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

PLoS Genet. 2013 Jun;9(6):e1003548. doi: 10.1371/journal.pgen.1003548. Epub 2013 Jun 6.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcoholic Beverages / microbiology
  • Alleles
  • Cell Proliferation*
  • Chromosome Mapping
  • DNA Damage / drug effects
  • DNA Damage / genetics
  • DNA Repair / drug effects
  • DNA Repair / genetics
  • Drug Tolerance / genetics
  • Ethanol / metabolism*
  • Ethanol / pharmacology
  • Genome
  • Polymorphism, Single Nucleotide
  • Protein-Serine-Threonine Kinases / genetics
  • Quantitative Trait Loci / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics

Substances

  • Saccharomyces cerevisiae Proteins
  • URA3 protein, S cerevisiae
  • Ethanol
  • KIN3 protein, S cerevisiae
  • Protein-Serine-Threonine Kinases

Grant support

This work has been supported by predoctoral fellowships to TMP, financed by Mark Anthony Group (Vancouver) and SS, financed by the Agency for Innovation by Science and Technology (IWT-Flanders), and by SBO grants (IWT 50148 and IWT 90043) from IWT-Flanders, the EC 7th Framework program (NEMO project), IOF-Knowledge platform (IKP/10/002 ZKC 1836) and BOF-Program financing (project NATAR) to JMT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.