Back to Search
Start Over
Adaptation to High Ethanol Reveals Complex Evolutionary Pathways
- Source :
- PLoS Genetics, PLoS Genetics, Vol 11, Iss 11, p e1005635 (2015), PLOS GENETICS, PLoS Genetics, 11(11), e1005635
- Publication Year :
- 2015
- Publisher :
- Public Library of Science (PLoS), 2015.
-
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.<br />Author Summary Organisms can evolve resistance to specific stress factors, which allows them to thrive in environments where non-adapted organisms fail to grow. However, the molecular mechanisms that underlie adaptation to complex stress factors that interfere with basic cellular processes are poorly understood. In this study, we reveal how yeast populations adapt to high ethanol concentrations, an ecologically and industrially relevant stress that is still poorly understood. We exposed six independent populations of genetically identical yeast cells to gradually increasing ethanol levels, and we monitored the changes in their DNA sequence over a two-year period. Together with novel computational analyses, we could identify the mutational dynamics and molecular mechanisms underlying increased ethanol resistance. Our results show how adaptation to high ethanol is complex and can be reached through different mutational pathways. Together, our study offers a detailed picture of how populations adapt to a complex continuous stress and identifies several mutations that increase ethanol resistance, which opens new routes to obtain superior biofuel yeast strains.
- Subjects :
- Cancer Research
BUDDING YEAST
GENE DISRUPTION
lcsh:QH426-470
DNA repair
Haploidy
YEAST SACCHAROMYCES-CEREVISIAE
Quantitative trait locus
Biology
medicine.disease_cause
CLONAL INTERFERENCE
03 medical and health sciences
0302 clinical medicine
GENOME-WIDE IDENTIFICATION
HIGH MUTATION-RATES
Genetics
medicine
Copy-number variation
Molecular Biology
Genetics (clinical)
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
2. Zero hunger
0303 health sciences
Mutation
Experimental evolution
Ethanol
TOLERANT MUTANTS
Clonal interference
Biology and Life Sciences
Aneuploidy
Adaptation, Physiological
Phenotype
ADAPTIVE EVOLUTION
lcsh:Genetics
ESCHERICHIA-COLI
E. COLI
Adaptation
030217 neurology & neurosurgery
Research Article
Subjects
Details
- ISSN :
- 15537404
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- PLOS Genetics
- Accession number :
- edsair.doi.dedup.....c6784ad07b75212827477b5467b612ba