title: Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.
abstract: Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts.
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Karin
authors.initials: K
authors.lastname: Voordeckers
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Jacek
authors.initials: J
authors.lastname: Kominek
authors.affiliation: CMPG Laboratory of Predictive Genetics and Multicellular Systems, KU Leuven, Leuven, Belgium.
authors.forename: Anupam
authors.initials: A
authors.lastname: Das
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico.
authors.forename: Adriana
authors.initials: A
authors.lastname: Espinosa-Cantú
authors.affiliation: CMPG Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.|Department of Information Technology (INTEC, iMINDS), University of Ghent, Ghent, Belgium.
authors.forename: Dries
authors.initials: D
authors.lastname: De Maeyer
authors.affiliation: CMPG Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Arslan
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Michiel
authors.initials: M
authors.lastname: Van Pee
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Elisa
authors.initials: E
authors.lastname: van der Zande
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Meert
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Yudi
authors.initials: Y
authors.lastname: Yang
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhu
authors.affiliation: CMPG Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.|Department of Information Technology (INTEC, iMINDS), University of Ghent, Ghent, Belgium.|Department of Plant Biotechnology and Bioinformatics, University of Ghent, Ghent, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.affiliation: Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico.
authors.forename: Alexander
authors.initials: A
authors.lastname: DeLuna
authors.affiliation: CMPG Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium.
authors.forename: Vera
authors.initials: V
authors.lastname: Van Noort
authors.affiliation: CMPG Laboratory of Predictive Genetics and Multicellular Systems, KU Leuven, Leuven, Belgium.
authors.forename: Rob
authors.initials: R
authors.lastname: Jelier
authors.affiliation: VIB Laboratory for Systems Biology, Leuven, Belgium.|CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Verstrepen
mesh_terms: D000222:Adaptation, Physiological; D000782:Aneuploidy; D000431:Ethanol / Q000494:pharmacology*; D006238:Haploidy
chemical_list: D000431:Ethanol