Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ACCESS DATA

Json Xml

Publications

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

Similar Datasets

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

Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

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.

2012-09-20 | E-GEOD-40219 | biostudies-arrayexpress

Comparative transcriptome analysis of yeast expressing the fungal desaturases

Project description:To study how the presence of PUFAs influences central cellular processes, and in order to perform lipidome, transcriptome and molecular studies we decided to use yeast as a model organism. We therefore co-expressed Δ12-desaturase and Δ6- desaturase genes from Mucor rouxii in S. cerevisiae with the objective to obtain a yeast strain that contains PUFAs, especially linoleic acid (LA, C18:2Δ9,12) and γ-linolenic acid (GLA, C18:3Δ6,9,12), in its membranes. The resulting yeast strain was analyzed in details in order to quantify the fluxes through the fatty acid biosynthetic pathways and the genome-wide transcriptional response to production of LA and GLA. Three recombinant yeasts were constructed and grown in glucose-limited condition. Steady-state cultures were harvested for RNA extraction and hybridization on Affymetrix microarrays. Comparative transcriptome analysis between S. cerevisiae recombinants expressing M. rouxii D12-desaturase (D12) and co-expressing D12-desaturase and D6-desaturase genes (D126) and the reference strain (REF) was implemented.

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

Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner

Project description:Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus. Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.

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

Interaction of Snf1 with TORC1 in yeast Saccharomyces cerevisiae

Project description:Snf1 and TORC1 are two global regulators that sense the nutrient availability and regulate the cell growth in yeast Saccharomyces cerevisiae. Here we undertook a systems biology approach to study the effect of deletion of these genes and investigate the interaction between Snf1 and TORC1 in regulation of gene expression and cell metabolism. 3 mutant strains (snf1?, tor1?, snf1?tor1?) together with 1 reference strain grown under both glucose-limited or amonia-limited defined media with three biological replicates for each strain

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

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

Project description:We undertook an inter-laboratory effort to generate high-quality quantitative data for a very large number of cellular components in yeast using transcriptome and metabolome analysis. We ensured the high-quality of the experimental data by evaluating a wide range of sampling and measurement techniques. The data were generated for two different yeast strains, each growing under two different growth conditions and based on integrated analysis of the high-throughput data we hypothesize that differences in growth rates and yields on glucose between the two strains are due to differences in protein metabolism. Two yeast strains, YSBN2 and CEN.PK 113-7D, were grown in aerobical batch as well as glucose-limited chemostat (dilution rate 0.1h-1) in biological triplicates

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

A tri-species Aspergillus array (oryzae arrays)

Project description:The full genome sequencing of the ﬁlamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Aﬀymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identiﬁed to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response Two conditions (glucose and xylose) and three biological replicates

2008-02-15 | E-GEOD-9277 | biostudies-arrayexpress

A tri-species Aspergillus array (niger arrays)

2008-02-15 | E-GEOD-9276 | biostudies-arrayexpress