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Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains.

Carreto L, Eiriz MF, Domingues I, Schuller D, Moura GR, Santos MA - BMC Genomics (2011)

Bottom Line: Saccharomyces cerevisiae (Baker's yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments.Nitrogen metabolism genes showed significant variation in expression among the environmental isolates.Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: RNA Biology Laboratory, CESAM & Department of Biology, Universidade de Aveiro, Portugal.

ABSTRACT

Background: Saccharomyces cerevisiae (Baker's yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments. In spite of recent advances on the study of yeast genome diversity, little is known about the underlying gene expression plasticity. In order to shed new light onto this biological question, we have compared transcriptome profiles of five environmental isolates, clinical and laboratorial strains at different time points of fermentation in synthetic must medium, during exponential and stationary growth phases.

Results: Our data unveiled diversity in both intensity and timing of gene expression. Genes involved in glucose metabolism and in the stress response elicited during fermentation were among the most variable. This gene expression diversity increased at the onset of stationary phase (diauxic shift). Environmental isolates showed lower average transcript abundance of genes involved in the stress response, assimilation of nitrogen and vitamins, and sulphur metabolism, than other strains. Nitrogen metabolism genes showed significant variation in expression among the environmental isolates.

Conclusions: Wild type yeast strains respond differentially to the stress imposed by nutrient depletion, ethanol accumulation and cell density increase, during fermentation of glucose in synthetic must medium. Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.

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Gene expression variability distinguishes yeast strains. Expression of genes involved in flocculation, transport and cell division distinguished strains J940047 and S288C from the environmental and commercial strains. When compared to the environmental strains (06L3FF02, 06L6FF20) and the commercial strains (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118), strains J940047 and S288C showed higher relative transcript abundance for genes included in cluster VIII of Figure 2A throughout fermentation. Among these were Ty, flocculation (FLO5 and FLO9), transport (SEO1 and SUL1), cell wall organization and biogenesis (EXG2) and meiosis (RME1 and CEP3) genes. All strains up-regulated these genes at the transition from exponential to stationary phase, but the increase in expression was more pronounced in the case of strains J940047 and S288C. Only the genes with annotated functions are depicted in the heat map, for comparison.
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Figure 3: Gene expression variability distinguishes yeast strains. Expression of genes involved in flocculation, transport and cell division distinguished strains J940047 and S288C from the environmental and commercial strains. When compared to the environmental strains (06L3FF02, 06L6FF20) and the commercial strains (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118), strains J940047 and S288C showed higher relative transcript abundance for genes included in cluster VIII of Figure 2A throughout fermentation. Among these were Ty, flocculation (FLO5 and FLO9), transport (SEO1 and SUL1), cell wall organization and biogenesis (EXG2) and meiosis (RME1 and CEP3) genes. All strains up-regulated these genes at the transition from exponential to stationary phase, but the increase in expression was more pronounced in the case of strains J940047 and S288C. Only the genes with annotated functions are depicted in the heat map, for comparison.

Mentions: Environmental and commercial strains differed markedly from J940047 and S288C in the expression of genes belonging to cluster VIII. Genes involved in flocculation, cell wall organization/biogenesis, transport and cell division (Figure 3), together with many Ty element ORFs, showed higher expression levels in strains J940047 and S288C relative to the environmental and commercial strains regardless of the fermentation time point. In a previous study [37], we identified gene copy number variation in the genomes of these strains which included some of the genes present in cluster VIII, namely SEO1 and RSC30 genes (see Additional file 3 for details on relative genome hybridization pattern). Meanwhile, cluster X grouped the expression profiles of genes that could be used to distinguish strain S288C from the other strains throughout the fermentation process. Most of the 79 genes of this cluster corresponded to non annotated ORFs while annotated ORFs were linked to sexual reproduction (Table 1), Ty elements and included the ASP3 tandem genes which are copy number depleted in the other strains relatively to strain S288C [37].


Expression variability of co-regulated genes differentiates Saccharomyces cerevisiae strains.

Carreto L, Eiriz MF, Domingues I, Schuller D, Moura GR, Santos MA - BMC Genomics (2011)

Gene expression variability distinguishes yeast strains. Expression of genes involved in flocculation, transport and cell division distinguished strains J940047 and S288C from the environmental and commercial strains. When compared to the environmental strains (06L3FF02, 06L6FF20) and the commercial strains (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118), strains J940047 and S288C showed higher relative transcript abundance for genes included in cluster VIII of Figure 2A throughout fermentation. Among these were Ty, flocculation (FLO5 and FLO9), transport (SEO1 and SUL1), cell wall organization and biogenesis (EXG2) and meiosis (RME1 and CEP3) genes. All strains up-regulated these genes at the transition from exponential to stationary phase, but the increase in expression was more pronounced in the case of strains J940047 and S288C. Only the genes with annotated functions are depicted in the heat map, for comparison.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3094312&req=5

Figure 3: Gene expression variability distinguishes yeast strains. Expression of genes involved in flocculation, transport and cell division distinguished strains J940047 and S288C from the environmental and commercial strains. When compared to the environmental strains (06L3FF02, 06L6FF20) and the commercial strains (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118), strains J940047 and S288C showed higher relative transcript abundance for genes included in cluster VIII of Figure 2A throughout fermentation. Among these were Ty, flocculation (FLO5 and FLO9), transport (SEO1 and SUL1), cell wall organization and biogenesis (EXG2) and meiosis (RME1 and CEP3) genes. All strains up-regulated these genes at the transition from exponential to stationary phase, but the increase in expression was more pronounced in the case of strains J940047 and S288C. Only the genes with annotated functions are depicted in the heat map, for comparison.
Mentions: Environmental and commercial strains differed markedly from J940047 and S288C in the expression of genes belonging to cluster VIII. Genes involved in flocculation, cell wall organization/biogenesis, transport and cell division (Figure 3), together with many Ty element ORFs, showed higher expression levels in strains J940047 and S288C relative to the environmental and commercial strains regardless of the fermentation time point. In a previous study [37], we identified gene copy number variation in the genomes of these strains which included some of the genes present in cluster VIII, namely SEO1 and RSC30 genes (see Additional file 3 for details on relative genome hybridization pattern). Meanwhile, cluster X grouped the expression profiles of genes that could be used to distinguish strain S288C from the other strains throughout the fermentation process. Most of the 79 genes of this cluster corresponded to non annotated ORFs while annotated ORFs were linked to sexual reproduction (Table 1), Ty elements and included the ASP3 tandem genes which are copy number depleted in the other strains relatively to strain S288C [37].

Bottom Line: Saccharomyces cerevisiae (Baker's yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments.Nitrogen metabolism genes showed significant variation in expression among the environmental isolates.Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: RNA Biology Laboratory, CESAM & Department of Biology, Universidade de Aveiro, Portugal.

ABSTRACT

Background: Saccharomyces cerevisiae (Baker's yeast) is found in diverse ecological niches and is characterized by high adaptive potential under challenging environments. In spite of recent advances on the study of yeast genome diversity, little is known about the underlying gene expression plasticity. In order to shed new light onto this biological question, we have compared transcriptome profiles of five environmental isolates, clinical and laboratorial strains at different time points of fermentation in synthetic must medium, during exponential and stationary growth phases.

Results: Our data unveiled diversity in both intensity and timing of gene expression. Genes involved in glucose metabolism and in the stress response elicited during fermentation were among the most variable. This gene expression diversity increased at the onset of stationary phase (diauxic shift). Environmental isolates showed lower average transcript abundance of genes involved in the stress response, assimilation of nitrogen and vitamins, and sulphur metabolism, than other strains. Nitrogen metabolism genes showed significant variation in expression among the environmental isolates.

Conclusions: Wild type yeast strains respond differentially to the stress imposed by nutrient depletion, ethanol accumulation and cell density increase, during fermentation of glucose in synthetic must medium. Our results support previous data showing that gene expression variability is a source of phenotypic diversity among closely related organisms.

Show MeSH
Related in: MedlinePlus