Project description:Short-read RNA-seq was performed on rRNA-depleted RNA isolated from spores of the budding yeast Saccharomyces cerevisiae that were sorted by mating type.
Project description:The budding yeast Saccharomyces cerevisiae is a popular host to be used to produce recombinant proteins. Here we studied three yeast strains with different productivity using the RNA-seq data to elucidate the mechanisms for improving protein production.
Project description:To characterize cellular response to the anti-cancer ruthinium complex KP1019, budding yeast Saccharomyces cerevisiae transcripitonal response to KP1019 was measured using microarray analysis. Although KP1019 molecular mechanism of action remains a matter of debate, the drug has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to characterize KP1019 induced transcriptional changes.
Project description:To characterize cellular response to the anti-cancer ruthinium complex KP1019, budding yeast Saccharomyces cerevisiae transcripitonal response to KP1019 was measured using microarray analysis. Although KP1019 molecular mechanism of action remains a matter of debate, the drug has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to characterize KP1019 induced transcriptional changes. Two concentrations of KP1019 (40 micrograms/mL and 80 micrograms/ml were assayed by microarray analysis to obtain comparative expression data for treated and untreated cells of the budding yeast Saccharomyces cerevisiae (strain BY4741). Two biological replicates of each concentration were done. Each biological replicate was done in duplicate to allow for dye reversal controls.
Project description:<p>Aging is a complex biological process influenced by genetic factors, environmental conditions, and interactions between organisms and their associated microbes. The budding yeast Saccharomyces cerevisiae and the fruit fly Drosophila melanogaster provide complementary model systems for investigating conserved metabolic processes associated with aging and longevity. However, comprehensive metabolomic resources describing how aging-associated microbial genetic alterations influence host metabolic states remain limited.</p><p>In this study, we generated a comprehensive untargeted metabolomics dataset to characterize metabolic alterations associated with aging-related S. cerevisiae deletion strains and their interactions with the D. melanogaster host. The dataset includes liquid chromatography–mass spectrometry (LC–MS)-based metabolomic profiles from 15 yeast strains, including the BY4743 control strain and 14 aging-associated deletion strains, as well as host metabolomic profiles from Drosophila tissues exposed to different yeast interventions. Host samples include intestinal and non-intestinal tissues collected at different life stages, enabling assessment of tissue-specific and age-associated metabolic responses to yeast genetic perturbations.</p><p>The generated dataset contains raw and processed metabolomics data, metabolite annotation information, and comprehensive sample metadata describing biological conditions, genetic backgrounds, tissue sources, intervention groups, and experimental parameters. These data provide a reusable resource for studying yeast-derived metabolic regulation, microbe–host interactions, and age-associated metabolic remodeling.</p><p>This metabolomics resource facilitates integrative analyses of microbial genetic variation, host metabolic adaptation, and conserved aging-related pathways, and supports future investigations into the molecular connections between microbial factors and host physiology.</p>
Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and Y´ subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y´ mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.
