Yeast meiotic transcriptional profile
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE221451 | GEO | 2023/02/01
REPOSITORIES: GEO
Similar Datasets
Project description:RNAseq across a time course of meiosis of cells with and without Kfc1p. The overexpression of either IME1 or both IME1 and RIM4 was used to determine how overexpression of the two genes functions to resuce the meiotic defect associated with the loss of Kar4p.
2023-02-01 | GSE222684 | GEO
Project description:Transcriptional profiling of wild type and kar4 deletion yeast mutants across a meiotic time course. Including samples with IME1 and RIM4 overexpression
2023-02-01 | GSE220125 | GEO
Project description:Ray2013 - Meiotic initiation in S. cerevisiae
A mathematical representation of early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signalling molecules for regulating protein activities, is described here
This model is described in the article:
Dynamic modeling of yeast meiotic initiation.
Ray D, Su Y, Ye P.
BMC Syst Biol. 2013 May 1;7:37
Abstract:
BACKGROUND:
Meiosis is the sexual reproduction process common to eukaryotes. The diploid yeast Saccharomyces cerevisiae undergoes meiosis in sporulation medium to form four haploid spores. Initiation of the process is tightly controlled by intricate networks of positive and negative feedback loops. Intriguingly, expression of early meiotic proteins occurs within a narrow time window. Further, sporulation efficiency is strikingly different for yeast strains with distinct mutations or genetic backgrounds. To investigate signal transduction pathways that regulate transient protein expression and sporulation efficiency, we develop a mathematical model using ordinary differential equations. The model describes early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signaling molecules for regulating protein activities.
RESULTS:
The mathematical model is capable of simulating the orderly and transient dynamics of meiotic proteins including Ime1, the master regulator of meiotic initiation, and Ime2, a kinase encoded by an early gene. The model is validated by quantitative sporulation phenotypes of single-gene knockouts. Thus, we can use the model to make novel predictions on the cooperation between proteins in the signaling pathway. Virtual perturbations on feedback loops suggest that both positive and negative feedback loops are required to terminate expression of early meiotic proteins. Bifurcation analyses on feedback loops indicate that multiple feedback loops are coordinated to modulate sporulation efficiency. In particular, positive auto-regulation of Ime2 produces a bistable system with a normal meiotic state and a more efficient meiotic state.
CONCLUSIONS:
By systematically scanning through feedback loops in the mathematical model, we demonstrate that, in yeast, the decisions to terminate protein expression and to sporulate at different efficiencies stem from feedback signals toward the master regulator Ime1 and the early meiotic protein Ime2. We argue that the architecture of meiotic initiation pathway generates a robust mechanism that assures a rapid and complete transition into meiosis. This type of systems-level regulation is a commonly used mechanism controlling developmental programs in yeast and other organisms. Our mathematical model uncovers key regulations that can be manipulated to enhance sporulation efficiency, an important first step in the development of new strategies for producing gametes with high quality and quantity.
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2024-09-02 | BIOMD0000000626 | BioModels
Project description:We used pCUP1-IME1 pCUP1-IME4 strain to generate synchronized yeast meiotic culture and measure the RNA expression through meiotic progression
2016-11-18 | GSE90008 | GEO
Project description:Starvation in diploid budding yeast cells triggers a cell-fate program culminating in meiosis and spore formation. Transcription activation of early meiotic genes (EMGs) hinges on the transcription activator Ime1, its DNA-binding partner Ume6, and GSK-3 kinase Rim11. Phosphorylation of Ume6 by Rim11 is key for EMG activation. We report that Rim11 functions as the central signal integrator for controlling Ume6 phosphorylation and EMG transcription. In nutrient-rich conditions, PKA suppresses Rim11 levels, while TORC1 retains Rim11 in the cytoplasm. Inhibiting PKA and TORC1 induces Rim11 expression and nuclear localization. Remarkably, nuclear Rim11 is required, but not sufficient, for Rim11-dependent Ume6 phosphorylation. Additionally, Ime1 is an essential anchor protein for phosphorylating Ume6. Subsequently, Ume6-Ime1 coactivator complexes form, which drive EMG transcription. Our results demonstrate how varied signalling inputs (PKA/TORC1/Ime1) converge through Rim11 to regulate EMG expression and meiosis initiation. We posit that the signalling-regulatory network elucidated here generates robustness in cell-fate control.
2024-03-06 | PXD049212 | Pride
Project description:The Kar4 protein has been identified as being a component of the yeast N6A mRNA methyltransferase, homologous to human METTL14. Mutations in KAR4 cause blocks in meiosis due to 1) reduced expression of Ime1p-induced transcripts, and 2) reduced levels of a subset of meiotic proteins, independent of their transcript levels. The reduced levels of the proteins are partially suppressed by increased levels of a translational regulator, Rim4. This proteomic study was aimed at identifying the spectrum of meiotic proteins affected by the absence of Kar4. The defect in Ime1p-depedent transcription was suppressed by over-expression of Ime1p. Proteins present in wildtype and kar4 deletion strains at two different times in meiosis were fractionated using reverse-phase chromatography and identified by MS/MS. Some 4068 proteins expressed during meiosis were identified. At 8 hours, 432 proteins were present at less than 50% the levels in kar4Δ/Δ compared to wild type. GO term analysis of the low proteins at 8 hours returned “meiotic cell cycle” as the sixth term with a P value of 7.74x10^-5. At 12 hours, 318 proteins were present at less than 50% the levels in kar4Δ/Δ relative to wild type. GO term analysis returned “meiotic cell cycle” as the second term with a P value less than 0.001. Proteins that were low at both 8 and 12 hours in kar4∆/∆ comprise proteins required for meiotic recombination and sporulation including Sps2p, Gas4p, Gmc2p, Mei5p, and Sae3p. Other meiotic proteins were expressed at or above wild type levels at 8 hours, but went down to lower than wild type levels at 12 hours, including Ecm11p, Hed1p, Spo11p, and Rec8p. In each case the levels of the proteins were reduced to much greater extents that can be explained by changes in transcript levels. Taken together these data suggest that Kar4 plays a role in the regulation of transcription and translation during yeast meiosis.
2023-08-22 | PXD043798 | Pride
Project description:Yeast meiotic transcriptional profile
| PRJNA914324 | ENA
Project description:Early meiotic genes (EMGs) encompass an important subset within the developmental program of gametogenesis. Regulation of EMGs is achieved through the recognition of a common regulatory element in their promoters by the transcription factor Ume6. Proper meiotic execution requires the timely expression of EMGs, which is achieved through the adoption of the meiotic regulator Ime1 by Ume6. While it is known that Ime1’s binding to Ume6 promotes EMG expression, the mechanism of EMG activation remains unclear. Two competing models have been proposed: (1) Ime1 converts Ume6 to a coactivator complex, and (2) Ime1 binding targets Ume6 for degradation. Using a combination of tools including meiotic synchronization, temporally controlled protein depletion, protein-protein interaction engineering, and transcriptomics, here we address this conundrum. We identify 160 genes that are directly regulated by Ime1-Ume6, including UME6 itself. Removal of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and to generate viable gametes in the absence of Ime1. We conclude that Ime1-Ume6 functions as a coactivator complex. While Ume6 is indispensable for EMGs expression, Ime1 primarily serves as an evolutionarily tuned activation domain for Ume6.
2023-06-30 | GSE226769 | GEO
Project description:In eukaryotes, chromosomal DNA is equally distributed to daughter cells during mitosis, whereas the number of chromosomes is halved during meiosis. Despite considerable progress in understanding the molecular mechanisms that regulate mitosis, there is currently a lack of complete understanding of the molecular mechanisms regulating meiosis. Here, we took advantage of the fission yeast Schizosaccharomyces pombe, for which highly synchronous meiosis can be induced, and performed quantitative proteomics and phosphoproteomics analyses to track changes in protein expression and phosphorylation during meiotic cell divisions. We compared the proteomes and phosphoproteomes of mitotic cells with cells harvested around meiosis I, or meiosis II in strains bearing either the temperature-sensitive pat1-114 allele or conditional ATP analog-sensitive pat1-as2 allele of the Pat1 kinase. Comparing pat1-114 with pat1-as2 also allowed us to investigate the impact of elevated temperature (25°C versus 34°C) on meiosis, an issue that sexually reproducing organisms face due to climate change. Using TMTpro 18plex labeling and phosphopeptide enrichment strategies, we performed quantification of a total of 4673 proteins and 7172 phosphosites in S. pombe. We found that the protein level of 2680 proteins and the rate of phosphorylation of 4005 phosphosites significantly changed during progression of S. pombe cells through meiosis. The proteins exhibiting changes in expression and phosphorylation during meiotic cell divisions were represented mainly by those involved in the meiotic cell cycle, meiotic recombination, meiotic nuclear division, meiosis I, centromere clustering, microtubule cytoskeleton organization, ascospore formation, organonitrogen compound biosynthetic process, carboxylic acid metabolic process, gene expression, and ncRNA processing, among others. In summary, our findings provide global overview of changes in the levels and phosphorylation of proteins during progression of S. pombe cells through meiosis at normal and elevated temperatures, laying the groundwork for further elucidation of the functions and importance of specific proteins and their phosphorylation in regulating meiotic cell divisions in this yeast.
2024-10-09 | PXD053920 | Pride
Project description:Dynamic proteome in diploid yeast cells undergoing mitotic growth and meiotic development. The proteome of growing (YPA) and differentiating yeast cells at 6 hours (SPII 6, middle meiosis) and 8 hours (SPII8, late meiosis) were compared using the TOP3 GeLC-MS/MS method.
2017-01-16 | PXD001275 | Pride