the accumulation of urea in Saccharomyces cerevisiae

Rice wine is a popular traditional alcoholic drink with a long history in China. However, the presence of the potential carcinogen ethyl carbamate (EC) raises a series of food safety concerns. Although the metabolic pathway of urea (the major precusor of EC) has been characterized in Saccharomyces cerevisiae, the regulation of urea accumulation remains unclear, making the efficient elimination of urea difficult. To demonstrate the regulatory mechanisms governing urea accumulation, three key nitrogen sources that can inhibit urea utilization for a commercial S. cerevisiae strain were identified. In addition, regulators of nitrogen catabolite repression (NCR) and target of rapamycin (TOR) pathways were identified as being involved in urea accumulation by real-time quantitative PCR. Based on these results, preferred nitrogen sources were found to repress urea utilization by converting them to glutamine or glutamate. Moreover, the results indicated that the manner of urea metabolism regulation was different for two positive regulators involved in NCR; Gln3p can be retained in the cytoplasm by glutamine, while Gat1p can be retained by glutamine and glutamate. Furthermore, this was confirmed by fluorescence location detection. These new findings provide new targets for eliminating EC and other harmful nitrogen-containing compounds in fermented foods.

Impact of assimilable nitrogen availability in glucose uptake kinetics in Saccharomyces cerevisiae during alcoholic fermentation

Background

The expression and activity of the different Saccharomyces cerevisiae hexose uptake systems (Hxt) and the kinetics of glucose uptake are considered essential to industrial alcoholic fermentation performance. However, the dynamics of glucose uptake kinetics during the different stages of fermentation, depending on glucose and nitrogen availability, is very poorly characterized. The objective of the present work was to examine thoroughly the alterations occurring in glucose uptake kinetics during alcoholic fermentation, by the wine strain S. cerevisiae PYCC 4072, of a synthetic grape juice basal medium with either a limiting or non-limiting initial nitrogen concentration and following nitrogen supplementation of the nitrogen-depleted sluggish fermentation.

Results

Independently of the initial concentration of the nitrogen source, glucose transport capacity is maximal during the early stages of fermentation and presumably sustained by the low-affinity and high-capacity glucose transporter Hxt1p. During nitrogen-limited sluggish fermentation, glucose uptake capacity was reduced to approximately 20% of its initial values (V_max = 4.9 ± 0.8 compared to 21.9 ± 1.2 μmol h^-1 10^-8 cells), being presumably sustained by the low-affinity glucose transporter Hxt3p (considering the calculated K_m = 39.2 ± 8.6 mM). The supplementation of the sluggish fermentation broth with ammonium led to the increase of glucose transport capacity associated to the expression of different glucose uptake systems with low and high affinities for glucose (K_m = 58.2 ± 9.1 and 2.7 ± 0.4 mM). A biclustering analysis carried out using microarray data, previously obtained for this yeast strain transcriptional response to equivalent fermentation conditions, indicates that the activation of the expression of genes encoding the glucose transporters Hxt2p (during the transition period to active fermentation) and Hxt3p, Hxt4p, Hxt6p and Hxt7p (during the period of active fermentation) may have a major role in the recovery of glucose uptake rate following ammonium supplementation. These results suggest a general derepression of the glucose-repressible HXT genes and are consistent with the downregulation of Mig1p and Rgt1p.

Conclusions

Although reduced, glucose uptake rate during nitrogen-limited fermentation is not abrogated. Following ammonium supplementation, sluggish fermentation recovery is associated to the increase of glucose uptake capacity, related to the de novo synthesis of glucose transporters with different affinity for glucose and capacity, presumably of Hxt2p, Hxt3p, Hxt4p, Hxt6p and Hxt7p. This study is a contribution to the understanding of yeast response to different stages of alcoholic fermentation at the level of glucose uptake kinetics, in particular under nitrogen limitation or replenish, which is useful knowledge to guide fermentation practices.

Genetics of yeast impacting wine quality

The availability of the sequence of the Saccharomyces genome in combination with the development of chemical analytical technologies with dynamic ranges sensitive enough to detect volatile aromatic compounds has generated a renewed interest in defining the role of yeast in the generation of wine aroma and flavor. Genetic differences among wine strains are well documented and aroma profiles also appear to vary, implying that specific allelic alterations may exist and impact the production of compounds associated with flavor. Partial or complete sequencing data on several wine strains are available and reveal underlying genetic differences across strains in key genes implicated in flavor formation. This review discusses the current understanding of the roles of Saccharomyces in wine flavor with an emphasis on positive contributions to flavor and highlights the discoveries of the underlying enzymatic and metabolic mechanisms responsible for the yeast contribution to wine quality.

Protein trafficking, ergosterol biosynthesis and membrane physics impact recombinant protein secretion in Pichia pastoris

Background

The increasing availability of 'omics' databases provide important platforms for yeast engineering strategies since they offer a lot of information on the physiology of the cells under diverse growth conditions, including environmental stresses. Notably, only a few of these approaches have considered a performance under recombinant protein production conditions. Recently, we have identified a beneficial effect of low oxygen availability on the expression of a human Fab fragment in Pichia pastoris. Transcriptional analysis and data mining allowed for the selection of potential targets for strain improvement. A first selection of these candidates has been evaluated as recombinant protein secretion enhancers.

Results

Based on previous transcriptomics analyses, we selected 8 genes for co-expression in the P. pastoris strain already secreting a recombinant Fab fragment. Notably, WSC4 (which is involved in trafficking through the ER) has been identified as a novel potential target gene for strain improvement, with up to a 1.2-fold increase of product yield in shake flask cultures. A further transcriptomics-based strategy to modify the yeast secretion system was focused on the ergosterol pathway, an aerobic process strongly affected by oxygen depletion. By specifically partially inhibiting ergosterol synthesis with the antifungal agent fluconazole (inhibiting Erg11p), we tried to mimic the hypoxic conditions, in which the cellular ergosterol content was significantly decreased. This strategy led to an improved Fab yield (2-fold) without impairing cellular growth. Since ergosterol shortage provokes alterations in the plasma membrane composition, an important role of this cellular structure in protein secretion is suggested. This hypothesis was additionally supported by the fact that the addition of non-ionic surfactants also enhanced Fab secretion.

Conclusions

The current study presents a systems biotechnology-based strategy for the engineering of the industrially important yeast P. pastoris combining the use of host specific DNA microarray technologies and physiological studies under well defined environmental conditions. Such studies allowed for the identification of novel targets related with protein trafficking and ergosterol biosynthesis for improved recombinant protein production. Nevertheless, further studies will be required to elucidate the precise mechanisms whereby membrane biogenesis and composition impact on protein secretion in P. pastoris.

Identification of genes related to nitrogen uptake in wine strains of Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae is the main microorganism responsible for wine fermentation and its development influences the quality of wine. A problem affecting these types of fermentations, generating important losses in this industry, are the slow or stuck fermentations which may result from low nitrogen availability in the must. Therefore, several studies have been directed towards identifying genes involved in nitrogen metabolism using high throughput strategies which include subjecting the yeast to changes in the type or concentration of the available nitrogen source. However, this type of approach can also generate responses in the yeast that do not necessarily alter the expression of genes related to nitrogen metabolism. In this work, by using intraspecific hybridisation of wild wine yeast strains we obtained genetically and oenologically similar strains with differences in the consumption of nitrogen sources. Using the same must, the global expression patterns of these yeasts were compared by microarrays, the analysis of which identified 276 genes that varied in their expression between the strains analysed. The functional analysis of the genes with a known function indicates that some participate in nitrogen metabolism, alcoholic fermentation, ion transport and transcriptional regulation. Furthermore, differences were observed in the expression of genes which have been partially associated to nitrogen, as in the case of ZRT1 and ATO2. Interestingly, many of the genes identified have no known function or have not been previously associated to this phenotype.

The impact of co-inoculation with Oenococcus oeni on the trancriptome of Saccharomyces cerevisiae and on the flavour-active metabolite profiles during fermentation in synthetic must

Co-inoculation of commercial yeast strains with a bacterial starter culture at the beginning of fermentation of certain varietal grape juices is rapidly becoming a preferred option in the global wine industry, and frequently replaces the previously dominant sequential inoculation strategy where bacterial strains, responsible for malolactic fermentation, are inoculated after alcoholic fermentation has been completed. However, while several studies have highlighted potential advantages of co-inoculation, such studies have mainly focused on broad fermentation properties of the mixed cultures, and no data exist regarding the impact of this strategy on many oenologically relevant attributes of specific wine yeast strains such as aroma production. Here we investigate the impact of co-inoculation on a commercial yeast strain during alcoholic fermentation by comparing the transcriptome of this strain in yeast-only and in co-inoculated fermentations of synthetic must. The data show that a significant number of genes are differentially expressed in this strain in these two conditions. Some of the differentially expressed genes appear to respond to chemical changes in the fermenting must that are linked to bacterial metabolic activities, whereas others might represent a direct response of the yeast to the presence of a competing organism.

Molecular response of Saccharomyces cerevisiae wine and laboratory strains to high sugar stress conditions

One of the stress conditions that can affect Saccharomyces cerevisiae cells during their growth is osmotic stress. Under particular environments (for instance, during the production of alcoholic beverages) yeasts have to cope with osmotic stress caused by high sugar concentrations. Although the molecular changes and pathways involved in the response to saline or sorbitol stress are widely understood, less is known about how cells respond to high sugar concentrations. In this work we present a comprehensive study of the response to this form of stress which indicates important transcriptomic changes, especially in terms of the genes involved in both stress response and respiration, and the implication of the HOG pathway. We also describe several genes of an unknown function which are more highly expressed under 20% (w/v) glucose than under 2% (w/v) glucose. In this work we focus on the YHR087w (RTC3) gene and its encoded protein. Proteomic analysis of the mutant deletion strain reveals lower levels of several yeast Hsp proteins, which establishes a link between this protein and the response to several forms of stress. The relevance of YHR087W for the response to high sugar and other stress conditions and the relationship of the encoded protein with several Hsp proteins suggest applications of this gene in biotechnological processes in which response to stress is important.

Accumulation of non-superoxide anion reactive oxygen species mediates nitrogen-limited alcoholic fermentation by Saccharomyces cerevisiae

Throughout alcoholic fermentation, nitrogen depletion is one of the most important environmental stresses that can negatively affect the yeast metabolic activity and ultimately leads to fermentation arrest. Thus, the identification of the underlying effects and biomarkers of nitrogen limitation is valuable for controlling, and therefore optimizing, alcoholic fermentation. In this study, reactive oxygen species (ROS), plasma membrane integrity, and cell cycle were evaluated in a wine strain of Saccharomyces cerevisiae during alcoholic fermentation in nitrogen-limiting medium under anaerobic conditions. The results indicated that nitrogen limitation leads to an increase in ROS and that the superoxide anion is a minor component of the ROS, but there is increased activity of both Sod2p and Cta1p. Associated with these effects was a decrease in plasma membrane integrity and a persistent cell cycle arrest at G(0)/G(1) phases. Moreover, under these conditions it appears that autophagy, evaluated by ATG8 expression, is induced, suggesting that this mechanism is essential for cell survival but does not prevent the cell cycle arrest observed in slow fermentation. Conversely, nitrogen refeeding allowed cells to reenter cell cycle by decreasing ROS generation and autophagy. Altogether, the results provide new insights on the understanding of wine fermentations under nitrogen-limiting conditions and further indicate that ROS accumulation, evaluated by the MitoTracker Red dye CM-H(2)XRos, and plasma membrane integrity could be useful as predictive markers of fermentation problems.

Genome-wide transcriptional analysis of Saccharomyces cerevisiae during industrial bioethanol fermentation

Saccharomyces cerevisiae is widely applied in large-scale industrial bioethanol fermentation; however, little is known about the molecular responses of industrial yeast during large-scale fermentation processes. We investigated the global transcriptional responses of an industrial strain of S. cerevisiae during industrial continuous and fed-batch fermentation by oligonucleotide-based microarrays. About 28 and 62% of all genes detected showed differential gene expression during continuous and fed-batch fermentation, respectively. The overrepresented functional categories of differentially expressed genes in continuous fermentation overlapped with those in fed-batch fermentation. Downregulation of glycosylation as well as upregulation of the unfolded protein stress response was observed in both fermentation processes, suggesting dramatic changes of environment in endoplasmic reticulum during industrial fermentation. Genes related to ergosterol synthesis and genes involved in glycogen and trehalose metabolism were downregulated in both fermentation processes. Additionally, changes in the transcription of genes involved in carbohydrate metabolism coincided with the responses to glucose limitation during the early main fermentation stage in both processes. We also found that during the late main fermentation stage, yeast cells exhibited similar but stronger transcriptional changes during the fed-batch process than during the continuous process. Furthermore, repression of glycosylation has been suggested to be a secondary stress in the model proposed to explain the transcriptional responses of yeast during industrial fermentation. Together, these findings provide insights into yeast performance during industrial fermentation processes for bioethanol production.

Effect of nitrogen supplementation and Saccharomyces species on hydrogen sulfide and other volatile sulfur compounds in shiraz fermentation and wine

A Shiraz must with low yeast assimilable nitrogen (YAN) was supplemented with two increasing concentrations of diammonium phosphate (DAP) and fermented with one Saccharomyces cerevisiae and one Saccharomyces bayanus strain, with maceration on grape skins. Hydrogen sulfide (H(2)S) was monitored throughout fermentation, and a total of 16 volatile sulfur compounds (VSCs) were quantified in the finished wines. For the S. cerevisiae yeast strain, addition of DAP to a final YAN of 250 or 400 mg/L resulted in an increased formation of H(2)S compared to nonsupplemented fermentations (100 mg/L YAN). For this yeast, DAP-supplemented fermentations also showed prolonged formation of H(2)S into the later stage of fermentation, which was associated with increased H(2)S in the final wines. The S. bayanus strain showed a different H(2)S production profile, in which production was inversely correlated to initial YAN. No correlation was found between total H(2)S produced by either yeast during fermentation and H(2)S concentration in the final wines. For both yeasts, DAP supplementation yielded higher concentrations of organic VSCs in the finished wines, including sulfides, disulfides, mercaptans, and mercaptoesters. PCA analysis indicated that nitrogen supplementation before fermentation determined a much clearer distinction between the VSC profiles of the two yeasts compared to nonsupplemented fermentations. These results raise questions concerning the widespread use of DAP in the management of low YAN fermentations with respect to the formation of reductive characters in wine.

(1)H NMR-based metabolomic approach for understanding the fermentation behaviors of wine yeast strains

(1)H NMR spectroscopy coupled with multivariate statistical analysis was used for the first time to investigate metabolic changes in musts during alcoholic fermentation and wines during aging. Three Saccharomyces cerevisiae yeast strains (RC-212, KIV-1116, and KUBY-501) were also evaluated for their impacts on the metabolic changes in must and wine. Pattern recognition (PR) methods, including PCA, PLS-DA, and OPLS-DA scores plots, showed clear differences for metabolites among musts or wines for each fermentation stage up to 6 months. Metabolites responsible for the differentiation were identified as valine, 2,3-butanediol (2,3-BD), pyruvate, succinate, proline, citrate, glycerol, malate, tartarate, glucose, N-methylnicotinic acid (NMNA), and polyphenol compounds. PCA scores plots showed continuous movements away from days 1 to 8 in all musts for all yeast strains, indicating continuous and active fermentation. During alcoholic fermentation, the highest levels of 2,3-BD, succinate, and glycerol were found in musts with the KIV-1116 strain, which showed the fastest fermentation or highest fermentative activity of the three strains, whereas the KUBY-501 strain showed the slowest fermentative activity. This study highlights the applicability of NMR-based metabolomics for monitoring wine fermentation and evaluating the fermentative characteristics of yeast strains.

The proteome of a wine yeast strain during fermentation, correlation with the transcriptome

AIMS

Although wine yeast gene expression has been thoroughly investigated only few data are available on the evolution the proteome during alcoholic fermentation. This work aimed at specifying the change in proteome during fermentation and to assess its connection with transcriptome.

METHODS AND RESULTS

The proteome of a wine yeast was monitored by 2-D gel electrophoresis throughout alcoholic fermentation. Proteome was analysed in exponential growth and stationary phase. Among 744 spots, detected we observed significant changes in abundance with 89 spots displaying an increase in intensity and 124 a decrease. We identified 59 proteins among the most regulated and/or the most expressed. Glycolysis and ethanol production, amino acid and sulfur metabolism were the most represented functional categories. We found only a weak correlation between changes in mRNA and protein abundance, which is strongly dependent on the functional category.

CONCLUSIONS

There are substantial changes in protein abundance during alcoholic fermentation, but they are not directly associated with changes at transcript level suggesting that mRNA is selectively processed and/or translated in stationary phase.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data show that proteome is a relevant level of analysis to gain insight into wine yeast adaptation to alcoholic fermentation.

Genetic manipulation of HSP26 and YHR087W stress genes may improve fermentative behaviour in wine yeasts under vinification conditions

Throughout wine production yeast cells are affected by a plethora of stress conditions that compromise their ability to carry out the whole process. In recent years important knowledge about the mechanisms involved in stress response in both laboratory and wine yeast strains has been obtained. Several studies have indicated that a correlation exists between stress resistance, expression of stress response genes and fermentative behaviour. In this work we introduce several genetic manipulations in two genes induced by several stress conditions: HSP26 (which encodes a heat shock protein) and YHR087W (encoding a protein of unknown function) in two different wine yeasts, ICV16 and ICV27. These manipulations include expression in multicopy and centromeric plasmids, and substitution of the promoter in one of the genomic copies of these genes for that of the SPI1 gene, encoding for a cell wall protein of unknown function, or the PGK1 gene, which encodes the phosphoglycerate kinase glycolytic enzyme. Our results indicate that some of these modifications result in strains with higher expression of these genes, better resistance to certain stress conditions, and even improved fermentative behaviour. The modifications of the YHR087W gene are particularly interesting, and suggest an important role of this gene in the vinification process.

Nitrogen depletion causes up-regulation of glutathione content and gamma-glutamyltranspeptidase in Schizosaccharomyces pombe

This work aims to elucidate the relationship between nitrogen depletion and Glutathione (GSH) level in Schizosaccharomyces pombe. The total GSH level was much higher in the Pap1-positive KP1 cells than in the Pap1-negative TP108-3C cells, suggesting that synthesis of GSH is dependent on Pap1. When the Pap1-positive KP1 cells were transferred to the nitrogen-depleted medium, total GSH level significantly increased up to 6 h and then slightly declined after 9 h. Elevation of the total GSH level was observed to be much less with the Pap1-negative cells. However, glucose deprivation was not able to enhance the GSH level in the KP1 cells. Activity of gamma-glutamyltranspeptidase (gamma-GT), an enzyme in the first step of GSH catabolism, also increased during nitrogen depletion. The total GSH level was more significantly enhanced in the KP1 cells overexpressing gamma-GT2 than gamma-GT1 during nitrogen starvation. Reactive oxygen species (ROS) levels were not changed during nitrogen starvation in both Pap1-positive and Pap1-negative cells. Collectively, nitrogen depletion causes up-regulation of GSH synthesis and gamma-GT in a Pap1-dependent manner.

A modified DNA isolation protocol for obtaining pure RT-PCR grade RNA

We provide a simple but very efficient method for RNA preparation from Saccharomyces cerevisiae based on a standard chromosomal DNA isolation protocol. The method yields DNA-free total RNA, including mRNA, rRNA, and tRNA but can easily be adjusted to considerably enrich low molecular weight RNAs, such as tRNAs and the small rRNA species (5S and 5.8S). The procedure was proven and validated by verification of cDNAs belonging to four different genes, two of which encoding polypeptides and two tRNA genes. Besides its simplicity, the method is further advantageous in terms of safety (omitting hazardous phenol) and cost efficiency.

Addition of ammonia or amino acids to a nitrogen-depleted medium affects gene expression patterns in yeast cells during alcoholic fermentation

Yeast cells require nitrogen and are capable of selectively using good nitrogen sources in preference to poor ones by means of the regulatory mechanism known as nitrogen catabolite repression (NCR). Herein, the effect of ammonia or amino acid addition to nitrogen-depleted medium on global yeast expression patterns in yeast cells was studied using alcoholic fermentation as a system. The results indicate that there is a differential reprogramming of the gene expression depending on the nitrogen source added. Ammonia addition resulted in a higher expression of genes involved in amino acids biosynthesis while amino acid addition prepares the cells for protein biosynthesis. Therefore, a high percentage of the genes regulated by the transcription factors involved in the regulation of amino acid biosynthesis are more expressed during the first hours after ammonia addition compared with amino acid addition. The opposite occurs for those genes regulated by the transcription factor Sfp1p, related to ribosome biosynthesis. Although both additions include rich nitrogen sources, most NCR-regulated genes are more expressed after adding ammonia than amino acids. One of the differentially expressed genes, YBR174W, is required for optimal growth in synthetic medium.

Saccharomyces cerevisiae signature genes for predicting nitrogen deficiency during alcoholic fermentation

Genome-wide analysis of the wine yeast strain Saccharomyces cerevisiae PYCC4072 identified 36 genes highly expressed under conditions of low or absent nitrogen in comparison with a nitrogen-replete condition. Reverse transcription-PCR analysis for four of these transcripts with this strain and its validation with another wine yeast strain underlines the usefulness of these signature genes for predicting nitrogen deficiency and therefore the diagnosis of wine stuck/sluggish fermentations.