Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA308295 | ENA |
REPOSITORIES: ENA
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Project description:The yeast Saccharomyces cerevisiae is a model for biology and is also one of the most important microorganisms for food and drink production. Surprisingly, only a few genes involved in the adaptation to anthropic niches have been described until now. Wine fermentation and flor aging, which are performed by strains from two closely related groups of yeast, are two technologies that have opposite approaches toward oxygen, which results in contrasting lifestyles for yeast: fermentation growth on grape for wine yeast, and biofilm aerobic growth on ethanol and glycerol contained in wine for flor strains. This pair of environments and the associated yeast populations can be a model for studying adaptation to anthropic environments. In this project, we have obtained high-quality genome sequences of 20 yeast strains from 9 flor yeast, 9 wine yeast as well as EC1118 and haploid derivative 59A. Phylogeny and population structure analysis, based on GATK genotyping, enable us to characterize a group of flor yeast that is clearly different from wine yeast. A comparison of the genomes of wine and flor yeasts using various methods (PCA, nucleotidic diversity, McDonald Kreitman test, potentially impacted genes according to SIFT) enabled us to note divergent regions, or genes, with potential non-neutral evolution, and highly variant genes. The results of these genomic comparisons are echoed by the comparison of a wine and a flor yeast transcriptome. These methods, as expected, highlight key genes that are involved in FLO11 regulation as well as in biofilm growth, but they also revealed the presence of many allelic variations in genes that are involved in the sensing and regulation of osmotic pressure (such as SLN1, HKR1, SSK22, AQY2) and specific metabolic traits, such as the fructophily of flor yeast, which carry a fructophile allele of HXT3. More remarkable is the accumulation of mutations in multiple genes, which creates a pattern of convergent mutations in regulatory networks, as seen in FLO11 regulation or the HOG MAP kinase pathway. The rewiring of these regulatory networks is clearly one of the hallmarks of domestication for the flor yeast genome. Data presented here correspond to the comparison of Flor yeast P3-D5 and wine yeast K1-280-2B transcriptomes under conditions potentially enabling the production of a biofilm.
2018-01-31 | GSE76667 | GEO
Project description:Wine biological aging is a wine making process used to produce specific beverages in several countries in Europe, including Spain, Italy, France, and Hungary. This process involves the formation of a velum at the surface of the wine. Here, we present the first large scale comparison of all European flor strains involved in this process. We inferred the population structure of these European flor strains from their microsatellite genotype diversity and analyzed their ploidy. We show that almost all of these flor strains belong to the same cluster and are diploid, except for a few Spanish strains. Comparison of the array hybridization profile of six flor strains originating from these four countries, with that of three wine strains did not reveal any large segmental amplification. Nonetheless, some genes, including YKL221W/MCH2 and YKL222C, were amplified in the genome of four out of six flor strains. Finally, we correlated ICR1 ncRNA and FLO11 polymorphisms with flor yeast population structure, and associate the presence of wild type ICR1 and a long Flo11p with thin velum formation in a cluster of Jura strains. These results provide new insight into the diversity of flor yeast and show that combinations of different adaptive changes can lead to an increase of hydrophobicity and affect velum formation.
2014-06-01 | GSE55925 | GEO
Project description:Fungal group III histidine kinases are the molecular targets of some classes of fungicides. In contrast to the yeast Saccharomyces cerevisiae, the fungal pathogen Candida albicans possesses a group III histidine kinase, CaNik1p, also called Cos1p. To investigate the function of CaNIK1, the gene was expressed in S. cerevisiae. The transformants became susceptible to antifungal compounds to which the wild-type strain is resistant. The susceptibility was related to the activation of the MAP kinase Hog1p of the osmotic stress response pathway. Gene expression analysis revealed a strong overlap of the responses to osmotic stress and to fludioxonil at early time points. While the response to fludioxonil persisted, the response to osmotic stress was diminished with time.
2014-02-01 | GSE25002 | GEO
Project description:Combined therapy with anti-BRAF plus anti-MEK is currently used as first-line treatment of patients with metastatic melanomas harboring the somatic BRAF V600E mutation. However, the main issue with targeted therapy is the acquisition of tumor cell resistance. In 70% of resistant melanoma cells, the resistant process consists in epithelial-to-mesenchymal transition (EMT). This process called phenotype switching makes melanoma cells more invasive. Its signature is characterized by MITF low, AXL high, and actin cytoskeleton reorganization through RhoA activation. In parallel of this phenotype switching phase, the resistant cells exhibit an anarchic cell proliferation due to hyper-activation of the MAP kinase pathway. We show that a majority of human melanoma overexpress discoidin domain receptor 2 (DDR2) after treatment. The same result was found in resistant cell lines presenting phenotype switching compared to the corresponding sensitive cell lines. We demonstrate that DDR2 inhibition induces a decrease in AXL expression and reduces stress fiber formation in resistant melanoma cell lines. In this phenotype switching context, we report that DDR2 control cell and tumor proliferation through the MAP kinase pathway in resistant cells in vitro and in vivo. Therefore, inhibition of DDR2 could be a new and promising strategy for countering this resistance mechanism.
2023-05-02 | PXD028292 | Pride
Project description:The role of the protein kinase-A pathway in the response to alkaline pH stress in yeast
| PRJNA137841 | ENA
Project description:Wine biological ageing is led in different countries in Europe: Spain, Italy, France, and Hungary, but until now no comparison of all these flor strains has been led. In this manuscript we investigated the population structure of these European flor strains from their microsatellite genotypes and analysed as well as their ploidy. We showed that almost all of these strains belong to the same cluster, and are mainly diploids. In order to detect a shared amplification pattern, we compared the hybridization profile on array of 6 flor strains from these four countries, and found only 2 genes amplified in the genome of 4 strains. Finally FLO11 polymorphism analysis revealed that most strains carry a 111 deletion in ICR1 non coding RNA, except a group of Jura Flor strains, which in contrast presented longer central core of the protein Flo11p. These results show that amplification is very likely not the main mechanism leading to the adaptation of flor yeast, and suggest that different adaptive itineraries can leading to an increase of hydrophobicity and velum formation. Wine and flor strains hybridization on affymetrix yeast2 arrays are compared to S288C Each strain is compared to S288C and is hybridized in duplicate or triplicate
2014-06-01 | E-GEOD-55925 | biostudies-arrayexpress
Project description:Expression profiling of yeast kinase and phosphatase knockouts
| PRJNA133899 | ENA
Project description:In response to carbon source switching from glucose to non-glucose, such as ethanol and galactose, yeast cells can directionally preprogram cellular metabolism to efficiently utilize the nutrients. However, the understanding of cellular responsive network to utilize a non-natural carbon source, such as xylose, is limited due to the incomplete knowledge on the xylose response mechanisms. Here, through optimization of the xylose assimilation pathway together with combinational evaluation of reported targets, we generated a series of mutants with varied growth ability. However, understanding how cells respond to xylose and remodel cellular metabolic network is far insufficient based on current information. Therefore, genome-scale transcriptional analysis was performed to unravel the cellular reprograming mechanisms underlying the improved growth phenotype.
2021-01-01 | GSE151478 | GEO
Project description:Fungal group III histidine kinases are the molecular targets of some classes of fungicides. In contrast to the yeast Saccharomyces cerevisiae, the fungal pathogen Candida albicans possesses a group III histidine kinase, CaNik1p, also called Cos1p. To investigate the function of CaNIK1, the gene was expressed in S. cerevisiae. The transformants became susceptible to antifungal compounds to which the wild-type strain is resistant. The susceptibility was related to the activation of the MAP kinase Hog1p of the osmotic stress response pathway. Gene expression analysis revealed a strong overlap of the responses to osmotic stress and to fludioxonil at early time points. While the response to fludioxonil persisted, the response to osmotic stress was diminished with time. S. cerevisiae expressing Candida albicans Nik1p were treated with 10 µg/ml fludioxonil. As a comparison, another culture of S. cerevisiae expressing Candida albicans Nik1p was treated with 1 M sorbitol to induce osmotic stress response. One culture remained untreated as a control. From all cultures, samples were taken after a duration of 15, 30 and 60 min.
2014-02-01 | E-GEOD-25002 | biostudies-arrayexpress