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Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast.

Pais TM, Foulquié-Moreno MR, Hubmann G, Duitama J, Swinnen S, Goovaerts A, Yang Y, Dumortier F, Thevelein JM - PLoS Genet. (2013)

Bottom Line: From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced.Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different.Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders, Belgium.

ABSTRACT
The yeast Saccharomyces cerevisiae is able to accumulate ≥17% ethanol (v/v) by fermentation in the absence of cell proliferation. The genetic basis of this unique capacity is unknown. Up to now, all research has focused on tolerance of yeast cell proliferation to high ethanol levels. Comparison of maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 yeast strains showed a poor correlation, but higher ethanol tolerance of cell proliferation clearly increased the likelihood of superior maximal ethanol accumulation capacity. We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced. Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different. Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity. These genes, as well as the previously identified MKT1 gene, were not linked in this genetic background to tolerance of cell proliferation to high ethanol levels. The superior KIN3 allele contained two SNPs, which are absent in all yeast strains sequenced up to now. This work provides the first insight in the genetic basis of maximal ethanol accumulation capacity in yeast and reveals for the first time the importance of DNA damage repair in yeast ethanol tolerance.

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Maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 different yeast strains.(A) Distribution of relative maximal ethanol production capacity of 68 different yeast strains compared to the wine strain V1116. The semi-static fermentations were performed in 250 mL of YP+33% glucose at 25°C. The V1116 strain produced 18.4% (±0.4%) (v/v) ethanol. (B) Ethanol tolerance of cell proliferation (X-axis) versus maximal ethanol accumulation capacity (Y-axis), expressed as maximal ethanol titer reached, in the 68 yeast strains. The highest ethanol concentration for which there was growth in all dilutions was taken as the maximal ethanol tolerance of cell proliferation. The possible correlation between the two traits was tested with a Spearman test, because of the non-normality of the ethanol accumulation trait. The (one-tailed) Spearman test indicated a weak correlation (90% confidence interval, P-value = 0.0984).
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pgen-1003548-g001: Maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 different yeast strains.(A) Distribution of relative maximal ethanol production capacity of 68 different yeast strains compared to the wine strain V1116. The semi-static fermentations were performed in 250 mL of YP+33% glucose at 25°C. The V1116 strain produced 18.4% (±0.4%) (v/v) ethanol. (B) Ethanol tolerance of cell proliferation (X-axis) versus maximal ethanol accumulation capacity (Y-axis), expressed as maximal ethanol titer reached, in the 68 yeast strains. The highest ethanol concentration for which there was growth in all dilutions was taken as the maximal ethanol tolerance of cell proliferation. The possible correlation between the two traits was tested with a Spearman test, because of the non-normality of the ethanol accumulation trait. The (one-tailed) Spearman test indicated a weak correlation (90% confidence interval, P-value = 0.0984).

Mentions: We have evaluated 68 different yeast strains in small-scale fermentations for maximal ethanol accumulation capacity under very high gravity (VHG) conditions [17], using 33% (w/v) glucose. The robust wine strain V1116 was used as reference in each series of fermentation experiments. Figure 1A shows the number of strains able to accumulate a certain maximal ethanol level expressed as percentage of the ethanol level accumulated by V1116 in the same experiment, which was 18.4±0.4% (v/v). There was no correlation between the final glycerol and ethanol levels produced but there was an inverse correlation between the final glycerol level and the ethanol yield. Table 1 shows the fermentation results for a number of representative strains ranked according to the maximal ethanol level produced in comparison with the reference V1116.


Comparative polygenic analysis of maximal ethanol accumulation capacity and tolerance to high ethanol levels of cell proliferation in yeast.

Pais TM, Foulquié-Moreno MR, Hubmann G, Duitama J, Swinnen S, Goovaerts A, Yang Y, Dumortier F, Thevelein JM - PLoS Genet. (2013)

Maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 different yeast strains.(A) Distribution of relative maximal ethanol production capacity of 68 different yeast strains compared to the wine strain V1116. The semi-static fermentations were performed in 250 mL of YP+33% glucose at 25°C. The V1116 strain produced 18.4% (±0.4%) (v/v) ethanol. (B) Ethanol tolerance of cell proliferation (X-axis) versus maximal ethanol accumulation capacity (Y-axis), expressed as maximal ethanol titer reached, in the 68 yeast strains. The highest ethanol concentration for which there was growth in all dilutions was taken as the maximal ethanol tolerance of cell proliferation. The possible correlation between the two traits was tested with a Spearman test, because of the non-normality of the ethanol accumulation trait. The (one-tailed) Spearman test indicated a weak correlation (90% confidence interval, P-value = 0.0984).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3675000&req=5

pgen-1003548-g001: Maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 different yeast strains.(A) Distribution of relative maximal ethanol production capacity of 68 different yeast strains compared to the wine strain V1116. The semi-static fermentations were performed in 250 mL of YP+33% glucose at 25°C. The V1116 strain produced 18.4% (±0.4%) (v/v) ethanol. (B) Ethanol tolerance of cell proliferation (X-axis) versus maximal ethanol accumulation capacity (Y-axis), expressed as maximal ethanol titer reached, in the 68 yeast strains. The highest ethanol concentration for which there was growth in all dilutions was taken as the maximal ethanol tolerance of cell proliferation. The possible correlation between the two traits was tested with a Spearman test, because of the non-normality of the ethanol accumulation trait. The (one-tailed) Spearman test indicated a weak correlation (90% confidence interval, P-value = 0.0984).
Mentions: We have evaluated 68 different yeast strains in small-scale fermentations for maximal ethanol accumulation capacity under very high gravity (VHG) conditions [17], using 33% (w/v) glucose. The robust wine strain V1116 was used as reference in each series of fermentation experiments. Figure 1A shows the number of strains able to accumulate a certain maximal ethanol level expressed as percentage of the ethanol level accumulated by V1116 in the same experiment, which was 18.4±0.4% (v/v). There was no correlation between the final glycerol and ethanol levels produced but there was an inverse correlation between the final glycerol level and the ethanol yield. Table 1 shows the fermentation results for a number of representative strains ranked according to the maximal ethanol level produced in comparison with the reference V1116.

Bottom Line: From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced.Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different.Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Flanders, Belgium.

ABSTRACT
The yeast Saccharomyces cerevisiae is able to accumulate ≥17% ethanol (v/v) by fermentation in the absence of cell proliferation. The genetic basis of this unique capacity is unknown. Up to now, all research has focused on tolerance of yeast cell proliferation to high ethanol levels. Comparison of maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 yeast strains showed a poor correlation, but higher ethanol tolerance of cell proliferation clearly increased the likelihood of superior maximal ethanol accumulation capacity. We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced. Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different. Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity. These genes, as well as the previously identified MKT1 gene, were not linked in this genetic background to tolerance of cell proliferation to high ethanol levels. The superior KIN3 allele contained two SNPs, which are absent in all yeast strains sequenced up to now. This work provides the first insight in the genetic basis of maximal ethanol accumulation capacity in yeast and reveals for the first time the importance of DNA damage repair in yeast ethanol tolerance.

Show MeSH
Related in: MedlinePlus