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Dynamic mRNA gene expression during a nutritional upshift from proline to glutamine

ABSTRACT: Dynamic mRNA gene expression from the wildtype YSBN6 during a nutritional upshift from proline to glutamine. Glutamine was added to yeast cells growing exponentially on proline as the sole nitrogen source.

ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe

PROVIDER: GSE54844 | GEO | 2015/04/07

SECONDARY ACCESSION(S): PRJNA237816

REPOSITORIES: GEO

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Dynamic mRNA gene expression during a nutritional upshift from proline to glutamine

Project description:Dynamic mRNA gene expression from the wildtype YSBN6 during a nutritional upshift from proline to glutamine. Glutamine was added to yeast cells growing exponentially on proline as the sole nitrogen source. A sample was taken at steady-state 10 minutes before the shift, and then 3, 7, 10, 14, 24, 56 and 120 minutes after the glutamine addition. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 14 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points. Other dynamic omics data are associated with this dataset. Consult the publication for more details.

2015-04-07 | E-GEOD-54844 | biostudies-arrayexpress

Dynamic mRNA gene expression during a nutritional downshift from glutamine to proline

2015-04-07 | GSE54850 | GEO

Dynamic mRNA gene expression during a nutritional downshift from glutamine to proline

Project description:Dynamic mRNA gene expression from the wildtype YSBN6 during a nutritional downshift from glutamine to proline. Glutamine and proline were initially together in the media, with cells consuming exlusively glutamine (proline utilization inhibited due to nitrogen catabolite repression). The concentration of glutamine was frequently evaluated at-line, and the moment at which glutamine was not detected anymore is referred to as the time of the shift. Given the uncertainty of the exact time of the shift, two samples were taken at steady-state, approximately 10 and 5 minutes before the shift. Once the shift was identified, samples were taken 3, 7, 10, 14, 24, 56 and 120 minutes after the glutamine depletion. Biological triplicate gene expression was measured for samples -10, 7 and 24 minutes after shift, for a total of 15 chips. Changes were generally evaluated relative to the steady-state point (-10 minutes). Biological variability can be assessed from the replicates time points. Other dynamic omics data are associated with this dataset. Consult the publication for more details.

2015-04-07 | E-GEOD-54850 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Dynamic mRNA gene expression during a nutritional upshift from proline to glutamine

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Dynamic mRNA gene expression following a rapamycin treatment

Project description:Dynamic mRNA gene expression from the wildtype YSBN6 during a rapamycin treatment (rapamycin-induced downshift). Rapamycin was added to yeast cells growing exponentially on glutamine as sole nitrogen source.

2015-04-07 | GSE54851 | GEO

L-Glutamine metabolism and its regulation in C. glutamicum

Project description:Corynebacterium glutamicum, a gram-positive soil bacterium used for the industrial production of amino acids such as L-glutamate and L-lysine, is able to use a number of different nitrogen sources, such as ammonium, urea, or creatinine. In this communication, we show that L-glutamine serves as an excellent nitrogen source for C. glutamicum and allows similar growth rates in glucose minimal medium as ammonium. A transcriptome comparison revealed a strong induction of the nitrogen starvation response when glutamine was used as nitrogen source. Subsequent growth experiments with a variety of mutants defective in nitrogen metabolism showed that glutamate synthase is crucial for glutamine utilization, while a putative glutaminase is dispensable under the experimental conditions used. The fact that the glutamate synthase encoding gltBD operon is under strict nitrogen control explains the necessity for induction of the nitrogen starvation response. The paradox situation that the nitrogen starvation response is induced although intracellular L-glutamine levels are high has implications on nitrogen sensing. In contrast to other gram-positive and gram-negative bacteria such as Bacillus subtilis, Salmonella typhimurium, and Klebsiella pneumoniae, a drop in glutamine concentration obviously does not serve as a nitrogen starvation signal in C. glutamicum. Three biological replicates were performed. To analyse how L-glutamine influences global gene expression when used as sole nitrogen source instead of ammonium, DNA microarray analyses were performed. For this purpose RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either L-glutamine or ammonium sulphate as nitrogen source.

2010-10-05 | E-GEOD-19779 | biostudies-arrayexpress

Temperature Upshift

Project description:Determine if cells in stationary-phase cultures respond to increased temperature. Yeast cells in stationary-phase cultures were exposed to temperature upshift (30C to 39C) with samples harvested every 30-minutes over 8 hours. All experimental samples are over an common reference. There are two replicates for each time point and six replicates of T0.

2010-06-30 | E-GEOD-3687 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Dynamic mRNA gene expression during a nutritional downshift from glutamine to proline

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Gene expression of subpopulations arising from a nitrogen down-shift with proline as a nitrogen source in S. cerevisiae

Project description:When S. cerevisiae cells growing exponentially in rich media (YPD) are shifted to nitrogen-limited media with proline (0.8 mM) as a nitrogen source, they differentiate into two subpopulations of different phenotypes including cell size, growth and survival capabilities. The RNA-seq data presented here are for each subpopulation (5 biological replicates per subpopulation) sampled 1 hour after the shift and separated by FACS.

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