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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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System level characterization of galactose mutants of yeast

ABSTRACT: Adaptively evolved mutants of yeast on galactose were characterized by feremtation physiology and tools from systems biology. Three evolved mutants of yeast grown on aerobic batch with galactose as carbon source

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Kuk-Ki Hong

PROVIDER: E-GEOD-27185 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis.

Hong Kuk-Ki KK Vongsangnak Wanwipa W Vemuri Goutham N GN Nielsen Jens J

Proceedings of the National Academy of Sciences of the United States of America 20110629 29

Identification of the underlying molecular mechanisms for a derived phenotype by adaptive evolution is difficult. Here, we performed a systems-level inquiry into the metabolic changes occurring in the yeast Saccharomyces cerevisiae as a result of its adaptive evolution to increase its specific growth rate on galactose and related these changes to the acquired phenotypic properties. Three evolved mutants (62A, 62B, and 62C) with higher specific growth rates and faster specific galactose uptake we ...[more]

PMID: 21715660

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Adaptively evolved yeast mutants on galactose shows trade-offs in carbon utilization on glucose.

Project description: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. Yeast galactose evolved mutants having improved galactose availability were grown on aerobic batch with glucose as carbon source

2012-07-31 | E-GEOD-39065 | biostudies-arrayexpress

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Project description:Reconstructed mutants of yeast by inverse metabolic engineering were characterized by fermentation physiology and tools from systems biology. Six reconstructed mutants of yeast were grown on aerobic batch with galactose as carbon source

2012-02-29 | E-GEOD-36118 | biostudies-arrayexpress

System level characterization of galactose mutants of yeast

Project description:Adaptively evolved mutants of yeast on galactose were characterized by feremtation physiology and tools from systems biology.

2011-03-31 | GSE27185 | GEO

The galactose regulator GalX regulates the D-galactose oxido-reductive pathway in Aspergillus niger.

Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger . We aim to discover differentially expressed genes in A.niger wild type strain N402 and M-NM-^TgalX mutant while growing on galactose as carbon source. Biological duplicates were made for both strains. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.

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2010-12-27 | E-GEOD-20155 | biostudies-arrayexpress

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2014-10-07 | E-GEOD-46187 | biostudies-arrayexpress

Interaction of Snf1 with TORC1 in yeast Saccharomyces cerevisiae

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2011-10-19 | E-GEOD-24421 | biostudies-arrayexpress

Experimental systems biology: Lessons from an integrated, multi-laboratory study in yeast

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2010-12-01 | E-GEOD-24234 | biostudies-arrayexpress

A tri-species Aspergillus array (oryzae arrays)

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