Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering

Metab Eng. 2013 May;17:68-81. doi: 10.1016/j.ymben.2013.02.006. Epub 2013 Mar 18.


Engineering of metabolic pathways by genetic modification has been restricted largely to enzyme-encoding structural genes. The product yield of such pathways is a quantitative genetic trait. Out of 52 Saccharomyces cerevisiae strains phenotyped in small-scale fermentations, we identified strain CBS6412 as having unusually low glycerol production and higher ethanol yield as compared to an industrial reference strain. We mapped the QTLs underlying this quantitative trait with pooled-segregant whole-genome sequencing using 20 superior segregants selected from a total of 257. Plots of SNP variant frequency against SNP chromosomal position revealed one major and one minor locus. Downscaling of the major locus and reciprocal hemizygosity analysis identified an allele of SSK1, ssk1(E330N…K356N), expressing a truncated and partially mistranslated protein, as causative gene. The diploid CBS6412 parent was homozygous for ssk1(E330N…K356N). This allele affected growth and volumetric productivity less than the gene deletion. Introduction of the ssk1(E330N…K356N) allele in the industrial reference strain resulted in stronger reduction of the glycerol/ethanol ratio compared to SSK1 deletion and also compromised volumetric productivity and osmotolerance less. Our results show that polygenic analysis of yeast biodiversity can provide superior novel gene tools for metabolic engineering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodiversity
  • Chromosome Mapping / methods
  • Ethanol / metabolism*
  • Genetic Variation / genetics*
  • Glycerol / metabolism*
  • Metabolic Engineering / methods*
  • Quantitative Trait Loci / genetics*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism


  • SSK1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Ethanol
  • Glycerol