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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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Fine-mapping and bulk RHA of QTL2.(A) Genes present in QTL2 (pool 1), located on chromosome I, as determined by markers scored in the 22 segregants individually. (B) Bulk RHA (bRHA 1.1) of genes NUP60, ERP1, SWD1, RFA1 and SEN34. Two heterozygous diploids for the five genes were constructed: Seg5/BY710-bRHA1.1Δ (○) and Seg5-bRHA1.1Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C. (C) Bulk RHA (bRHA 1.2) of genes YARCdelta3/4/5, YARCTy1-1, YAR009c, YAR010c, tA(UGC), BUD14, ADE1, KIN3, and CDC15. Two heterozygous diploids for the previous genes were constructed: Seg5/BY710-bRHA1.2Δ (○) and Seg5-bRHA1.2Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C.
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pgen-1003548-g005: Fine-mapping and bulk RHA of QTL2.(A) Genes present in QTL2 (pool 1), located on chromosome I, as determined by markers scored in the 22 segregants individually. (B) Bulk RHA (bRHA 1.1) of genes NUP60, ERP1, SWD1, RFA1 and SEN34. Two heterozygous diploids for the five genes were constructed: Seg5/BY710-bRHA1.1Δ (○) and Seg5-bRHA1.1Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C. (C) Bulk RHA (bRHA 1.2) of genes YARCdelta3/4/5, YARCTy1-1, YAR009c, YAR010c, tA(UGC), BUD14, ADE1, KIN3, and CDC15. Two heterozygous diploids for the previous genes were constructed: Seg5/BY710-bRHA1.2Δ (○) and Seg5-bRHA1.2Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C.

Mentions: We have analysed in detail two QTLs (2 and 3) involved in high ethanol accumulation capacity (pool 1) because this trait is more relevant in industrial fermentations and because these two QTLs were among those with the strongest linkage. QTL2 is located on chromosome I and was fine-mapped by scoring selected markers in the 22 individual segregants. This reduced the length of the QTL to the area between chromosomal positions 151 kb and 178 kb (P-value<0.05) (Figure 5A). The association percentage of the markers, their genomic positions, the respective P-values and the genes located in the putative QTL 1 are shown in Figure 5A.


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)

Fine-mapping and bulk RHA of QTL2.(A) Genes present in QTL2 (pool 1), located on chromosome I, as determined by markers scored in the 22 segregants individually. (B) Bulk RHA (bRHA 1.1) of genes NUP60, ERP1, SWD1, RFA1 and SEN34. Two heterozygous diploids for the five genes were constructed: Seg5/BY710-bRHA1.1Δ (○) and Seg5-bRHA1.1Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C. (C) Bulk RHA (bRHA 1.2) of genes YARCdelta3/4/5, YARCTy1-1, YAR009c, YAR010c, tA(UGC), BUD14, ADE1, KIN3, and CDC15. Two heterozygous diploids for the previous genes were constructed: Seg5/BY710-bRHA1.2Δ (○) and Seg5-bRHA1.2Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1003548-g005: Fine-mapping and bulk RHA of QTL2.(A) Genes present in QTL2 (pool 1), located on chromosome I, as determined by markers scored in the 22 segregants individually. (B) Bulk RHA (bRHA 1.1) of genes NUP60, ERP1, SWD1, RFA1 and SEN34. Two heterozygous diploids for the five genes were constructed: Seg5/BY710-bRHA1.1Δ (○) and Seg5-bRHA1.1Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C. (C) Bulk RHA (bRHA 1.2) of genes YARCdelta3/4/5, YARCTy1-1, YAR009c, YAR010c, tA(UGC), BUD14, ADE1, KIN3, and CDC15. Two heterozygous diploids for the previous genes were constructed: Seg5/BY710-bRHA1.2Δ (○) and Seg5-bRHA1.2Δ/BY710 (▪). These two diploids were compared with the original strain Seg5/BY710 (•) in semi-static fermentations performed in 250 mL of YP+33% glucose at 25°C.
Mentions: We have analysed in detail two QTLs (2 and 3) involved in high ethanol accumulation capacity (pool 1) because this trait is more relevant in industrial fermentations and because these two QTLs were among those with the strongest linkage. QTL2 is located on chromosome I and was fine-mapped by scoring selected markers in the 22 individual segregants. This reduced the length of the QTL to the area between chromosomal positions 151 kb and 178 kb (P-value<0.05) (Figure 5A). The association percentage of the markers, their genomic positions, the respective P-values and the genes located in the putative QTL 1 are shown in Figure 5A.

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