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

Barbosa C, García-Martínez J, Pérez-Ortín JE, Mendes-Ferreira A - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Centre of Agricultural Genomics and Biotechnology (CGBA) Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal; Universitat de Valência, Departamento de Bioquímica y Biología Molecular y E.R.I. Biotecmed, València, Spain.

ABSTRACT
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.

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Genotype, environment, and genotype–environment interaction effects in wine yeast strains.Differentially expressed genes at each nitrogen regime studied (LN and HN), identified using two-way ANOVA. The number of genes significantly affected by genotype (strain), by environment (fermentation stage) and by the interaction between both factors is represented with bars. The selection of genes showing differential expression (with a significant effect of the different factors) was defined at FDR<0.05 using the Benjamini and Hochberg correction.
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pone.0122709.g002: Genotype, environment, and genotype–environment interaction effects in wine yeast strains.Differentially expressed genes at each nitrogen regime studied (LN and HN), identified using two-way ANOVA. The number of genes significantly affected by genotype (strain), by environment (fermentation stage) and by the interaction between both factors is represented with bars. The selection of genes showing differential expression (with a significant effect of the different factors) was defined at FDR<0.05 using the Benjamini and Hochberg correction.

Mentions: An analysis of variance (ANOVA) for each fermentation (LN and HN) was used to determine the effect of the strain (genotype—G), fermentation stage (environment—E), and the interaction between genotype and environment (GEI) on gene expression variation. The two-way ANOVA allowed us to determine how a response is affected by the two factors and whether or not they are intertwined. For the LN fermentation, of the 5764 genes analyzed, 759 genes (13%), 708 genes (12%), and 141 (2%) showed significant effects (false discovery rate (FDR) <0.05) due to genotype, environment and genotype- environment interaction, respectively. Similarly, for the HN fermentation, we identified 479 genes (8%), 1065 genes (18%), and 310 (5%) as being affected by the genotype, environment and genotype- environment interaction, respectively (Fig 2). The 141 and 310 genes which responded differently to the environments examined, depending on the strain, represent genes that are genetically variable for transcriptional plasticity [40].


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

Barbosa C, García-Martínez J, Pérez-Ortín JE, Mendes-Ferreira A - PLoS ONE (2015)

Genotype, environment, and genotype–environment interaction effects in wine yeast strains.Differentially expressed genes at each nitrogen regime studied (LN and HN), identified using two-way ANOVA. The number of genes significantly affected by genotype (strain), by environment (fermentation stage) and by the interaction between both factors is represented with bars. The selection of genes showing differential expression (with a significant effect of the different factors) was defined at FDR<0.05 using the Benjamini and Hochberg correction.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401569&req=5

pone.0122709.g002: Genotype, environment, and genotype–environment interaction effects in wine yeast strains.Differentially expressed genes at each nitrogen regime studied (LN and HN), identified using two-way ANOVA. The number of genes significantly affected by genotype (strain), by environment (fermentation stage) and by the interaction between both factors is represented with bars. The selection of genes showing differential expression (with a significant effect of the different factors) was defined at FDR<0.05 using the Benjamini and Hochberg correction.
Mentions: An analysis of variance (ANOVA) for each fermentation (LN and HN) was used to determine the effect of the strain (genotype—G), fermentation stage (environment—E), and the interaction between genotype and environment (GEI) on gene expression variation. The two-way ANOVA allowed us to determine how a response is affected by the two factors and whether or not they are intertwined. For the LN fermentation, of the 5764 genes analyzed, 759 genes (13%), 708 genes (12%), and 141 (2%) showed significant effects (false discovery rate (FDR) <0.05) due to genotype, environment and genotype- environment interaction, respectively. Similarly, for the HN fermentation, we identified 479 genes (8%), 1065 genes (18%), and 310 (5%) as being affected by the genotype, environment and genotype- environment interaction, respectively (Fig 2). The 141 and 310 genes which responded differently to the environments examined, depending on the strain, represent genes that are genetically variable for transcriptional plasticity [40].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Centre of Agricultural Genomics and Biotechnology (CGBA) Universidade de Trás-os-Montes e Alto Douro, Vila Real, Portugal; Universitat de Valência, Departamento de Bioquímica y Biología Molecular y E.R.I. Biotecmed, València, Spain.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus