Saccharomyces cerevisiae
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PROVIDER: PRJNA119459 | ENA |
REPOSITORIES: ENA
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Project description:Despite the scientific and applied interest in anaerobic metabolism of Saccharomyces cerevisiae, not all genes whose transcription is up-regulated under anaerobic conditions have yet been linked to known transcription factors. Experiments with a reporter construct in which the promoter of the anaerobically up-regulated TIR1 gene was fused to LacZ revealed a complete loss of anaerobic up-regulation in a snf7Δ mutant. Anaerobic up-regulation was restored by expression of a truncated allele of RIM101 that encodes for a constitutively active Rim101p transcription factor. Analysis of LacZ expression in several deletion mutants confirmed that the effect of Snf7p on anaerobic up-regulation of TIR1 involved Rim101p and did not require a functional multi-vesicular body sorting pathway (in which Snf7p also participates). Transcriptome analysis in anaerobic chemostat cultures revealed that 26 additional genes exhibited a Snf7p/Rim101p dependent anaerobic up-regulation. Since, in its activated form, Rim101p is generally known as a transcriptional repressor, its role in anaerobic up regulation of TIR1 and other ‘anaerobic’ yeast genes must involve additional factors. Further studies with deletion mutants in NRG1, NRG2 and SMP1, which were previously shown to be regulated by Rim101p, showed that these genes were not involved in the regulation of TIR1. However, the aerobic repression mechanism of TIR1 involved the general repressor Ssn6p-Tup1p complex. The physiological relevance of Snf7p/Rim101p-mediated transcriptional up-regulation of several genes in anaerobic yeast cultures was evident from reduced growth of a snf7Δ under anaerobic conditions.
2009-09-25 | GSE18128 | GEO
Project description:Identification of ploidy-regulated genes in budding yeast
| PRJNA122517 | ENA
Project description:Yeast replicative aging is a process resembling replicative aging in mammalian cells. During aging, wild type haploid yeast cells enlarge, become sterile, and undergo nucleolar enlargement and fragmentation; we sought gene expression changes during the time of these phenotypic changes. Gene expression studied via microarrays and qPCR has shown reproducible, statistically significant changes in mRNA of genes at 12 and 18-20 generations. Our findings support previously described changes towards aerobic metabolism, decreased ribosome gene expression, and a partial Environmental Stress Response. Our novel findings include a pseudo-stationary phase, down-regulation of methylation-related metabolism, increased Nucleotide Excision Repair related mRNA, and a strong up-regulation of many of the regulatory subunits of protein phosphatase I (Glc7). These findings are correlated with aging changes in higher organisms as well as with the known involvement of protein phosphorylation states during yeast aging. J Gerontol, Jan, 2008, vol 63A, no. 1. Keywords: aging time course
2008-02-01 | GSE10018 | GEO
Project description:Despite the scientific and applied interest in anaerobic metabolism of Saccharomyces cerevisiae, not all genes whose transcription is up-regulated under anaerobic conditions have yet been linked to known transcription factors. Experiments with a reporter construct in which the promoter of the anaerobically up-regulated TIR1 gene was fused to LacZ revealed a complete loss of anaerobic up-regulation in a snf7Δ mutant. Anaerobic up-regulation was restored by expression of a truncated allele of RIM101 that encodes for a constitutively active Rim101p transcription factor. Analysis of LacZ expression in several deletion mutants confirmed that the effect of Snf7p on anaerobic up-regulation of TIR1 involved Rim101p and did not require a functional multi-vesicular body sorting pathway (in which Snf7p also participates). Transcriptome analysis in anaerobic chemostat cultures revealed that 26 additional genes exhibited a Snf7p/Rim101p dependent anaerobic up-regulation. Since, in its activated form, Rim101p is generally known as a transcriptional repressor, its role in anaerobic up regulation of TIR1 and other ‘anaerobic’ yeast genes must involve additional factors. Further studies with deletion mutants in NRG1, NRG2 and SMP1, which were previously shown to be regulated by Rim101p, showed that these genes were not involved in the regulation of TIR1. However, the aerobic repression mechanism of TIR1 involved the general repressor Ssn6p-Tup1p complex. The physiological relevance of Snf7p/Rim101p-mediated transcriptional up-regulation of several genes in anaerobic yeast cultures was evident from reduced growth of a snf7Δ under anaerobic conditions. Experiment Overall Design: The aim of the present study is to investigate the role of SNF7 in the regulation of TIR1, to assess whether this role involves the Rim101p pathway, and to investigate whether Snf7p and/or Rim101p are also involved in regulation of other ‘anaerobic’ S. cerevisiae genes. After analyzing transcriptional regulation of TIR1 in several genetic backgrounds, a chemostat-based transcriptome analysis was performed on snf7Δ and rim101Δ strains as well as on the isogenic reference strain. Sets of genes that were differentially expressed in the snf7 and rim101 deletion strains were then compared to sets of genes that were previously shown to be transcriptionally up-regulated in anaerobic chemostat cultures of S. cerevisiae (Piper et al., 2002; Tai et al., 2005) Experiment Overall Design: Piper MD, Daran-Lapujade P, Bro C, Regenberg B, Knudsen S, Nielsen J & Pronk JT (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277: 37001-37008. Experiment Overall Design: Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM & Pronk JT (2005) Two-dimensional transcriptome analysis in chemostat cultures. Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem 280: 437-447.
2009-10-02 | E-GEOD-18128 | biostudies-arrayexpress
Project description:Identification and distinct regulation of yeast TATA-box containing genes
| PRJNA87891 | ENA
Project description:When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.
2012-04-28 | GSE36151 | GEO
Project description:The main objective was to identify genes regulated after the BY4742 yeast cells were exposed to 0.125% for 5 or 10 min. The experiment was further valited by microbiological assays.
2011-11-29 | GSE33971 | GEO
Project description:When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much recent attention. In this study, we use a genome-wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signaling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, one notable exception being FLO11, a gene encoding a cell-surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters to tune FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive looks at the complex genetic network that underlies the diversity in the morphologies of yeast colonies. Microarrays were used to measure gene expression between WT and FLO11 mutants in both liquid and solid medium to assess which genes induce altered colony morphology through FLO11.
2012-04-27 | E-GEOD-36151 | biostudies-arrayexpress
Project description:The Saccharomyces cerevisiae MYO1 gene encodes the myosin type II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Deletion of the MYO1 gene prevents actomyosin-driven cytokinesis thereby activating an alternative mechanism that involves the synthesis of a remedial septum. Myo1p deficiency in yeast (myo1) also causes the formation of attached cells, abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, and increased chitin synthesis. To determine how the differential expression of genes is related to these diverse phenotypes, we analyzed the global mRNA expression profile of myo1 strains. Global mRNA expression profiles of myo1 strains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes were identified with 263 up-regulated and 284 down regulated genes in the myo1 strains. Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories. Genes involved in cell wall assembly (GAS1, PSA1, CIS3, FIT1, WSC2), MAP kinase activity (SLT2), Rho1p Guanine Exchange Factor (ROM1), and regulation of cell proliferation (RAS1) were also differentially expressed in myo1 strains. Conclusions: We have presented a global mRNA expression analysis of yeast myo1 strains and hypothesized about possible correlations with morphological and biochemical phenotypes observed in these strains. We report 547 differentially regulated genes in the myo1 mutant strains. Genes involved in the control of cell proliferation, protein synthesis and maturation, DNA replication, and cell division processes were largely down regulated, suggesting a mechanism for delayed cell cycle progression and growth that involves coordinated regulation of these processes in myo1 strains. Other genes involved in the cellular response to cell wall stress and cell wall organization were largely up-regulated suggesting that cell wall biogenesis is important for the completion of cytokinesis and cell wall morphogenetic processes that may also be affected by myosin II deficiency. Gene set enrichment analysis indicates that stress response and protein biosynthesis gene categories are inversely correlated in this mutant. Keywords: Comparative genomic hybridization
2008-09-18 | GSE5931 | GEO