Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA307668 | ENA |
REPOSITORIES: ENA
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Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.
2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress
Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions.
2014-07-28 | GSE56622 | GEO
Project description:Ribosome profiling upon glucose starvation in S. cerevisiae
| PRJNA244101 | ENA
Project description:Ribosome profiling provides an opportunity to not only assess how the relative abundance of ribosome association with mRNAs changes in different conditions, but to look more closely at where along mRNAs those ribosomes bind. Here, we used ribosome profiling to calculate the ribosome polarity scores and changes in ribosome footprint read density in both aggregate and gene-specific ways. We profiled a time course of acute glucose starvation followed by glucose readdition and a multi-day growth course through the diauxic shift into stationary phase. We found that ribosome polarity became positive in postdiauxic shift conditions relative to log phase. In acute starvation, polarity shifted positive at our earliest time points but did not continue to do so at later time points. This is consistent with a read density analysis which demonstrated increased density on the 3’ half of genes after glucose starvation. Additionally, we performed ribosome profiling in samples that had glucose added back following acute starvation and observed a wave of new ribosome movement near the start codon and approximately 2,000 nucleotides downstream on open reading frames after one and five minutes of readdition, respectively. Our ribosome profiling analysis suggested that elongation slows during starvation which leads to a buildup of ribosomes on the 3’ halves of mRNAs. Further, it also indicated ribosomes previously built up can resume translation upon glucose readdition. We used reporter assays to corroborate these findings in vivo. Together, these results demonstrate how yeast regulate translation in response to glucose starvation.
2022-04-11 | GSE200491 | GEO
Project description:In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-10-15 | GSE3456 | GEO
Project description:In Saccharomyces cerevisiae, the Ca2+/calmodulin-dependent protein phosphatase, calcineurin, is activated by specific environmental conditions, including exposure to Ca2+ and Na+, and induces gene expression by regulating the Crz1p/Tcn1p transcription factor. We used DNA microarrays to perform a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca2+ (200 mM) or Na+ (0.8 M) to yeast. 163 genes exhibited increased expression that was reduced 50% or more by calcineurin inhibition. These calcineurin dependent genes function in signaling pathways, ion/small molecule transport, cell wall maintenance, vesicular transport, and include many open reading frames of heretofore-unknown function. Three distinct gene classes were defined: 28 genes displayed calcineurin-dependent induction in response to Ca2+ and Na+, 125 showed calcineurin-dependent expression following Ca2+ but not Na+ addition, and 10 were regulated by calcineurin in response to Na+ but not Ca2+. Analysis of crz1D cells established Crz1p as the major effecter of calcineurin-regulated gene expression in yeast. We identified the Crz1p binding site as 5-GNGGC(G/T)CA-3 by in vitro site selection. A similar sequence, 5-GAGGCTG-3, was identified as a common sequence motif in the upstream regions of calcineurin/Crz1p-dependent genes. This finding is consistent with direct regulation of these genes by Crz1p. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-10-15 | E-GEOD-3456 | biostudies-arrayexpress
Project description:Inflammation and infection can trigger local tissue Na+-accumulation. This Na+-rich environment boosts pro-inflammatory activation of monocyte/macrophage-like cells (MΦ) and their antimicrobial activity. Enhanced Na+-driven MΦ-function requires the osmoprotective transcription factor nuclear factor of activated T cells 5 (NFAT5), which augments NO production and contributes to increased autophagy. However, the mechanism of Na+-sensing in MΦ remained unclear. High extracellular Na+ levels (HS) trigger a substantial Na+-influx and Ca2+ loss. Here, we show that the Na+/ Ca2+-exchanger 1 (NCX1/ solute carrier family 8 member A1 (SLC8A1)) plays a critical role in HS-triggered Na+-influx, concomitant Ca2+ efflux and subsequent NFAT5 accumulation. Moreover, interfering with NCX1-activity impairs HS-boosted inflammatory signaling, infection-triggered autolysosome formation and subsequent antibacterial activity. Taken together, this demonstrates that NCX1 is able to sense Na+ and is required for amplifying inflammatory and antimicrobial MΦ responses upon HS exposure. Manipulating NCX1 offers a new strategy to regulate MΦ function.
2020-06-29 | GSE136662 | GEO
Project description:Post-transcriptional modifications to messenger RNAs (mRNAs) have the potential to alter the biological function of this important class of biomolecules. The study of mRNA modifications is a rapidly emerging field, and the full complement of chemical modifications in mRNAs is not yet established. We sought to identify and quantify the modifications present in yeast mRNAs using an ultra-high performance liquid chromatography tandem mass spectrometry method to detect 40 nucleoside variations in parallel. We observe six modified nucleosides with high confidence in highly purified mRNA samples (N7-methylguanosine, N6-methyladenosine, 2’-O-methylguanosine, 2’-O-methylcytidine, N4-acetylcytidine and 5-formylcytidine), and identify the yeast protein responsible for N4-acetylcytidine incorporation in mRNAs, Rra1. Additionally, we find that mRNA modification levels change in response to heat shock, glucose starvation and/or oxidative stress. This work expands the repertoire of potential chemical modifications in mRNAs, and highlights the value of integrating mass spectrometry tools in the mRNA modification discovery and characterization pipeline.
2019-06-20 | GSE126405 | GEO
Project description:Autophagy phenomenon is an essential mechanism to regulate cell homeostasis and is activated by various stresses such as nutrient starvation. It is well known that when autophagy is activated and how important components in the cytoplasm cause a series of reactions, but the regulatory mechanism of transcription in the nucleus is poorly known. Here, we identify that histone demethylase KDM3A plays a crucial role in the transcription of autophagy and lysosomal genes. Notably, KDM3A is increased in transcriptional levels in both glucose and amino acid starvation. Especially, transcriptional increase of histone demethylase in response to glucose starvation is dependent on AMP-activated protein kinase (AMPK). Furthermore, genome-wide analysis reveals that KDM3A acts as a co-activator in the expression of autophagy and lysosomal genes. Our finding of histone demethylase signaling cascade in nucleus, modulating histone demethylation signature is one of the predominant epigenetic event in autophagy activation, thereby providing the functional and mechanistic link between epigenetic control and transcriptional regulation of autophagy upon nutrient starvation.
2020-08-30 | GSE103573 | GEO
Project description:To learn about the cellular processes involved in Mg2+ transport and the mechanisms allowing cells to cope with low Mg2+ availability, we performed RNA expression profiling experiments, and followed changes in gene activity upon Mg2+ depletion on a genome-wide scale. A striking portion of genes up-regulated under Mg2+ depletion is also induced by high Ca2+ and/or alkalinization. Among the genes significantly up-regulated by Mg2+ starvation, Ca2+ stress and alkalinization are ENA1 (encoding a P-type ATPase sodium pump) and PHO89 (encoding a sodium/phosphate cotransporter). We show that up-regulation of these genes is dependent on the calcineurin/Crz1p signaling pathway. Similarly to Ca2+ stress, Mg2+ starvation induces translocation of the transcription factor Crz1p from the cytoplasm into the nucleus. The up-regulation of ENA1 and PHO89 upon Mg2+ starvation depends on extracellular Ca2+. Using fluorescence resonance energy transfer microscopy we demonstrate that removal of Mg2+ results in an immediate increase in free cytoplasmic Ca2+. This effect is dependent on external Ca2+. Results presented indicate that Mg2+ depletion in yeast cells leads to enhanced cellular Ca2+ concentrations, which activate the Crz1p/calcineurin pathway. We provide evidence that calcineurin/Crz1p signaling is crucial for yeast cells to cope with Mg2+ depletion stress. Keywords: stress response (magnesium starvation)
2007-03-08 | GSE6687 | GEO