Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE64468 | GEO | 2014/12/24
SECONDARY ACCESSION(S): PRJNA271078
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. 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:In oenological conditions, yeasts are exposed to several stresses and Saccharomyces cerevisiae strains respond modifying their transcriptional program. Yeast flocculation is a social trait that permits to the cells to escape to hostile conditions by sedimentation. This behaviour is mainly due to the presence in the genome of FLO greenbeards genes. In order to understand the role of flocculation in stress response a flocculent S. cerevisiae wine strain and his FLO5 deleted strain were submitted to standard and second fermentation. At the middle of these two processes a genome wide expression analysis was performed. Results showed that while the FLO5 deleted strain was engaged to a re-organization of cell wall and to find a different way to adhere, flocculent yeast presented a proteic stress response and an up-regulation of genes involved in superior alcohols production. Obtained data confirmed the importance of FLO5 in flocculation phenotype and highlight the role of flocculation in stress response.
2017-11-30 | GSE99465 | GEO
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: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: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: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. We generated 2 overexpression microarrays and 1 deletion microarray with dye swaps, 2 overexpression single replicate microarray experiments, 3 deletion single replicate microarray experiments, and 3 single replicate ChIP-chip experiments. The effect of the mutant strains were all compared to wild type or empty vector strains.
2012-11-02 | E-GEOD-41730 | biostudies-arrayexpress
Project description:The transcriptome from a S. cerevisiae tup1 deletion mutant was one of the first comprehensive yeast transcriptomes published. Subsequent transcriptomes from tup1 and cyc8 mutants firmly established the Tup1-Cyc8 complex as predominantly acting as a repressor of gene transcription. However, transcriptomes from tup1/cyc8 gene deletion or conditional mutants would all have been influenced by the striking flocculation phenotypes that these mutants display. In this study, we have separated the impact of flocculation from the transcriptome in a cyc8 conditional mutant to reveal those genes (i) subject solely to Cyc8p dependent regulation, (ii) regulated by flocculation only, and (iii) regulated by Cyc8p and further influenced by flocculation. We reveal an improved Cyc8p transcriptome that includes newly identified Cyc8p-regulated genes that were masked by the flocculation phenotype and excludes genes which were indirectly influenced by flocculation and not regulated by Cyc8p. Furthermore, we show evidence to suggest that flocculation exerts a complex and potentially dynamic influence upon global gene transcription. These data should be of interest to future studies into the mechanism of action of the Tup1-Cyc8 complex and to those involved in understanding the development of flocculation and its impact upon cell function.
2023-12-05 | GSE248550 | GEO
Project description:Sexual reproduction can promote genetic diversity in eukaryotes, and yet many pathogenic fungi have been labeled as obligate asexual species. It is becoming increasingly clear, however, that cryptic sexual programs may exist in some species, and that efficient mating requires the necessary developmental switch to be triggered. In this study we investigate Candida tropicalis, an important human fungal pathogen that has been reported to be asexual. Significantly, we demonstrate that C. tropicalis uses a phenotypic switch to regulate a cryptic program of sexual mating. Thus, diploid a and α cells must undergo a developmental transition to the mating-competent form, and only then does efficient cell-cell conjugation take place resulting in the formation of stable a/α tetraploids. We show that both the phenotypic switch and sexual mating depend on the conserved transcriptional regulator Wor1, which is regulated by temperature in other fungal species. In contrast, C. tropicalis mating occurs efficiently at both 25 °C and 37 °C, suggesting that it could occur in the mammalian host and have direct consequences for the outcome of an infection. Transcriptional profiling further reveals that ≈400 genes are differentially expressed between the two phenotypic states, including the regulatory factor Wor1. Taken together, our results demonstrate that C. tropicalis has a unique sexual program, and that entry to this program is controlled via a Wor1-mediated, metastable switch. These observations have direct implications for the regulation and evolution of cryptic sexual programs in related fungal pathogens.
2012-08-28 | GSE40179 | GEO
Project description:Daphnia infochemicals can induce defensive responses in microalgae Scenedesmus spp., including colony formation and flocculation. We investigated the phenomenon using a combination of microalgal biology, physiological ecology, and quantitative isobaric tagging (iTRAQ) proteomics. We have discovered that flocculation as a defense response occurs at the early ‘alarm’ phase and requires increased energy resources, with an important role proposed in cysteine synthesis. It appears to be initially stimulated by the production of an extracellular matrix (mainly composed ofby polysaccharides and fatty acids), and later sustained at the ‘acclimation’ stage through Mitogen-activated protein kinase (MAPK) signalling cascades. Defensive strategies leading to colony formation required investment into fatty acids metabolism, to ensure the accurate separation of membranes during cell division. Furthermore, higher energy demands were required at the alarm phase which subsequently decreased at the acclimation stage, thus suggesting a trade-off between colony formation and support of floc form.
2020-05-06 | PXD014153 | Pride
Project description:Photoautotrophic cyanobacteria assimilate the greenhouse gas carbon dioxide as their sole carbon source for producing useful bioproducts. However, harvesting the cells from their liquid media is a major bottleneck in the process. Thus, an easy-to-harvest method, such as auto-flocculation, is desirable. Here, we found that cyanobacterium Synechocystis sp. PCC 6803 co-flocculated with a natural fungal contamination in the presence of the antibiotic erythromycin (EM) but not without EM. The fungi in the co-flocculated biomass were isolated and found to consist of five species with the filamentous Purpureocillium lilacinum and Aspergillus protuberus making up 71% of the overall fungal population. The optimal co-cultivation for flocculation was an initial 5 mg (fresh weight) of fungi, an initial cell density of Synechocystis of 0.2 OD730, 10 µM EM, and 14 days of cultivation in 100 mL of BG11 medium with no organic compound. This yielded 248 ± 28 mg/L of the Synechocystis-fungi flocculated biomass from 560 ± 35 mg/L of total biomass, a 44 ± 2 % biomass flocculation efficiency. Furthermore, the EM treated Synechocystis cells in the Synechocystis-fungi flocculate had a normal cell color and morphology, while those in the axenic suspension exhibited strong chlorosis. Thus, the occurrence of the Synechocystis-fungi flocculation was mediated by EM, and the co-flocculation with the fungi helped Synechocystis to alleviate the negative effect of EM. Transcriptomic analysis of suspended and flocculated (with the fungi) Synechocystis cells suggested that the EM-mediated co-flocculation was a result of down-regulation of the minor pilin genes and up-regulation of several genes including the chaperone gene for pilin regulation, the S-layer protein genes, the exopolysaccharide-polymerization gene, and the genes for signaling proteins involved in cell attachment and abiotic-stress responses. The EM treatment may be applied in the co-culture between other cyanobacteria and fungi to mediate cell bio-flocculation.
2024-05-01 | GSE256451 | GEO