Overexpression of stress-related genes enhances cell viability and velum formation in Sherry wine yeasts

Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses

During the fermentation process, yeast cells face different stresses, and their survival and fermentation efficiency depend on their adaptation to these challenging conditions. Yeast cells must tolerate not only a single stress but also multiple simultaneous and sequential stresses. However, the adaptation and cellular response when cells are sequentially stressed are not completely understood. To explore this, we exposed a multi-stress-tolerant strain (BT0510) to different consecutive stresses to globally explore a common response, focusing on the genes induced in both stresses. Gene Ontology, pathway analyses, and common transcription factor motifs identified many processes linked to this common response. A metabolic shift to the pentose phosphate pathway, peroxisome activity, and the oxidative stress response were some of the processes found. The SYM1, STF2, and HSP genes and the transcription factors Adr1 and Usv1 may play a role in this response. This study presents a global view of the transcriptome of a multi-resistance yeast and provides new insights into the response to sequential stresses. The identified response genes can indicate future directions for the genetic engineering of yeast strains, which could improve many fermentation processes, such as those used for bioethanol production and beverages.

Protective Effects of Melatonin on Saccharomyces cerevisiae under Ethanol Stress

During alcoholic fermentation, Saccharomyces cerevisiae is subjected to several stresses, among which ethanol is of capital importance. Melatonin, a bioactive molecule synthesized by yeast during alcoholic fermentation, has an antioxidant role and is proposed to contribute to counteracting fermentation-associated stresses. The aim of this study was to unravel the protective effect of melatonin on yeast cells subjected to ethanol stress. For that purpose, the effect of ethanol concentrations (6 to 12%) on a wine strain and a lab strain of S. cerevisiae was evaluated, monitoring the viability, growth capacity, mortality, and several indicators of oxidative stress over time, such as reactive oxygen species (ROS) accumulation, lipid peroxidation, and the activity of catalase and superoxide dismutase enzymes. In general, ethanol exposure reduced the cell growth of S. cerevisiae and increased mortality, ROS accumulation, lipid peroxidation and antioxidant enzyme activity. Melatonin supplementation softened the effect of ethanol, enhancing cell growth and decreasing oxidative damage by lowering ROS accumulation, lipid peroxidation, and antioxidant enzyme activities. However, the effects of melatonin were dependent on strain, melatonin concentration, and growth phase. The results of this study indicate that melatonin has a protective role against mild ethanol stress, mainly by reducing the oxidative stress triggered by this alcohol.

Stress Resistance and Adhesive Properties of Commercial Flor and Wine Strains, and Environmental Isolates of Saccharomyces cerevisiae

Flor strains of Saccharomyces cerevisiae represent a special group of yeasts used for producing biologically aged wines. We analyzed the collection of commercial wine and flor yeast strains, as well as environmental strains isolated from the surface of grapes growing in vineyards, for resistance to abiotic stresses, adhesive properties, and the ability to form a floating flor. The degree of resistance of commercial strains to ethanol, acetaldehyde, and hydrogen peroxide was generally not higher than that of environmental isolates, some of which had high resistance to the tested stress agents. The relatively low degree of stress resistance of flor strains can be explained both by the peculiarities of their adaptive mechanisms and by differences in the nature of their exposure to various types of stress in the course of biological wine aging and under the experimental conditions we used. The hydrophobicity and adhesive properties of cells were determined by the efficiency of adsorption to polystyrene and the distribution of cells between the aqueous and organic phases. Flor strains were distinguished by a higher degree of hydrophobicity of the cell surface and an increased ability to adhere to polystyrene. A clear correlation between biofilm formation and adhesive properties was also observed for environmental yeast isolates. The overall results of this study indicate that relatively simple tests for cell hydrophobicity can be used for the rapid screening of new candidate flor strains in yeast culture collections and among environmental isolates.

Next Generation Winemakers: Genetic Engineering in Saccharomyces cerevisiae for Trendy Challenges

The most famous yeast of all, Saccharomyces cerevisiae, has been used by humankind for at least 8000 years, to produce bread, beer and wine, even without knowing about its existence. Only in the last century we have been fully aware of the amazing power of this yeast not only for ancient uses but also for biotechnology purposes. In the last decades, wine culture has become and more demanding all over the world. By applying as powerful a biotechnological tool as genetic engineering in S. cerevisiae, new horizons appear to develop fresh, improved, or modified wine characteristics, properties, flavors, fragrances or production processes, to fulfill an increasingly sophisticated market that moves around 31.4 billion € per year.

Metabolic Engineering of Wine Strains of Saccharomyces cerevisiae

Modern industrial winemaking is based on the use of starter cultures of specialized wine strains of Saccharomyces cerevisiae yeast. Commercial wine strains have a number of advantages over natural isolates, and it is their use that guarantees the stability and reproducibility of industrial winemaking technologies. For the highly competitive wine market with new demands for improved wine quality, it has become increasingly critical to develop new wine strains and winemaking technologies. Novel opportunities for precise wine strain engineering based on detailed knowledge of the molecular nature of a particular trait or phenotype have recently emerged due to the rapid progress in genomic and "postgenomic" studies with wine yeast strains. The review summarizes the current achievements of the metabolic engineering of wine yeast, the results of recent studies and the prospects for the application of genomic editing technologies for improving wine S. cerevisiae strains.

Rethinking about flor yeast diversity and its dynamic in the "criaderas and soleras" biological aging system

Fino wine is one of the most important Sherry wines and it is obtained through a complex and dynamic biological aging system. In this study, wine and veil of flor samples from fifty-two barrels with different aging levels and distributed in three different wineries from the Jerez-Xèrés-Sherry winemaking area have been analyzed during two years. Some of the wine compounds most deeply involved in flor yeast metabolism were analyzed to take into account the blending effect of this system. On the other hand, veil of flor was analyzed by molecular methods, finding five different species: S. cerevisiae, W. anomalus, P. membranaefaciens, P. kudriavzevii and P. manshurica, being the first time that the three last species have been reported in this biological aging system. Since S. cerevisiae was the vast majority of the isolates, its intraspecies variability was also analyzed by the simultaneous amplification of three microsatellite loci, obtaining nine different S. cerevisiae genotypes, also differentiated according to their physiological properties. Biodiversity analysis showed there were significant differences between the three wineries in the three aging scales, although the overall diversity was relatively low. Moreover, variations in the relative frequency of the different S. cerevisiae genotypes were found to be seasonal-dependent.

Transcriptome Profile of Yeast Strain Used for Biological Wine Aging Revealed Dynamic Changes of Gene Expression in Course of Flor Development

Flor strains of Saccharomyces cerevisiae are principal microbial agents responsible for biological wine aging used for production of sherry-like wines. The flor yeast velum formed on the surface of fortified fermented must is a major adaptive and technological characteristic of flor yeasts that helps them to withstanding stressful winemaking conditions and ensures specific biochemical and sensory oxidative alterations typical for sherry wines. We have applied RNAseq technology for transcriptome analysis of an industrial flor yeast strain at different steps of velum development over 71 days under experimental winemaking conditions. Velum growth and maturation was accompanied by accumulation of aldehydes and acetales. We have identified 1490 differentially expressed genes including 816 genes upregulated and 674 downregulated more than 2-fold at mature biofilm stage as compared to the early biofilm. Distinct expression patterns of genes involved in carbon and nitrogen metabolism, respiration, cell cycle, DNA repair, cell adhesion, response to various stresses were observed. Many genes involved in response to different stresses, oxidative carbon metabolism, high affinity transport of sugars, glycerol utilization, sulfur metabolism, protein quality control and recycling, cell wall biogenesis, apoptosis were induced at the mature biofilm stage. Strong upregulation was observed for FLO11 flocculin while expression of other flocculins remained unaltered or moderately downregulated. Downregulated genes included those for proteins involved in glycolysis, transportation of ions, metals, aminoacids, sugars, indicating repression of some major transport and metabolic process at the mature biofilm stage. Presented results are important for in-depth understanding of cell response elicited by velum formation and sherry wine manufacturing conditions, and for the comprehension of relevant regulatory mechanisms. Such knowledge may help to better understand the molecular mechanisms that flor yeasts use to adapt to winemaking environments, establish the functions of previously uncharacterized genes, improve the technology of sherry- wine production, and find target genes for strain improvement.

Comparative analysis of intracellular metabolites, proteins and their molecular functions in a flor yeast strain under two enological conditions

Flor yeasts confer a wide range of organoleptic properties to Sherry-type wines during a process called "biological aging" that takes place after alcoholic fermentation. These kinds of yeasts adapt to a biological aging condition by forming a biofilm known as "flor velum" and by changing from fermentative to oxidative metabolism. It has been reported that some functions such as increase of cell surface hydrophobicity or changes to lipid metabolism are enhanced when yeasts switch to biofilm lifestyle. Here, we attempt to reveal intracellular metabolites and protein molecular functions not documented before that are relevant in biofilm formation and in fermentation by an endometabolome and proteome screening. We report that at early stages of biofilm formation, flor yeasts accumulate mannose, trehalose, glycerol, oleic and stearic acids and synthesize high amounts of GTPases, glycosylases and lipoproteins. On the other hand, in early fermentation, flor yeasts rapidly consume glucose and phosphoric acid; and produce abundant proteins related to chromatin binding, transcription factors and methyl transferases.

Flor Yeast Diversity and Dynamics in Biologically Aged Wines

Wine biological aging is characterized by the development of yeast strains that form a biofilm on the wine surface after alcoholic fermentation. These yeasts, known as flor yeasts, form a velum that protects the wine from oxidation during aging. Thirty-nine velums aged from 1 to 6 years were sampled from “Vin jaune” from two different cellars. We show for the first time that these velums possess various aspects in term of color and surface aspects. Surprisingly, the heterogeneous velums are mostly composed of one species, S. cerevisiae. Scanning electron microscope observations of these velums revealed unprecedented biofilm structures and various yeast morphologies formed by the sole S. cerevisiae species. Our results highlight that different strains of Saccharomyces are present in these velums. Unexpectedly, in the same velum, flor yeast strain succession occurred during aging, supporting the assumption that environmental changes are responsible for these shifts. Despite numerous sample wine analyses, very few flor yeasts could be isolated from wine following alcoholic fermentation, suggesting that flor yeast development results from the colonization of yeast present in the aging cellar. We analyzed the FLO11 and ICR1 sequence of different S. cerevisiae strains in order to understand how the same strain of S. cerevisiae could form various types of biofilm. Among the strains analyzed, some were heterozygote at the FLO11 locus, while others presented two different alleles of ICR1 (wild type and a 111 bp deletion). We could not find a strong link between strain genotypes and velum characteristics. The same strain in different wines could form a velum having very different characteristics, highlighting a matrix effect.

The Microbial Diversity of Sherry Wines

The principal role of wine yeast is to transform efficiently the grape-berries’ sugars to ethanol, carbon dioxide, and other metabolites, without the production of off-flavors. Wine yeast strains are able to ferment musts, while other commercial or laboratory strains fail to do so. The genetic differences that characterize wine yeast strains in contrast to the biological ageing of the veil-forming yeasts in Sherry wines are poorly understood. Saccharomyces cerevisiae strains frequently exhibit rather specific phenotypic features needed for adaptation to a special environment, like fortified wines with ethanol up to 15% (v/v), known as Sherry wines. Factors that affect the correct development of the veil of flor during ageing are also reviewed, along with the related aspects of wine composition, biofilm formation processes, and yeast autolysis. This review highlights the importance of yeast ecology and yeast metabolic reactions in determining Sherry wine quality and the wealth of untapped indigenous microorganisms co-existing with the veil-forming yeast strains. It covers the complexity of the veil forming wine yeasts’ genetic features, and the genetic techniques often used in strain selection and monitoring during fermentation or biological ageing. Finally, the outlook for new insights to protect and to maintain the microbiota of the Sherry wines will be discussed.

Potential Application of the Oryza sativa Monodehydroascorbate Reductase Gene (OsMDHAR) to Improve the Stress Tolerance and Fermentative Capacity of Saccharomyces cerevisiae

Monodehydroascorbate reductase (MDHAR; EC 1.6.5.4) is an important enzyme for ascorbate recycling. To examine whether heterologous expression of MDHAR from Oryza sativa (OsMDHAR) can prevent the deleterious effects of unfavorable growth conditions, we constructed a transgenic yeast strain harboring a recombinant plasmid carrying OsMDHAR (p426GPD::OsMDHAR). OsMDHAR-expressing yeast cells displayed enhanced tolerance to hydrogen peroxide by maintaining redox homoeostasis, proteostasis, and the ascorbate (AsA)-like pool following the accumulation of antioxidant enzymes and molecules, metabolic enzymes, and molecular chaperones and their cofactors, compared to wild-type (WT) cells carrying vector alone. The addition of exogenous AsA or its analogue isoascorbic acid increased the viability of WT and ara2Δ cells under oxidative stress. Furthermore, the survival of OsMDHAR-expressing cells was greater than that of WT cells when cells at mid-log growth phase were exposed to high concentrations of ethanol. High OsMDHAR expression also improved the fermentative capacity of the yeast during glucose-based batch fermentation at a standard cultivation temperature (30°C). The alcohol yield of OsMDHAR-expressing transgenic yeast during fermentation was approximately 25% (0.18 g·g^-1) higher than that of WT yeast. Accordingly, OsMDHAR-expressing transgenic yeast showed prolonged survival during the environmental stresses produced during fermentation. These results suggest that heterologous OsMDHAR expression increases tolerance to reactive oxygen species-induced oxidative stress by improving cellular redox homeostasis and improves survival during fermentation, which enhances fermentative capacity.

Flor Yeast: New Perspectives Beyond Wine Aging

The most important dogma in white-wine production is the preservation of the wine aroma and the limitation of the oxidative action of oxygen. In contrast, the aging of Sherry and Sherry-like wines is an aerobic process that depends on the oxidative activity of flor strains of Saccharomyces cerevisiae. Under depletion of nitrogen and fermentable carbon sources, these yeast produce aggregates of floating cells and form an air–liquid biofilm on the wine surface, which is also known as velum or flor. This behavior is due to genetic and metabolic peculiarities that differentiate flor yeast from other wine yeast. This review will focus first on the most updated data obtained through the analysis of flor yeast with -omic tools. Comparative genomics, proteomics, and metabolomics of flor and wine yeast strains are shedding new light on several features of these special yeast, and in particular, they have revealed the extent of proteome remodeling imposed by the biofilm life-style. Finally, new insights in terms of promotion and inhibition of biofilm formation through small molecules, amino acids, and di/tri-peptides, and novel possibilities for the exploitation of biofilm immobilization within a fungal hyphae framework, will be discussed.

The complex genetic and molecular basis of a model quantitative trait

Sixty‐four genomic loci and seven genes that contribute to heritable variation in a model quantitative trait—resistance to oxidative stress—are identified across three yeast strains. The high‐resolution understanding of this phenotype provides new insight into the genetic and molecular basis of quantitative traits.

Quantitative traits are often influenced by many loci with small effects. Identifying most of these loci and resolving them to specific genes or genetic variants is challenging. Yet, achieving such a detailed understanding of quantitative traits is important, as it can improve our knowledge of the genetic and molecular basis of heritable phenotypic variation. In this study, we use a genetic mapping strategy that involves recurrent backcrossing with phenotypic selection to obtain new insights into an ecologically, industrially, and medically relevant quantitative trait—tolerance of oxidative stress, as measured based on resistance to hydrogen peroxide. We examine the genetic basis of hydrogen peroxide resistance in three related yeast crosses and detect 64 distinct genomic loci that likely influence the trait. By precisely resolving or cloning a number of these loci, we demonstrate that a broad spectrum of cellular processes contribute to hydrogen peroxide resistance, including DNA repair, scavenging of reactive oxygen species, stress-induced MAPK signaling, translation, and water transport. Consistent with the complex genetic and molecular basis of hydrogen peroxide resistance, we show two examples where multiple distinct causal genetic variants underlie what appears to be a single locus. Our results improve understanding of the genetic and molecular basis of a highly complex, model quantitative trait.

Secretion expression of SOD1 and its overlapping function with GSH in brewing yeast strain for better flavor and anti-aging ability

Superoxide dismutase (SOD) is a significant antioxidant, but unlike glutathione (GSH), SOD cannot be secreted into beer by yeast cells during fermentation, this directly leads to the limited application of SOD in beer anti-aging. In this investigation, we constructed the SOD1 secretion cassette in which strong promoter PGK1p and the sequence of secreting signal factor from Saccharomyces cerevisiae were both harbored to the upstream of coding sequence of SOD1 gene, as a result, the obtained strains carrying this cassette successfully realized the secretion of SOD1. In order to overcome the limitation of previous genetic modification on yeast strains, one new comprehensive strategy was adopted targeting the suitable homologous sites by gene deletion and SOD1 + GSH1 co-overexpression, and the new strain ST31 (Δadh2::SOD1 + Δilv2::GSH1) was constructed. The results of the pilot-scale fermentation showed that the diacetyl content of ST31 was lower by 42 % than that of the host, and the acetaldehyde content decreased by 29 %, the GSH content in the fermenting liquor of ST31 increased by 29 % compared with the host. Both SOD activity test and the positive and negative staining assay after native PAGE indicated that the secreted active SOD in the fermenting liquor of ST31 was mainly a dimer with the size of 32,500 Da. The anti-aging indexes such as the thiobarbituric acid and the resistance staling value further proved that the flavor stability of the beer brewed with strain ST31 was not only better than that of the original strain, but also better than that of the previous engineering strains. The multi-modification and comprehensive improvement of the beer yeast strain would greatly enhance beer quality than ever, and the self-cloning strain would be attractive to the public due to its bio-safety.

Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering

Excessive oxidative stress poses significant damage to yeast cells during fermentation process, and finally affects fermentation efficiency and the quality of products. In this paper, global transcription machinery engineering was employed to elicit Saccharomyces cerevisiae phenotypes of higher tolerance against oxidative stress caused by H2O2. Two strains from two plasmid-based mutagenesis libraries (Spt15 and Taf25), which exhibited significant increases in oxidative stress tolerance, were successfully isolated. At moderate H2O2 shock (≤3.5 mM), a positive correlation was found between the outperformance in cell growth of the oxidation-tolerate strains and H2O2 concentration. Several mutations were observed in the native transcription factors, which resulted in a different transcriptional profile compared with the control. Catalase and superoxide dismutase activities of the two mutants increased under H2O2 stress conditions. Fermentation experiments revealed that the mutant strain taf25-3 has a shorter lag phase compared to the control one, indicating that taf25-3 had improved adaptation ability to H2O2-induced oxidative stress and higher fermentation efficiency. Our study demonstrated that several amino acid substitutions in general transcription factors (Spt15 and Taf25) could modify the cellular oxidation defense systems and improve the anti-oxidation ability of S. cerevisiae. It could make the industrial ethanol fermentation more efficient and cost-effective by using the strain of higher stress tolerance.

Relationship of trehalose accumulation with ethanol fermentation in industrial Saccharomyces cerevisiae yeast strains

The protective effect and the mechanisms of trehalose accumulation in industrial Saccharomyces cerevisiae strains were investigated during ethanol fermentation. The engineered strains with more intercellular trehalose achieved significantly higher fermentation rates and ethanol yields than their wild strain ZS during very high gravity (VHG) fermentation, while their performances were not different during regular fermentation. The VHG fermentation performances of these strains were consistent with their growth capacity under osmotic stress and ethanol stress, the key stress factors during VHG fermentation. These results suggest that trehalose accumulation is more important for VHG fermentation of industrial yeast strains than regular one. The differences in membrane integrity and antioxidative capacity of these strains indicated the possible mechanisms of trehalose as a protectant under VHG condition. Therefore, trehalose metabolic engineering may be a useful strategy for improving the VHG fermentation performance of industrial yeast strains.