Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA140577 | ENA |
REPOSITORIES: ENA
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Project description:Gene expression in Eukaryotic cells is profoundly shaped by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. Here we report the use of a splicing isoform specific microarray platform to investigate the effects of a host of diverse stress conditions on both splicing pre-mRNA fate. Interestingly, We find that diverse stresses cause distinct patterns of changes at the level of pre- mRNA processing. The responses we observed are most dramatic for the RPGs and can be categorized into three major classes. The first is characterized by accumulation of RPG pre-mRNA and is seen in multiple types of amino acid starvation regimes; the magnitude of splicing inhibition correlates with the severity of the stress. The second class is characterized by a rapid decrease in both pre- and mature RPG mRNA and is seen in many stresses that inactivate the TORC1 kinase complex. These decreases depend on nuclear turn-over of the intron-containing pre-RNAs. The third class is characterized by a decrease in RPG pre-mRNA with only a modest reduction in the mature species; this response is observed in hyperosmotic and cation-toxic stresses. We show that casein kinase 2 (CK2) makes important contributions to the changes in pre-mRNA processing, particularly for the first two classes of stress responses. In total, our data suggest that complex post-transcriptional programs cooperate to fine-tune expression of intron-containing transcripts in budding yeast. Splicing-specific microarrays were used to assay the changes to splicing caused by a wide variety of environmental stresses and nutrient conditions.
2011-07-01 | E-GEOD-28919 | biostudies-arrayexpress
Project description:Gene expression in Eukaryotic cells is profoundly shaped by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. Here we report the use of a splicing isoform specific microarray platform to investigate the effects of a host of diverse stress conditions on both splicing pre-mRNA fate. Interestingly, We find that diverse stresses cause distinct patterns of changes at the level of pre- mRNA processing. The responses we observed are most dramatic for the RPGs and can be categorized into three major classes. The first is characterized by accumulation of RPG pre-mRNA and is seen in multiple types of amino acid starvation regimes; the magnitude of splicing inhibition correlates with the severity of the stress. The second class is characterized by a rapid decrease in both pre- and mature RPG mRNA and is seen in many stresses that inactivate the TORC1 kinase complex. These decreases depend on nuclear turn-over of the intron-containing pre-RNAs. The third class is characterized by a decrease in RPG pre-mRNA with only a modest reduction in the mature species; this response is observed in hyperosmotic and cation-toxic stresses. We show that casein kinase 2 (CK2) makes important contributions to the changes in pre-mRNA processing, particularly for the first two classes of stress responses. In total, our data suggest that complex post-transcriptional programs cooperate to fine-tune expression of intron-containing transcripts in budding yeast.
2011-07-01 | GSE28919 | GEO
Project description:The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. cerevisiae strains, and elucidated the genetic variations correlated with its advantaged traits (higher ethanol yield under sever conditions and better tolerance to multiple stresses compared to an S288c derived laboratory strain BYZ1). Firstly, pulse-field gel electrophoresis combined with array-comparative genomic hybridization was used to compare the genome structure of industrial strains and the laboratory strain BYZ1.
2011-09-15 | GSE31872 | GEO
Project description:Theory and experiment suggest that organisms would benefit from pre-adaptation to future stressors based on reproducible environmental fluctuations experienced by their ancestors. Yet mechanisms driving pre-adaptation remain enigmatic. We report that the [SMAUG+] prion allows yeast to anticipate nutrient repletion after periods of starvation, providing a strong selective advantage. By transforming the landscape of post-transcriptional gene expression, [SMAUG+] regulates the decision between two broad growth and survival strategies: mitotic proliferation or meiotic differentiation into a stress-resistant state. [SMAUG+] is common in laboratory yeast strains, where standard propagation practice produces regular cycles of nutrient scarcity followed by repletion. Distinct [SMAUG+] variants are also widespread in wild yeast isolates from multiple niches, establishing that prion polymorphs can be utilized in natural populations. Our data provide a striking example of how protein-based epigenetic switches, hidden in plain sight, can establish a transgenerational memory that integrates adaptive prediction into developmental decisions.
2020-02-05 | GSE138559 | GEO
Project description:Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other.
2012-04-17 | GSE30054 | GEO
Project description:The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. cerevisiae strain YJS329, and elucidated the genetic variations correlated with its advantaged traits (higher ethanol yield under sever conditions and better tolerance to multiple stresses compared to an S288c derived laboratory strain BYZ1). Firstly, pulse-field gel electrophoresis combined with array-comparative genomic hybridization was used to compare the genome structure of YJS329 and the laboratory strain BYZ1. Yeast cells were cultured in YPD medium. Genome DNA of YJS329 and BYZ1 was isolated and sonicated. The average length of DNA fragments was 200-1000bp. The shearing DNA was labeled with Cy5/Cy3 and hybridized to NimbleGen S.cerevisiae Whole-Genome Tiling arrays, which is single array design containing all chromosomes with 32bp median probe spacing and totally covered by ~385,000 probes. Scanning was performed with the Axon GenePix 4000B microarray scanner.
2011-09-14 | E-GEOD-31872 | biostudies-arrayexpress
Project description:Production of D-xylonate in the yeast S. cerevisiae represents an example of bioprocess development for more sustainable production of value-added chemicals from cheap raw material or waste. Previously it was shown that the production of D-xylonate led to its significant intracellular accumulation and to dramatic loss of viability during the production process. In order to identify the physiological or pathological responses associated with D-xylonate production, we performed a time-course transcriptome analysis of D-xylonate production in yeast cultivated in a bioreactor. Comparison of the transcriptomes of D-xylonate producing strain with control strain showed considerably higher expression in the xylonate producing strain of the genes controlled by the cell wall integrity pathway (CWI) and of some genes previously identified as upregulated in response to the organic acid stress. Surprisingly, also genes encoding proteins involved in translation, ribosome structure and RNA metabolism – the processes commonly found to be down-regulated under virtually every condition causing cellular stress – were upregulated during the D-xylonate production. The overall transcriptional responses were, therefore, very dissimilar to those previously reported as being associated with diverse stresses including the organic acid treatment and production. In addition, it was observed that the consumption of ethanol was slower and the level of trehalose was lower in the D-xylonate producing strain. Validation experiments including Slt2 kinase phosphorylation profiles and the quantitative PCR analyses of selected gene showed remarkably good match with our findings and confirmed the observations made in the transcriptome analysis. The production of organic acids has a major impact on the physiology of yeast cells. There is, however, very limited overlap at the transcriptional level in responses to treatment or production of different acids. The loss of viability, observed during production and accumulation of D-xylonate, seems to be caused by erroneous interpretation of environmental signals causing a failure in entering the stationary phase and eventually leading to depletion of scarce resources by the affected cells. This, together with intracellular acidification, inevitably results in cell death.
2014-11-18 | GSE52736 | GEO
Project description:Budding yeast mRNA export and processing factor localization
| PRJNA154681 | ENA
Project description:Genetic and environmental stresses are known factors that influence an organisms phenotype. Time is rarely taken into consideration when studying phenotypic changes in cells. Time-resolved microarray data revealed genome-wide transcriptional changes in yeast strain CEN.PK122 oscillating with~2 periods. We mapped the global patterns of transcriptional oscillationsinto a 3-dimensional map to represent different cellular phenotypes ofoscillation period. This map shows the dynamic nature of transcripts through time and concentration space, and that they are ordered and coupled to each other. High-resolution samples over time were collected for CEN.PK122 oscillating with 2 h period.
2012-04-16 | E-GEOD-30054 | biostudies-arrayexpress
Project description:We characterize the genome-wide transcription response of four related yeast species and two strains to equivalent environmental stresses. Keywords: Comparative analysis of gene expression across species.
2006-03-31 | GSE3406 | GEO