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Series GSE39065 Query DataSets for GSE39065
Status Public on Aug 01, 2012
Title Adaptively evolved yeast mutants on galactose shows trade-offs in carbon utilization on glucose.
Platform organisms Schizosaccharomyces pombe; Saccharomyces cerevisiae
Sample organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary Exploring molecular details of carbon utilization trade-offs in galactose-evolved yeast

Adaptively evolved yeast mutants on galactose for around 400 generations showed diminished growth and carbon uptake rates on glucose. Genome-scale approaches were applied to characterize the molecular genetic basis of these trade-offs in carbon source utilization. Engineered mutants showing trade-offs in a specific carbon uptake rate between both carbons were used as controls. The transcriptional responses of the evolved mutants were almost identical during growth on both carbon sources. These carbon-independent conserved patterns were clearly observed in specific pathways and genes. Up-regulation of PGM2, a confirmed beneficial genetic change for improving galactose utilization was preserved on both carbons. In addition, HXK1, GLK1 and genes involved in reserve carbohydrate metabolism were up-regulated, while HXK2 was down-regulated. Genes that have a transcription factor binding site for Gis1p, Rph1p, Msn2/4p and Nrg1p were up-regulated. These results indicated changes in the metabolic pathways involved in metabolism of both carbons and in nutrient signaling pathway. The concentration profile of trehalose and glycogen supported these findings. Mutations in RAS2 and ERG5 genes were selected because of their beneficial and neutral effect on galactose utilization, respectively in our previous study. Site-directed mutants containing galactose-beneficial mutations in RAS2 only resulted in a significant decrease in glucose utilization. Integration of all these analyses clearly suggest an antagonistic pleiotropic trade-off in carbon source utilization caused by changes in regulatory region, and we hereby demonstrate how systems biology can be used to gain insight into evolutionary processes at the molecular level.
 
Overall design Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source
 
Contributor(s) Hong KK, Nielsen J
Citation(s) 23376593
Submission date Jul 03, 2012
Last update date Feb 21, 2017
Contact name Kuk-Ki Hong
E-mail(s) kukki@chalmers.se
Organization name Chalmers University of Technology
Department Department of Chemical and Biological Engineering
Lab Nielsen's Laboratory for Systems Biology
Street address Kemiv├Ągen 10
City Gothenburg
ZIP/Postal code 412 96
Country Sweden
 
Platforms (1)
GPL2529 [Yeast_2] Affymetrix Yeast Genome 2.0 Array
Samples (6)
GSM954977 Glc-62A
GSM954978 Glc-62B1
GSM954979 Glc-62B2
Relations
BioProject PRJNA169865

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
GSE39065_RAW.tar 4.5 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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