Saccharomyces cerevisiae
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PROVIDER: PRJNA84715 | ENA |
REPOSITORIES: ENA
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Project description:Expression profile of hsp31∆, hsp32∆, hsp33∆ during diauxic shift
| PRJNA242536 | ENA
Project description:Yeast (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.st (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
2015-06-20 | PXD002093 | Pride
Project description:Yeast (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.st (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
2015-06-20 | PXD001334 | Pride
Project description:Protein phosphorylation has long been recognized as an essential regulator of protein activity, structure, complex formation, and sub-cellular localization among other cellular mechanisms. However, interpretation of the changes in protein phosphorylation is difficult. To address this difficulty, we measured protein and phosphorylation site changes across 11 points of a time course and developed a method for categorizing phosphorylation site behavior relative to protein level changes using the diauxic shift in yeast as a model and TMT11 sample multiplexing. We classified quantified proteins into behavioral categories that reflected differences in kinase activity, protein complex structure, and growth and metabolic pathway regulation across different phases of the diauxic shift. These data also provide a valuable resource for the study of fermentative versus respiratory growth and set a new benchmark for temporal quantitative proteomics and phosphoproteomics for Diauxic Shift in Saccharomyces cerevisiae.
2021-03-04 | PXD022741 | Pride
Project description:Yeast (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics
2015-06-22 | PXD001338 | Pride
Project description:Yeast (Saccharomyces cerevisea) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct groups of proteins such as those of glyoxylate metabolism, as well as many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
2015-06-20 | PXD001335 | Pride
Project description:Yeast (Saccharomyces cerevisiae) has served as a key model system in biology and as a benchmark for “omics” technology. Although near-complete proteomes of log phase yeast have been measured, protein abundance in yeast is dynamic, particularly during the transition from log to stationary phase. Defining the dynamics of proteomic changes during this transition, termed the diauxic shift, is important to understand the basic biology of proliferative versus quiescent cells. Here, we perform temporal quantitative proteomics to fully capture protein induction and repression during the diauxic shift. Accurate and sensitive quantitation at a high temporal resolution and depth of proteome coverage was achieved using TMT10 reagents and LC-MS3 analysis on an Orbitrap Fusion tribrid mass spectrometer deploying synchronous precursor selection (SPS). We devised a simple template matching strategy to reveal temporal patterns of protein induction and repression. Within these groups are functionally distinct types of proteins such as those of glyoxylate metabolism and many proteins of unknown function not previously associated with the diauxic shift (e.g. YNR034W-A and FMP16). We also perform a dual time-course experiment to determine Hap2-dependent proteins during the diauxic shift. These data serve as an important basic model for fermentative versus respiratory growth of yeast and other eukaryotes and are a benchmark for temporal quantitative proteomics.
2015-06-20 | PXD002092 | Pride
Project description:Ire1 is an endoplasmic reticulum (ER)-located transmembrane protein that triggers the unfolded protein response. I recently noticed that Ire1 is activated not only in response to ER accumulation of unfolded proteins but also alongside diauxic shift in yeast Saccharomyces cerevisiae cells. I thus asked how different the Ire1-target genes upon two distinct scenes, a canonical ER -stressing stimuli and diauxic shift. Thus NGS transcriptome analysis was performed by using IRE1+ and ire1-delta mutant yeast cells under these conditions.
2019-03-01 | E-MTAB-6923 | biostudies-arrayexpress
Project description:<p>Despite extensive research on Saccharomyces cerevisiae functional genomics, approximately 880 out of ~6,000 open reading frames (ORFs) remain uncharacterised. In this study we propose a method for characterising genes with limited prior functional knowledge using an automated laboratory platform, in conjunction with several hypothesis instantiation methods. We demonstrate this method by investigating YGR067C, an uncharacterised ORF hypothesised to regulate respiration during the diauxic shift. Predictions of the first-order effects of deletion were obtained by curating a list of pathways relevant to the hypothesis. Higher-order effects were predicted using simulation models based on the GEM Yeast9. The predictions were tested using empirical data from biological experiments performed in the Robot Scientist Eve, which generated OD560, transcriptomics, and metabolomics data. </p><p>We observed that YGR067C deletion led to downregulation of transcripts in some ethanol consuming respiratory pathways during the glucose phase. During the ethanol phase we observed that NAD+, NADP+ and NADH accumulated, and several amino acid biosynthesis pathways were enriched for the ygr067c∆ strain, suggesting longer term consequences of YGR067C mediated regulation. Based on these observations we propose that the role of YGR067C during the diauxic shift is to regulate genes related to ethanol consumption and respiration in the glucose phase.</p>
2025-12-03 | MTBLS12663 | MetaboLights
Project description:Strand-specific RNA sequencing was performed on wild type yeast in log phase, after diauxic shift, and after entry into quiescence with incorporation of external ERCC RNA spike-in controls to account for global changes in RNA abundance. We find that RNA profiles undergo at least two transitions: 1) From log-to-diauxic shift where stress response genes are induced and translational machinery is massively repressed. 2) From diauxic shift-to-quiescence, where global transcript abundance is repressed 15-fold. The transition from diauxic shift to quiescence was found to require Rpd3, as deletion of Rpd3 prevented the global repression of the transcriptome after the diauxic shift.
2015-08-20 | GSE67149 | GEO