Transcriptional response to weak organic acids in chemostat cultures of Saccharomyces cerevisiae
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE5926 | GEO | 2007/02/27
SECONDARY ACCESSION(S): PRJNA97371
REPOSITORIES: GEO
Similar Datasets
Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with various weak organic acids Experiment Overall Design: The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 2-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume. All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming. The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH. The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1. To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas. A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of acetic acid, sodium benzoate, propionic acid or potassium sorbate to the reservoir media. Triplicate cultivations and microarrays were performed for each condition. Experiment Overall Design: Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications. Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. Experiment Overall Design: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0. **note 2014-04-02: file GSM137686.CEL is truncated.
2009-04-23 | E-GEOD-5926 | biostudies-arrayexpress
Project description:Candida albicans is the most important fungal pathogen of humans, causing severe infections especially in nosocomial and immunocompromised settings. However, it is also the most prevalent fungus of the normal human microbiome, where it shares its habitat with hundreds of trillions of other microbial cells. Despite weak organic acids (WOAs) being among the most abundant metabolites produced by bacterial microbiota, little is known about their effect on C. albicans. Here we employed a sequencing-based profiling strategy to systematically investigate the transcriptional stress response of C. albicans to lactic, acetic, propionic and butyric acid at several time points after treatment. Our data reveal a complex transcriptional response, with individual WOAs triggering unique gene expression profiles and with important differences between acute and chronic exposure. In spite of all these dissimilarities, we found significant overlaps between the gene expression changes induced by each WOA, which lead us to uncover a core transcriptional signature that was unrelated to the general response to low pH. Genes commonly up-regulated by WOAs were enriched in several iron transporters, which was associated with an overall decrease in intracellular iron concentrations. Moreover, chronic exposure to any WOA lead to down-regulation of RNA synthesis and ribosome biogenesis genes, which resulted in significant reduction of total RNA levels in general and of ribosomal RNA in particular. In conclusion, this study suggests that GI microbiota might directly influence C. albicans physiology via production of WOAs, with possible implications of how this fungus interacts with its hosts in both health and disease. Transcriptional profiling of wild-type Candida albicans strain SC5314 under 6 differents condition (2 controls, 4 weak acids) at 4 time points by cDNA deep-sequencing, with 4 biological replicates, on the Illumina HiSeq 2000 platform. 96 total samples were sequenced (6 x 4 x 4).
2015-01-28 | E-GEOD-49310 | biostudies-arrayexpress
Project description:Candida albicans is the most important fungal pathogen of humans, causing severe infections especially in nosocomial and immunocompromised settings. However, it is also the most prevalent fungus of the normal human microbiome, where it shares its habitat with hundreds of trillions of other microbial cells. Despite weak organic acids (WOAs) being among the most abundant metabolites produced by bacterial microbiota, little is known about their effect on C. albicans. Here we employed a sequencing-based profiling strategy to systematically investigate the transcriptional stress response of C. albicans to lactic, acetic, propionic and butyric acid at several time points after treatment. Our data reveal a complex transcriptional response, with individual WOAs triggering unique gene expression profiles and with important differences between acute and chronic exposure. In spite of all these dissimilarities, we found significant overlaps between the gene expression changes induced by each WOA, which lead us to uncover a core transcriptional signature that was unrelated to the general response to low pH. Genes commonly up-regulated by WOAs were enriched in several iron transporters, which was associated with an overall decrease in intracellular iron concentrations. Moreover, chronic exposure to any WOA lead to down-regulation of RNA synthesis and ribosome biogenesis genes, which resulted in significant reduction of total RNA levels in general and of ribosomal RNA in particular. In conclusion, this study suggests that GI microbiota might directly influence C. albicans physiology via production of WOAs, with possible implications of how this fungus interacts with its hosts in both health and disease.
2015-01-28 | GSE49310 | GEO
Project description:Candida albicans is a resident fungus of the human intestinal microflora. Commonly isolated at low abundance in healthy people, C. albicans outcompetes local microbiota during candidiasis episodes. Under normal conditions, members of the human gastrointestinal microbiota were shown to keep C. albicans colonization under control. By releasing weak organic acids (WOAs), bacteria are able to moderate yeast growth. This mechanism displayed a synergistic effect in vitro with the absence of glucose in medium of culture, which underline the complex interaction that C. albicans faces in its natural environment. Inactivation of the transcriptional regulator MIG1 in C. albicans results in a lack of sensitivity to this synergistic outcome. To decipher C. albicans transcriptional responses to glucose, WOAs and the role of MIG1, we performed RNA sequencing on four biological replicates exposed to combinations of these 3 parameters. We were able to characterise the i) glucose response, ii) response to acetic and butyric acid, iii) MIG1 regulation of C. albicans and iv) genes responsible for WOAs resistance. We identified a group of 6 genes linked to WOAs sensitivity in a glucose-MIG1-dependent manner and inactivated one of these genes, the putative glucose transporter HGT16, in a SC5314 wild-type background. As expected, the mutant displayed a partial complementation to WOAs resistance in absence of glucose. This result points towards a mechanism of WOAs sensitivity in C. albicans involving membrane transporters which could be exploited to control yeast colonisation in human body niches.
2017-10-03 | GSE99767 | GEO
Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5. Experiment Overall Design: The laboratory reference strain CEN.PK 113-7D (MATa) was grown at 30 °C in 1.5-L chemostat fermentors (Applikon, Schiedam, The Netherlands) with a working volume of 1-L using an electronic level sensor to maintain a constant volume. All cultures, including the reference, were fed with minimal medium as described by Verduyn et al. (1992) with 25 g L-1 glucose as the limiting nutrient and 0.15 ml L-1 silicone antifoam (BDH, Poole, England) to prevent excessive foaming. The dilution rate was set to 0.10 h-1 and the pH was controlled at 5.0 with the automatic addition (ADI 1031 bio controller, Applikon) of 2 M KOH. The stirrer speed was set at 800 RPM and anaerobicity was maintained by sparging the fermentor with N2 gas at 500 ml min-1. To prevent diffusion of oxygen, the fermentor was equipped with Norprene tubing and Viton O-rings and the medium vessel was also flushed with N2 gas. A comparable degree of weak acid uncoupling was ensured by decreasing the biomass yield to approximately 50% of the reference condition (no organic acids added) with the addition of the appropriate concentration of lactic acid to the reservoir media. Experiment Overall Design: Sampling of chemostat cultures, probe preparation and hybridization to Affymetrix GeneChip microarrays was performed as described previously (Piper et al., 2002), but with the following modifications. Double-stranded cDNA synthesis was carried out using 15 μg of total RNA and the components of the One Cycle cDNA Synthesis Kit (Affymetrix). The double-stranded cDNA was purified (Genechip Sample Cleanup Module, Qiagen) before in vitro transcription and labeling (GeneChip IVT Labeling Kit, Affymetrix). Finally, labeled cRNA was purified (GeneChip Sample Cleanup Module) prior to fragmentation and hybridization of 15 μg of biotinylated cRNA. Experiment Overall Design: Data acquisition was performed using the Affymetrix scanner 3000, quantification of array images and data filtering were performed with the Affymetrix software packages Microarray Suite v5.0, MicroDB v3.0 and Data Mining Tool v3.0.
2008-10-20 | E-GEOD-10066 | biostudies-arrayexpress
Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5. Keywords: response to lactic acid
2008-07-30 | GSE10066 | GEO
Project description:We show that combinations of organic acids and glucose trigger phenotypes associated with the late stage of biotrophy for the maize pathogen Ustilago maydis. These phenotypes include the expression of a set of effectors normally observed only during biotrophic development as well as the formation of melanin associated with sporulation in plant tumors.
2022-12-31 | GSE194157 | GEO
Project description:Rhizospheric organic acids as biostimulants: interactions with soil borne microorganisms and effect on soil biochemical properties
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Project description:Transcriptional response to weak organic acids in chemostat cultures of Saccharomyces cerevisiae
| PRJNA97371 | ENA
Project description:Organic acids production from starch waste by rumen microorganisms
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