Different genetic responses to oenological conditions between a flocculent wine yeast and its FLO5 deleted strain: insights from the transcriptome
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE99465 | GEO | 2017/11/30
SECONDARY ACCESSION(S): PRJNA388508
REPOSITORIES: GEO
Similar Datasets
Project description:Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper, the role of Flo1p in mating was demonstrated by showing that the mating efficiency, which contributes to the increased survival rate as well by generating genetic variability, is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation.
2014-12-24 | GSE64468 | GEO
Project description:Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper, the role of Flo1p in mating was demonstrated by showing that the mating efficiency, which contributes to the increased survival rate as well by generating genetic variability, is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation. S. cerevisiae strains BY4742 WT, BY4742::FLO8 and BY4742 [FLO1] were grown in microgravity and 1-g. A transcriptomic analysis was performed and the transcriptome data were integrated with the high quality protein-protein interaction networks. The identified high score sub-networks (qvalue < 0.001) were considered and further evaluated concerning their GO enrichment using a hypogeometric test.
2014-12-24 | E-GEOD-64468 | biostudies-arrayexpress
Project description:The regulation of flocculation, surface adhesion and invasive growth in the fission yeast Schizosaccharomyces pombe has focused primarily at the transcriptional level, but little is known with regards to posttranscriptional control. Here, we identified the Pumilio protein Pfr1 as a novel posttranscriptional regulator of these processes. Deletion of pfr1+ prevented flocculation, surface adhesion and invasive growth under inducing conditions, while overexpression of pfr1+ was sufficient to trigger flocculation. The flocculent phenotype of pfr1+ overexpression was dependent on the presence of the Gsf2 flocculin, but not on the Mbx2, Cbf12 and Adn3 transcription factors. In addition, we used RNA immunoprecipitation and expression microarrays to identify pvg1+ and SPBPB7E8.01, which encode a galactose pyruvyltransferase and glycophosphatidylinositol membrane protein, respectively, as putative mRNA targets potentially degraded by Pfr1. The mRNAs of these genes were upregulated and downregulated in the pfr1 deletion and overexpression strains, respectively, and contained putative binding sites in the 3’-untranslated region. We also discovered that ccr4+ and ste13+, which encode components of the mRNA decay machinery, were required for these processes, but did not suppress the pfr1+ overexpression flocculent phenotype when deleted. This data suggest that these processes in S. pombe involve multiple posttranscriptional-regulatory pathways of which one requires Pfr1.
2016-03-24 | GSE79537 | GEO
Project description:Effect of either FLO8 or MSS11 deletion and -overexpression on yeast transcript profiles compared to wild type in laboratory yeast strains Σ1278b and S288c - also the effect of FLO11 (MUC1) overexpression in the Σ1278b genetic background The aim of this study was to (1) perform a repeat analysis (to improve statistical analysis of these data sets) similar to data submitted previously (GSE17716) and also (2) study the effect of FLO11 over-expression on the transcriptome. Background: The outer cell wall of the yeast Saccharomyces cerevisiae serves as the interface with the surrounding environment and defines cell-cell and cell-surface interactions. Many of these interactions are facilitated by specific adhesins that belong to the Flo protein family. This family of mannoproteins has been implicated in phenotypes such as flocculation and substrate adhesion as well as pseudohyphal growth. Genetic data strongly suggest that individual Flo proteins are responsible for many specific cellular adhesion phenotypes. However, it remains unclear whether such phenotypes are determined solely by the nature of the expressed FLO genes or rather the result of a combination of FLO gene expression and other cell wall properties and cell wall proteins. Mss11p has been shown to be a central element of FLO1 and FLO11 gene regulation and acts together with the cAMP-PKA-dependent transcription factor Flo8p. We use genome wide transcript analysis to identify genes that are direct ly or indirectly regulated by Mss11p in the genetic backgrounds: Sigma1278b and S288c. Sigma 1278b is the strain historically used for the study of pseudohyphae (FLO11 expression) but we also included S288c as this strain is widely used in the research community and was used to determine the first full genome sequence (Thus correspond with SGD information). We also compare this data with transcriptome data from Sigma 1278b yeast over-expressing FLO8 to compare similarities/differences between these two signalling factors. Finally the effect of FLO11 over-expression in Sigma1278b on global transcription is studied so that we can differentiate between "direct" gene targets of Flo8p or Mss11p, and those regulated as a result by the "indirect" effect caused by modified cell wall Flo11p levels. We used two laboratory yeast strains that behave different with regard to adhesion phenotypes. By comparing yeast deleted in either FLO8 or MSS11 to wild type, or yeast overexpressing these genes, in both genetic backgrounds, we investigate the role of Flo8p and Mss11p on yeast transcription. In addition the effect of the over-expression of the adhesin gene FLO11 was studied in Sigma 1278b. By using similar growth conditions to what we use for adhesion phenotype determination we aim to correlate transcription profile changes to yeast behaviour (phenotypes).
2011-09-20 | E-GEOD-29371 | biostudies-arrayexpress
Project description:The regulation of flocculation, surface adhesion and invasive growth in the fission yeast Schizosaccharomyces pombe has focused primarily at the transcriptional level, but little is known with regards to posttranscriptional control. Here, we identified the Pumilio protein Pfr1 as a novel posttranscriptional regulator of these processes. Deletion of pfr1+ prevented flocculation, surface adhesion and invasive growth under inducing conditions, while overexpression of pfr1+ was sufficient to trigger flocculation. The flocculent phenotype of pfr1+ overexpression was dependent on the presence of the Gsf2 flocculin, but not on the Mbx2, Cbf12 and Adn3 transcription factors. In addition, we used RNA immunoprecipitation and expression microarrays to identify pvg1+ and SPBPB7E8.01, which encode a galactose pyruvyltransferase and glycophosphatidylinositol membrane protein, respectively, as putative mRNA targets potentially degraded by Pfr1. The mRNAs of these genes were upregulated and downregulated in the pfr1 deletion and overexpression strains, respectively, and contained putative binding sites in the 3â-untranslated region. We also discovered that ccr4+ and ste13+, which encode components of the mRNA decay machinery, were required for these processes, but did not suppress the pfr1+ overexpression flocculent phenotype when deleted. This data suggest that these processes in S. pombe involve multiple posttranscriptional-regulatory pathways of which one requires Pfr1. We generated 2 overexpression microarrays with dye swap that were biological replicates, 2 deletion microarrys with dye swap. Mutants samples were compared to empty vector control or wild type. 1 RIP-chip array was generated with IP rna compared to total RNA from the sample.
2016-03-24 | E-GEOD-79537 | biostudies-arrayexpress
Project description:Different genetic responses to oenological conditions between a flocculent wine yeast and its FLO5 deleted strain: insights from the transcriptome
| PRJNA388508 | ENA
Project description:The budding yeast, Saccharomyces cerevisiae, has emerged as an archetype of eukaryotic cell biology. Here we show that S. cerevisiae is also a model for the evolution of cooperative behavior by revisiting flocculation, a self-adherence phenotype lacking in most laboratory strains. Expression of the gene FLO1 in the laboratory strain S288C restores flocculation, an altered physiological state, reminiscent of bacterial biofilms. Flocculation protects the FLO1-expressing cells from multiple stresses, including antimicrobials and ethanol. Furthermore, FLO1+ cells avoid exploitation by non-expressing flo1 cells by self/non-self recognition: FLO1+ cells preferentially stick to one another, regardless of genetic relatedness across the rest of the genome. Flocculation, therefore, is driven by one of a few known “green beard genes”, which direct cooperation towards other carriers of the same gene. Moreover, FLO1 is highly variable among strains both in expression and in sequence, suggesting that flocculation in S. cerevisiae is a dynamic, rapidly-evolving social trait. This dataset contains raw transcriptome data of flocculating cells (that express FLO1 driven by the GAL1 promoter) and non-flocculating cells (that do not express FLO1).
2008-09-16 | GSE12786 | GEO
Project description:In the fission yeast Schizosaccharomyces pombe, the transcriptional-regulatory network that governs flocculation remains poorly understood. Here, we systematically screened an array of transcription factor deletion and overexpression strains for flocculation and performed microarray expression profiling and ChIP-chip analysis to identify the flocculin target genes. We identified five transcription factors that displayed novel roles in the activation or inhibition of flocculation (Rfl1, Adn2, Adn3, Sre2, and Yox1), in addition to the previously-known Mbx2, Cbf11 and Cbf12 regulators. Overexpression of mbx2+ and deletion of rfl1+ resulted in strong flocculation and transcriptional upregulation of gsf2+/pfl1+ and several other putative flocculin genes (pfl2+-pfl9+). Overexpression of the pfl+ genes singly was sufficient to trigger flocculation, and enhanced flocculation was observed in several combinations of double pfl+ overexpression. Among the pfl1+ genes, only loss of gsf2+ abrogated the flocculent phenotype of all the transcription factor mutants and prevented flocculation when cells were grown in inducing medium containing glycerol and ethanol as the carbon source, thereby indicating that Gsf2 is the dominant flocculin. In contrast, the mild flocculation of adn2+ or adn3+ overexpression was likely mediated by the transcriptional activation of cell wall-remodeling genes including gas2+, psu1+, and SPAC4H3.03c. We also discovered that Rfl1, Mbx2, and Cbf12 displayed transcriptional autoregulation, and Rfl1 repressed gsf2+ expression in an inhibitory feed-forward loop involving mbx2+. These results reveal that flocculation in S. pombe is regulated by a complex network of multiple transcription factors and target genes encoding flocculins and cell wall-remodeling enzymes. Moreover, comparisons between the flocculation transcriptional regulatory networks of Saccharomyces cerevisiae and S. pombe indicate substantial rewiring of transcription factors and cis-regulatory sequences.
2012-11-02 | GSE41730 | GEO
Project description:Second fermentation in a bottle supposes such specific conditions that undergo yeasts to a set of stress situations like high ethanol, low nitrogen, low pH or sub-optimal temperature. Also, yeast have to grow until 1 or 2 generations and ferment all sugar available while they resist increasing CO2 pressure produced along with fermentation. Because of this, yeast for second fermentation must be selected depending on different technological criteria such as resistance to ethanol, pressure, high flocculation capacity, and good autolytic and foaming properties. All of these stress factors appear sequentially or simultaneously, and their superposition could amplify their inhibitory effects over yeast growth. Considering all of the above, it has supposed interesting to characterize the adaptive response of commercial yeast strain EC1118 during second-fermentation experiments under oenological/industrial conditions by transcriptomic profiling. We have pointed ethanol as the most relevant environmental condition in the induction of genes involved in respiratory metabolism, oxidative stress, autophagy, vacuolar and peroxisomal function, after comparison between time-course transcriptomic analysis in alcoholic fermentation and transcriptomic profiling in second fermentation. Other examples of parallelism include overexpression of cellular homeostasis and sugar metabolism genes. Finally, this study brings out the role of low-temperature on yeast physiology during second-fermentation.
2011-05-31 | GSE29273 | GEO
Project description:Effect of either FLO8 or MSS11 deletion and -overexpression on yeast transcript profiles compared to wild type in laboratory yeast strains Σ1278b and S288c - also the effect of FLO11 (MUC1) overexpression in the Σ1278b genetic background The aim of this study was to (1) perform a repeat analysis (to improve statistical analysis of these data sets) similar to data submitted previously (GSE17716) and also (2) study the effect of FLO11 over-expression on the transcriptome. Background: The outer cell wall of the yeast Saccharomyces cerevisiae serves as the interface with the surrounding environment and defines cell-cell and cell-surface interactions. Many of these interactions are facilitated by specific adhesins that belong to the Flo protein family. This family of mannoproteins has been implicated in phenotypes such as flocculation and substrate adhesion as well as pseudohyphal growth. Genetic data strongly suggest that individual Flo proteins are responsible for many specific cellular adhesion phenotypes. However, it remains unclear whether such phenotypes are determined solely by the nature of the expressed FLO genes or rather the result of a combination of FLO gene expression and other cell wall properties and cell wall proteins. Mss11p has been shown to be a central element of FLO1 and FLO11 gene regulation and acts together with the cAMP-PKA-dependent transcription factor Flo8p. We use genome wide transcript analysis to identify genes that are direct ly or indirectly regulated by Mss11p in the genetic backgrounds: Sigma1278b and S288c. Sigma 1278b is the strain historically used for the study of pseudohyphae (FLO11 expression) but we also included S288c as this strain is widely used in the research community and was used to determine the first full genome sequence (Thus correspond with SGD information). We also compare this data with transcriptome data from Sigma 1278b yeast over-expressing FLO8 to compare similarities/differences between these two signalling factors. Finally the effect of FLO11 over-expression in Sigma1278b on global transcription is studied so that we can differentiate between "direct" gene targets of Flo8p or Mss11p, and those regulated as a result by the "indirect" effect caused by modified cell wall Flo11p levels.
2011-09-21 | GSE29371 | GEO