Quantification of global gene expression control by growth rate and metabolic cues
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ABSTRACT:
PROVIDER: PRJEB38463 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed a series of 14 steady-state chemostat cultures of S. cerevisiae in biological triplicates, which orthogonally modulated either the growth rate under nitrogen limitation, or the amino acid metabolism of the cell under nitrogen or carbon limitation. The nitrogen sources in the AA subset were chosen to represent those that are preferred (NH4 and Glu) and non-preferred (Phe and Ile). This dataset allows us to account for gene expression changes that arise from changing growth rate and metabolism, which is necessary for a complete understanding of gene regulation.
2021-03-16 | E-MTAB-9117 | biostudies-arrayexpress
Project description:We studied the relation between growth rate and genomewide gene expression, cell cycle progression, and glucose metabolism in 36 steady state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil or leucine). The expression of more than a quarter of all yeast genes is linearly correlated with growth rate, independently of the limiting nutrient. The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions. Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling. We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient. Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate or ammonia did not; this phenomenon (reminiscent of the "Warburg effect" in cancer cells) was confirmed in batch cultures. Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an "instantaneous growth rate". This concept is useful in interpreting the systemlevel connections among growth rate, metabolism, stress and the cell cycle. Keywords: growth condition design
2007-08-21 | GSE8825 | GEO
Project description:Here we quantitatively describe the influence of cell growth rate and amino acid metabolic context on gene expression in the eukaryal model organism Saccharomyces cerevisiae. We show that growth rate and metabolic cues regulate ~70% of the yeast transcriptome and proteome, thereby exerting gene expression control in a global manner. We find that the growth rate-dependent differential gene expression largely reflects changing availabilities of the mRNA and protein synthesis machineries, while metabolic cues influences gene expression through the availabilities of amino acids and nucleotides. Genes in central carbon metabolism, however, are regulated independently of these global physiological controls, demonstrating distinct mechanisms to control their expression levels.
2021-03-15 | PXD021218 | Pride
Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented. Adult fish were placed in six different 26L tanks with three fish per tank in a partially recirculating flow-through system. Half of the tanks were assigned to the control group and the other half to the experimental group.10 samples were selected for microarray analysis. The ten samples comprised five biological replicates in the experimental group (fish exposed to predator cues) and five biological replicates in the control group (fish not exposed to predator cues), and were evenly distributed across tanks. The cDNA labeling (single color), hybridization, washing and scanning steps were performed in the NimbleGen microarray gene expression service department.
2011-04-24 | E-GEOD-21599 | biostudies-arrayexpress
Project description:We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes. Examination of Ifh1p binding over two timepoints of the YMC (OX, RC) using Input as the control.
2013-07-05 | E-GEOD-39147 | biostudies-arrayexpress
Project description:Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside widespread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent ~55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.
2022-02-24 | PXD027835 | Pride
Project description:Absolute quantification of miRNAs
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Project description: Not available
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Project description:Clostridioides difficile (formerly Clostridium difficile) is a Gram-positive, spore-forming pathogen which cases drug-induced Clostridioides difficile-associated diseases in hospitals worldwide. A detailed analysis of the proteome may provide new targets for drug development or therapy strategies to combat this pathogen. So far, quantitative proteome analyses could only be carried out by label-free or chemical labeling methods. However, the application of metabolic labeling would allow for accurate quantification of significant differences, even in the case of very small changes. Additionally, it would be possible to perform bias free studies of the membrane or surface proteome which require elaborated preparations and are therefore prone to higher standard deviations during the quantification. Up to now, the implementation of metabolic labeling strategies of C. difficile was hampered by the very specific metabolic requirements of this anaerobic pathogen. To solve this problem, media were evaluated and the cultivation procedure with 15N labeled media for the C. difficile 630Δerm strain was optimized to gain a high incorporation rate. In the following proof-of-principle experiment, the cytosolic sub-proteomes of C. difficile cells of three different cultivation media and two growth phases were analyzed resulting in reproducible data which are shown in detail.
2018-10-25 | PXD010279 | Pride
Project description:In this study, we used whole genome comparative oligonucleotide microarrays to investigate the brain transcriptomic response to predator cues using the threespine stickleback, Gasteroteus aculeatus. We showed that exposure to olfactory, visual and tactile cues of a predator (rainbow trout, Oncorhynchus mykiss) for six days resulted in subtle but significant transcriptomic changes in the brain of sticklebacks. Gene functional analysis and gene ontology (GO) enrichment revealed that the majority of the transcripts differentially expressed between the fish exposed to predator cues and the control group are primarily related to antigen processing and presentation (involving primarily the major histocompatibility complex (MHC)), transmission of synaptic signals, brain metabolic processes, gene regulation, or visual perception. Pathway analysis identified synaptic long-term depression, RAN signaling, relaxin signaling and phototransduction as the top four pathways that were over-represented.
2011-04-24 | GSE21599 | GEO