Yeast systems biology: modelling the winemaker's art

Divergent Roles for cAMP-PKA Signaling in the Regulation of Filamentous Growth in Saccharomyces cerevisiae and Saccharomyces bayanus

The cyclic AMP - Protein Kinase A (cAMP-PKA) pathway is an evolutionarily conserved eukaryotic signaling network that is essential for growth and development. In the fungi, cAMP-PKA signaling plays a critical role in regulating cellular physiology and morphological switches in response to nutrient availability. We undertook a comparative investigation of the role that cAMP-PKA signaling plays in the regulation of filamentous growth in two closely related budding yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus Using chemical and genetic perturbations of this pathway and its downstream targets we discovered divergent roles for cAMP-PKA signaling in the regulation of filamentous growth. While cAMP-PKA signaling is required for the filamentous growth response in both species, increasing or decreasing the activity of this pathway leads to drastically different phenotypic outcomes. In S. cerevisiae, cAMP-PKA inhibition ameliorates the filamentous growth response while hyper-activation of the pathway leads to increased filamentous growth; the same perturbations in S. bayanus result in the obverse. Divergence in the regulation of filamentous growth between S. cerevisiae and S. bayanus extends to downstream targets of PKA, including several kinases, transcription factors, and effector proteins. Our findings highlight the potential for significant evolutionary divergence in gene network function, even when the constituent parts of such networks are well conserved.

Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes

In nature, microbes often need to "decide" which of several available nutrients to utilize, a choice that depends on a cell's inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes' decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wild S. cerevisiae strains. Using bulk segregant analysis, we found that a locus containing the galactose sensor GAL3 was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed that GAL3 is the major driver of GAL induction variation, and that GAL3 allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. The GAL3 variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.

Yeast's balancing act between ethanol and glycerol production in low-alcohol wines

Alcohol is fundamental to the character of wine, yet too much can put a wine off‐balance. A wine is regarded to be well balanced if its alcoholic strength, acidity, sweetness, fruitiness and tannin structure complement each other so that no single component dominates on the palate. Balancing a wine's positive fruit flavours with the optimal absolute and relative concentration of alcohol can be surprisingly difficult. Over the past three decades, consumers have increasingly demanded wine with richer and riper fruit flavour profiles. In response, grape and wine producers have extended harvest times to increase grape maturity and enhance the degree of fruit flavours and colour intensity. However, a higher degree of grape maturity results in increased grape sugar concentration, which in turn results in wines with elevated alcohol concentration. On average, the alcohol strength of red wines from many warm wine‐producing regions globally rose by about 2% (v/v) during this period. Notwithstanding that many of these ‘full‐bodied, fruit‐forward’ wines are well balanced and sought after, there is also a significant consumer market segment that seeks lighter styles with less ethanol‐derived ‘hotness’ on the palate. Consumer‐focussed wine producers are developing and implementing several strategies in the vineyard and winery to reduce the alcohol concentration in wines produced from well‐ripened grapes. In this context, Saccharomyces cerevisiae wine yeasts have proven to be a pivotal strategy to reduce ethanol formation during the fermentation of grape musts with high sugar content (> 240 g l⁻¹). One of the approaches has been to develop ‘low‐alcohol’ yeast strains which work by redirecting their carbon metabolism away from ethanol production to other metabolites, such as glycerol. This article reviews the current challenges of producing glycerol at the expense of ethanol. It also casts new light on yeast strain development programmes which, bolstered by synthetic genomics, could potentially overcome these challenges.

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.

Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a eukaryotic microorganism that is able to choose between different unicellular and multicellular lifestyles. The potential of individual yeast cells to switch between different growth modes is advantageous for optimal dissemination, protection and substrate colonization at the population level. A crucial step in lifestyle adaptation is the control of self- and foreign adhesion. For this purpose, S. cerevisiae contains a set of cell wall-associated proteins, which confer adhesion to diverse biotic and abiotic surfaces. Here, we provide an overview of different aspects of S. cerevisiae adhesion, including a detailed description of known lifestyles, recent insights into adhesin structure and function and an outline of the complex regulatory network for adhesin gene regulation. Our review shows that S. cerevisiae is a model system suitable for studying not only the mechanisms and regulation of cell adhesion, but also the role of this process in microbial development, ecology and evolution.

Yeast systems biology: the challenge of eukaryotic complexity

In this chapter, we present an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote for systems biology studies, with main molecular mechanisms, biological networks, and sub-cellular organization essentially conserved in all eukaryotes, derived from a complex common ancestor. The existence of advanced tools for molecular studies together with high-throughput experimental and computational methods, most of them being implemented and validated in yeast, with new ones being developed, is opening the way to the characterization of the core modular architecture and complex networks essential to all eukaryotes. Selected examples of the latest discoveries in eukaryote complexity and systems biology studies using yeast as a reference model and their applications in biotechnology and medicine are presented.

Volatile composition and sensory properties of Shiraz wines as affected by nitrogen supplementation and yeast species: rationalizing nitrogen modulation of wine aroma

The effects of yeast assimilable nitrogen (YAN) supplementation on Shiraz volatile composition and sensory properties have been investigated. A low YAN Shiraz must (YAN 100 mg/L) was supplemented with nitrogen in the form of diammonium phosphate (DAP) to a final YAN of either 250 or 400 mg/L. Fermentation was carried out with either Saccharomyces cerevisiae or Saccharomyces bayanus , with maceration on skins. For both yeast strains, high DAP additions increased the ratings of positive sensory attributes such as "red fruit" and "dark fruit" and decreased the "yeast/cheese", "vegetal", and "earth/dirty" attributes. For the S. cerevisiae yeast moderate DAP addition resulted in higher "reduced" attribute scores. DAP supplementation had a strong influence on formation of acetates, fatty acid ethyl esters, higher alcohols, hydrogen sulfide, ethyl mercaptan, methyl mercaptan, DMS, and DES. Partial least-squares regression analysis of chemical and sensory data indicated that esters, sulfides, and mercaptans were associated with fruit-related descriptors, whereas hydrogen sulfide was associated with the "reduced" attribute. Nitrogen-related variations in the concentration of other yeast metabolites such as ethanol and 2- and 3-methylbutanoic acids also affected perceived fruitiness. Depending on yeast species DAP supplementation to a low nitrogen must can result in increased reduction off-odor.

[Systems biology: from yesterday's concepts to tomorrow's discoveries]

The idea that genes and their products are the fundamental units of biology has profoundly influenced our scientific thinking during the second half of the past century. Today, this reductionism is challenged by a renaissance of a systems understanding of biology, focusing on the systems formed by interacting gene products rather than on individual gene products. This discipline, based on a complementary and more holistic approach, keeps expanding its scope thanks to biotechnological innovations as well as theoretical modeling. This review aims at showing how and why, since the beginning of the 21st century, in fundamental as well as biomedical research, systems biology is proving a promising paradigm for understanding emerging properties of complex biological systems.

Wine yeasts for the future

International competition within the wine market, consumer demands for newer styles of wines and increasing concerns about the environmental sustainability of wine production are providing new challenges for innovation in wine fermentation. Within the total production chain, the alcoholic fermentation of grape juice by yeasts is a key process where winemakers can creatively engineer wine character and value through better yeast management and, thereby, strategically tailor wines to a changing market. This review considers the importance of yeast ecology and yeast metabolic reactions in determining wine quality, and then discusses new directions for exploiting yeasts in wine fermentation. It covers criteria for selecting and developing new commercial strains, the possibilities of using yeasts other than those in the genus of Saccharomyces, the prospects for mixed culture fermentations and explores the possibilities for high cell density, continuous fermentations.