Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pgen.1000303
Title: The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
Authors: Gresham D.
Desai M.M.
Tucker C.M.
Jenq H.T.
Pai D.A.
Ward A. 
DeSevo C.G.
Botstein D.
Dunham M.J.
Keywords: glucose
nucleotide
phosphate
sulfate
glucose
phosphate
Saccharomyces cerevisiae protein
sulfate
article
chemostat
diploidy
DNA microarray
evolutionary adaptation
fungal genetics
fungus growth
gene amplification
gene expression
gene insertion
genetic variability
genotype
haploidy
molecular cloning
mutation rate
nonhuman
nutrient limitation
phenotype
point mutation
regulatory mechanism
reproducibility
retroposon
Saccharomyces cerevisiae
adaptation
gene deletion
gene duplication
gene expression profiling
genetic selection
genetics
growth, development and aging
metabolism
molecular evolution
molecular genetics
mutation
physiology
Saccharomyces cerevisiae
Saccharomyces cerevisiae
Adaptation, Physiological
Evolution, Molecular
Gene Deletion
Gene Duplication
Gene Expression Profiling
Genotype
Glucose
Molecular Sequence Data
Mutation
Oligonucleotide Array Sequence Analysis
Phenotype
Phosphates
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Selection (Genetics)
Sulfates
Issue Date: 2008
Citation: Gresham D., Desai M.M., Tucker C.M., Jenq H.T., Pai D.A., Ward A., DeSevo C.G., Botstein D., Dunham M.J. (2008). The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genetics 4 (12) : e1000303. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pgen.1000303
Rights: Attribution 4.0 International
Abstract: The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time. Until very recently, however, such studies have been limited by our inability to systematically find mutations in evolved organisms. We overcome this limitation by using a variety of DNA microarray-based techniques to characterize genetic changes - including point mutations, structural changes, and insertion variation - that resulted from the experimental adaptation of 24 haploid and diploid cultures of Saccharomyces cerevisiae to growth in either glucose, sulfate, or phosphate-limited chemostats for ?200 generations. We identified frequent genomic amplifications and rearrangements as well as novel retrotransposition events associated with adaptation. Global nucleotide variation detection in ten clonal isolates identified 32 point mutations. On the basis of mutation frequencies, we infer that these mutations and the subsequent dynamics of adaptation are determined by the batch phase of growth prior to initiation of the continuous phase in the chemostat. We relate these genotypic changes to phenotypic outcomes, namely global patterns of gene expression, and to increases in fitness by 5-50%. We found that the spectrum of available mutations in glucose- or phosphate-limited environments combined with the batch phase population dynamics early in our experiments allowed several distinct genotypic and phenotypic evolutionary pathways in response to these nutrient limitations. By contrast, sulfate-limited populations were much more constrained in both genotypic and phenotypic outcomes. Thus, the reproducibility of evolution varies with specific selective pressures, reflecting the constraints inherent in the system-level organization of metabolic processes in the cell. We were able to relate some of the observed adaptive mutations (e.g., transporter gene amplifications) to known features of the relevant metabolic pathways, but many of the mutations pointed to genes not previously associated with the relevant physiology. Thus, in addition to answering basic mechanistic questions about evolutionary mechanisms, our work suggests that experimental evolution can also shed light on the function and regulation of individual metabolic pathways. © 2008 Gresham et al.
Source Title: PLoS Genetics
URI: https://scholarbank.nus.edu.sg/handle/10635/161681
ISSN: 15537390
DOI: 10.1371/journal.pgen.1000303
Rights: Attribution 4.0 International
Appears in Collections:Elements
Staff Publications

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
10_1371_journal_pgen_1000303.pdf1.08 MBAdobe PDF

OPEN

NoneView/Download

SCOPUSTM   
Citations

321
checked on May 13, 2022

WEB OF SCIENCETM
Citations

285
checked on Oct 4, 2021

Page view(s)

195
checked on May 12, 2022

Download(s)

1
checked on May 12, 2022

Google ScholarTM

Check

Altmetric


This item is licensed under a Creative Commons License Creative Commons