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Series GSE52786 Query DataSets for GSE52786
Status Public on Nov 28, 2013
Title Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments [GE]
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that knowledge of the selective environment and the regulatory mechanisms important for growth and survival in that environment greatly increases the predictability of adaptive evolution.
 
Overall design mRNA from each evolved clone or from the ancestral strain growing in the specificied nitrogen-limited condition was co-hybridized with mRNA from the ancestral strain grown in ammonium limited media
 
Contributor(s) Gresham D, Hong J
Citation(s) 24415948
Submission date Nov 27, 2013
Last update date Feb 10, 2014
Contact name Jungeui Hong
E-mail(s) jh2663@nyu.edu
Organization name New York University
Department Biology
Lab Gresham Lab
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platforms (3)
GPL7293 Agilent-013384 Yeast Oligo Microarray (V2) G4140B (Probe Name version)
GPL9294 Agilent-015072 Yeast Oligo Microarray 4x44K G2519F (Probe Name version)
GPL11382 Agilent Yeast Microarray
Samples (22)
GSM1275995 FY4 in arginine limited media vs FY4 in ammonium limited media
GSM1275996 FY4 in glutamine limited media vs FY4 in ammonium limited media
GSM1275997 FY4 in proline limited media vs FY4 in ammonium limited media
This SubSeries is part of SuperSeries:
GSE52787 Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments
Relations
BioProject PRJNA230023

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52786_RAW.tar 107.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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