title: Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering.
abstract: 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.
authors.affiliation: Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Belgium.
authors.forename: Georg
authors.initials: G
authors.lastname: Hubmann
authors.forename: Maria R
authors.initials: MR
authors.lastname: Foulquié-Moreno
authors.forename: Elke
authors.initials: E
authors.lastname: Nevoigt
authors.forename: Jorge
authors.initials: J
authors.lastname: Duitama
authors.forename: Nicolas
authors.initials: N
authors.lastname: Meurens
authors.forename: Thiago M
authors.initials: TM
authors.lastname: Pais
authors.forename: Lotte
authors.initials: L
authors.lastname: Mathé
authors.forename: Sofie
authors.initials: S
authors.lastname: Saerens
authors.forename: Huyen Thi Thanh
authors.initials: HT
authors.lastname: Nguyen
authors.forename: Steve
authors.initials: S
authors.lastname: Swinnen
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Verstrepen
authors.forename: Luigi
authors.initials: L
authors.lastname: Concilio
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: de Troostembergh
authors.forename: Johan M
authors.initials: JM
authors.lastname: Thevelein
mesh_terms: D044822:Biodiversity; D002874:Chromosome Mapping / Q000379:methods; D000431:Ethanol / Q000378:metabolism*; D014644:Genetic Variation / Q000235:genetics*; D005990:Glycerol / Q000378:metabolism*; D060847:Metabolic Engineering / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: C087199:SSK1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D000431:Ethanol; D005990:Glycerol