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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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Variability in gene expression is enhanced at the beginning of fermentation and during early stationary phase. Variability in gene expression was compared from T1 to T6 fermentation time points, considering the average deviation from the mean expression value as a measure of amplitude of gene expression. Panel A shows the distribution of the average deviation values for all strains and Panel B represents the same distribution for the environmental (06L3FF02, 06L6FF20) and commercial (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118) strains only. Inserts in Panels A and B expand the scale to highlight the frequency of highly variable genes.
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Figure 6: Variability in gene expression is enhanced at the beginning of fermentation and during early stationary phase. Variability in gene expression was compared from T1 to T6 fermentation time points, considering the average deviation from the mean expression value as a measure of amplitude of gene expression. Panel A shows the distribution of the average deviation values for all strains and Panel B represents the same distribution for the environmental (06L3FF02, 06L6FF20) and commercial (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118) strains only. Inserts in Panels A and B expand the scale to highlight the frequency of highly variable genes.

Mentions: Gene expression differences between the yeast strains were investigated at the monitored growth stages (Figure 6). The highest amplitudes of gene expression were registered at T6 (Figure 6A), but this was a reflection of the extensive transcriptional repression that occurred in environmental and commercial strains at this stage of fermentation (Figure 6B). Variability was biased towards TATA box genes (Additional file 4), in agreement with what was reported by Basehoar and colleagues [54], who showed that TATA box containing genes comprise approximately 20% of the yeast ORFeome and are highly regulated in response to stress. Our results reinforce the hypothesis that this promoter element is an important generator of expression diversity under environmental pressure.


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)

Variability in gene expression is enhanced at the beginning of fermentation and during early stationary phase. Variability in gene expression was compared from T1 to T6 fermentation time points, considering the average deviation from the mean expression value as a measure of amplitude of gene expression. Panel A shows the distribution of the average deviation values for all strains and Panel B represents the same distribution for the environmental (06L3FF02, 06L6FF20) and commercial (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118) strains only. Inserts in Panels A and B expand the scale to highlight the frequency of highly variable genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Variability in gene expression is enhanced at the beginning of fermentation and during early stationary phase. Variability in gene expression was compared from T1 to T6 fermentation time points, considering the average deviation from the mean expression value as a measure of amplitude of gene expression. Panel A shows the distribution of the average deviation values for all strains and Panel B represents the same distribution for the environmental (06L3FF02, 06L6FF20) and commercial (AEB Fermol Rouge, Lalvin ICV D254 and Lalvin EC-1118) strains only. Inserts in Panels A and B expand the scale to highlight the frequency of highly variable genes.
Mentions: Gene expression differences between the yeast strains were investigated at the monitored growth stages (Figure 6). The highest amplitudes of gene expression were registered at T6 (Figure 6A), but this was a reflection of the extensive transcriptional repression that occurred in environmental and commercial strains at this stage of fermentation (Figure 6B). Variability was biased towards TATA box genes (Additional file 4), in agreement with what was reported by Basehoar and colleagues [54], who showed that TATA box containing genes comprise approximately 20% of the yeast ORFeome and are highly regulated in response to stress. Our results reinforce the hypothesis that this promoter element is an important generator of expression diversity under environmental pressure.

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