Phenotypic and genomic differences among S. cerevisiae strains in nitrogen requirements during wine fermentations

Evaluating cellular roles and phenotypes associated with trehalose degradation genes in Saccharomyces cerevisiae

In the yeast Saccharomyces cerevisiae, 2 types of trehalase activities have been described. Neutral trehalases (Nth1 and Nth2) are considered to be the main proteins that catalyze intracellular trehalose mobilization. In addition to Nth1 and Nth2, studies have shown that acid trehalase Ath1 is required for extracellular trehalose degradation. Although both neutral and acid-type trehalases have been predominantly investigated in laboratory strains of S. cerevisiae, we sought to examine the phenotypic consequences of disrupting these genes in wild strains. In this study, we constructed mutants of the trehalose degradation pathway (NTH1, NTH2, and ATH1) in 5 diverse S. cerevisiae strains to examine whether published lab strain phenotypes are also exhibited by wild strains. For each mutant, we assessed a number of phenotypes for comparison to trehalose biosynthesis mutants, including trehalose production, glycogen production, cell size, acute thermotolerance, high-temperature growth, sporulation efficiency, and growth on a variety of carbon sources in rich and minimal medium. We found that all trehalase mutants including single deletion nth1Δ, nth2Δ, and ath1Δ, as well as double deletion nth1nth2Δ, accumulated higher intracellular trehalose levels compared to their isogenic wild-type cells. Also, nth1Δ and nth1Δnth2Δ mutants exhibited mild thermal sensitivity, suggesting a potential minor role for trehalose mobilization when cells recover from stress. In addition, we evaluated phenotypes more directly relevant to trehalose degradation, including both extracellular and intracellular trehalose utilization. We discovered that intracellular trehalose hydrolysis is critical for typical spore germination progression, highlighting a role for trehalose in cell cycle regulation, likely as a storage carbohydrate providing glycolytic fuel. Additionally, our work provides further evidence suggesting Ath1 is indispensable for extracellular trehalose utilization as a carbon source, even in the presence of AGT1.

Effect of Yeast Assimilable Nitrogen Content on Fermentation Kinetics, Wine Chemical Composition and Sensory Character in the Production of Assyrtiko Wines

Two wild-type Saccharomyces cerevisiae yeast strains (Sa and Sb) were tested for white wine production using Assyrtiko grape of Santorini. A third commercial Saccharomyces strain was also studied for comparison reasons. Two concentrations of yeast extract and diammonium phosphate (DAP) were added to the must (150 and 250 mg/L) in order to evaluate the effect of nitrogen content on the final wine quality. Analytical methods (HPLC, GC-MS) and sensory analysis were employed to assess the quality of the wines. Fermentation kinetics were monitored throughout the experiment. By the second day of fermentation, all strains showed an approximate consumption of 70% of amino acids. Differences among strains were observed regarding inorganic nitrogen requirements. Sb strain resulted in higher concentrations of higher alcohols (1.9-fold) and ketones (5.6-fold) and lower concentrations of esters (1.2-fold) compared to the control, while Sa strain resulted in higher content of fatty acids (2.1-fold). Both indigenous strains scored better results in aroma quality, body and acidity compared to control. The overall evaluation of the data highlights the great potential of the indigenous S. cerevisiae strains as fermentation starters providing promising results in the sector of terroir wines.

Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity

Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism among natural yeast populations has been reported, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq (assay for transposase accessible chromatin) and RNA-seq (transcriptome sequencing). We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the nitrogen catabolite repression regulatory pathway and demonstrates a cis × environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility, and allelic differences in transcription factor binding in response to low nitrogen culture conditions. IMPORTANCE Historically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on noncoding variants demonstrated their ubiquitous role in adaptation. Here, we performed genome-wide regulatory variation profiles between two divergent yeast strains when facing nitrogen nutritional stress. The open chromatin availability of several regulatory regions changes in response to nitrogen scarcity. Importantly, we describe regulatory events that deviate between strains. Our results demonstrate a widespread variation in gene expression regulation between naturally occurring populations in response to stressful environments.

Impact of Nitrogen Addition on Wine Fermentation by S. cerevisiae Strains with Different Nitrogen Requirements

In modern oenology, supplementation of nitrogen sources is an important strategy to prevent sluggish or stuck fermentation. The present study thoroughly determined the effect of nitrogen addition timing and nitrogen source type on fermentation kinetics and aroma production, carried out by yeast strains with low and high nitrogen requirements. The results revealed that yeast strains with different nitrogen requirements have divergent reactions to nitrogen addition. Nitrogen addition clearly shortened the fermentation duration, especially for the high-nitrogen-demanding yeast strain. Nitrogen addition at 1/3 fermentation was the most effective in terms of fermentation activity, nitrogen assimilation, and production of acetate esters. Interestingly enough, yeast cells preferentially took up amino acids related to fermentative aroma synthesis with the addition at 2/3 fermentation. The addition of nitrogen sources also largely affected the production of important metabolites. Generally speaking, acetic acid, glycerol, and succinic acid reduced with the supplementation of nitrogen sources. The results revealed significant application importance for the winemaking industry.