Sake yeast strains have difficulty in entering a quiescent state after cell growth cessation

Sake yeast strains produce a high concentration of ethanol during sake brewing compared to laboratory yeast strains. As ethanol fermentation by yeast cells continues even after cell growth stops, analysis of the physiological state of the stationary phase cells is very important for understanding the mechanism of producing higher concentrations of ethanol. We compared the physiological characteristics of stationary phase cells of both sake and laboratory yeast strains in an aerobic batch culture and under sake brewing conditions. We unexpectedly found that sake yeast cells in the stationary phase had a lower buoyant density and stress tolerance than did the laboratory yeast cells under both experimental conditions. These results suggest that it is difficult for sake yeast cells to enter a quiescent state after cell growth has stopped, which may be one reason for the higher fermentation rate of sake yeast compared to laboratory yeast strains.     

Biomarkers for detecting nitrogen deficiency during alcoholic fermentation in different commercial wine yeast strains

Nitrogen deficiencies in grape musts are one of the main causes of stuck or sluggish wine fermentations. Several putative biomarkers were tested in order to analyze their appropriateness to detect nitrogen stress in the yeast. To this aim, four commercial wine strains (PDM, ARM, RVA and TTA) were grown in a synthetic grape must with different nitrogen concentrations. Trehalose accumulation, arginase activity and the expression of eleven genes were tested in these wine strains, known to have different nitrogen requirements. The overall response of the four strains was similar, with differences in response intensity (PDM and RVA with higher intensity) and response time (which was also related with nitrogen consumption time). Trehalose response was mostly related to entry into the stationary phase, whereas arginase activity was responsive to nitrogen depletion, although its measurement is too complicated to be used for routine monitoring during winemaking. The expression of the genes DAL4, DAL5, DUR3 and GAP1 was clearly related to nitrogen depletion and thus, GAP1 and DAL4 were selected as markers of nitrogen deficiency. In order to adapt expression analysis to winemaking conditions, the original strains were transformed into reporter strains based on the expression of green fluorescent protein (GFP) under control of the promoters for GAP1 and DAL4. The transformants had a similar fermentative capacity to the parental strains and were able to detect alterations in yeast physiological status due to nitrogen limitations.     

Identification of genes whose expressions are enhanced or reduced in baker's yeast during fed-batch culture process using molasses medium by DNA microarray analysis

Genes whose expression levels are enhanced or reduced during the cultivation process that uses cane molasses in baker's yeast production were identified in this study. The results showed that baker's yeast grown in molasses medium had higher fermentation ability and stress tolerance compared with baker's yeast grown in synthetic medium. Molasses apparently provided not only sugar as a carbon source but also provided functional components that enhanced or reduced expression of genes involved in fermentation ability and stress tolerance. To identify the genes whose expression is enhanced or reduced during cultivation in molasses medium, DNA microarray analysis was then used to compare the gene expression profile of cells grown in molasses with that of cells grown in synthetic medium. To simulate the commercial baker's yeast production process, cells were cultivated using a fed-batch culture system. In molasses medium, genes involved in the synthesis or uptake of vitamins (e.g., biotin, pyridoxine and thiamine) showed enhanced expression, suggesting that vitamin concentrations in molasses medium were lower than those in synthetic medium. Genes involved in formate dehydrogenase and maltose assimilation showed enhanced expression in molasses medium. In contrast, genes involved in iron utilization (e.g., siderophore, iron transporter and ferroxidase) showed enhanced expression in synthetic medium, suggesting that iron starvation occurred. The genes involved in the metabolism of amino acids also showed enhanced expression in synthetic medium. This identification of genes provides information that will help improve the baker's yeast production process.     

基于代谢组学和转录组学分析工业面包酵母（Saccharomyces cerevisiae）ABY3冷冻胁迫应答机制

为研究面包酵母（Saccharomyces cerevisiae）响应冷冻胁迫的机理，对面包酵母－20 ℃处理7 d前后的发酵菌液进行胞内的代谢组学和转录组学分析。在－20 ℃、7 d的环境胁迫下，面包酵母不加糖模拟面团发酵后的存活率为43%，发酵力下降42%。冷冻胁迫下，面包酵母胞内24 种代谢物的变化与494 种基因的表达差异与应答机制相关。通过差异代谢通路分析得出：冷冻胁迫下，胞内氨基酸的匮乏与质膜僵硬化可能是影响细胞生长和发酵性能的主要原因，而胞内不饱和脂肪酸相对含量的增加和海藻糖的积累并不能消除低温对细胞的损伤。研究结果可完善酵母冷冻胁迫应答机理，为耐性调节机制的研究提供思路，对冷冻面团的优化和技术发展具有重要意义。     

Functional genomics of commercial baker's yeasts that have different abilities for sugar utilization and high-sucrose tolerance under different sugar conditions

In the modern baking industry, high-sucrose-tolerant (HS) and maltose-utilizing (LS) yeast were developed using breeding techniques and are now used commercially. Sugar utilization and high-sucrose tolerance differ significantly between HS and LS yeasts. We analysed the gene expression profiles of HS and LS yeasts under different sucrose conditions in order to determine their basic physiology. Two-way hierarchical clustering was performed to obtain the overall patterns of gene expression. The clustering clearly showed that the gene expression patterns of LS yeast differed from those of HS yeast. Quality threshold clustering was used to identify the gene clusters containing upregulated genes (cluster 1) and downregulated genes (cluster 2) under high-sucrose conditions. Clusters 1 and 2 contained numerous genes involved in carbon and nitrogen metabolism, respectively. The expression level of the genes involved in the metabolism of glycerol and trehalose, which are known to be osmoprotectants, in LS yeast was higher than that in HS yeast under sucrose concentrations of 5-40%. No clear correlation was found between the expression level of the genes involved in the biosynthesis of the osmoprotectants and the intracellular contents of the osmoprotectants. The present gene expression data were compared with data previously reported in a comprehensive analysis of a gene deletion strain collection. Welch's t-test for this comparison showed that the relative growth rates of the deletion strains whose deletion occurred in genes belonging to cluster 1 were significantly higher than the average growth rates of all deletion strains.     

Glycerol formation during wine fermentation is mainly linked to Gpd1p and is only partially controlled by the HOG pathway

Glycerol 3-phosphate dehydrogenase, a key enzyme in the production of glycerol, is encoded by GPD1 and GPD2. The isoforms encoded by these genes have different functions, in osmoregulation and redox balance, respectively. We investigated the roles of GPD1, GPD2 and HOG1-the kinase involved in the response to osmotic stress-in glycerol production during wine fermentation. We found that the deletion of GPD2 in a wine yeast-derived strain did not affect growth or fermentation performance and reduced glycerol production by only 20%. In contrast, a gpd1delta mutant displayed a prolonged lag phase, and produced 40% less glycerol than the wild-type strain. The deletion of HOG1 resulted in a slight decrease in growth rate and a 20% decrease in glycerol production, indicating that the HOG pathway operates under wine fermentation conditions. However, the hog1delta mutant was not as severely affected as the gpd1delta mutant during the first few hours of fermentation, and continued to express GPD1 strongly. The hog1delta mutant was able to increase glycerol production in response to high sugar concentration (15-28% glucose), to almost the same extent as the wild-type, whereas this response was totally abolished in the gpd1delta mutant. These data show that Gpd1p plays a major role in glycerol formation, particularly during the first few hours of exposure to high sugar concentration, and that GPD2 is only of little significance in anaerobic fermentation by wine yeast. The results also demonstrate that the HOG pathway exerts only limited control over GPD1 expression and glycerol production during wine fermentation.     

Genome-wide expression analysis of Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays

The lager brewing yeast, Saccharomyces pastorianus, an allopolyploid species hybrid, contains 2 diverged sub-genomes; one derived from Saccharomyces cerevisiae (Sc-type) and the other from Saccharomyces bayanus (Sb-type). We analyzed the functional roles of these orthologous genes in determining the phenotypic features of S. pastorianus. We used a custom-made oligonucleotide microarray containing probes designed for both Sc-type and Sb-type ORFs for a comprehensive expression analysis of S. pastorianus in a pilot-scale fermentation. We showed a high degree of correlation between the expression levels and the expression changes for a majority of orthologous gene sets during the fermentation process. We screened the functional categories and metabolic pathways where Sc- or Sb-type genes have higher expression levels than the corresponding orthologous genes. Our data showed that, for example, pathways for sulfur metabolism, cellular import, and production of branched amino acids are dominated by Sb-type genes. This comprehensive expression analysis of orthologous genes can provide valuable insights on understanding the phenotype of S. pastorianus.     

Study of two wine strains rehydrated with different activators in sluggish fermentation conditions

Rehydration of active dry yeasts is essential in wine fermentation. To help yeast cells withstand the extreme conditions during alcoholic fermentation, adjuvants are added to the must. However, few commercial activators are added directly to the yeast rehydration water, even though this might render hydration more efficient due to a favorable osmotic gradient. The effect of five “metabolic activators” added directly to the water to rehydrate two commercial wine yeast strains in sluggish fermentation conditions was evaluated; these conditions were achieved by acid and osmotic stress. Cell vitality, sugar consumption, glycerol, ethanol and nitrogen contents at 8 and 15 days of process were determined. Furthermore, discrepancy in glucose and fructose consumption was also measured. Ergosterol at certain doses generally showed a favorable effect, so that it could be considered a good activator compared with other molecules involved in essential metabolic cycles.