Ontology highlight
ABSTRACT:
PROVIDER: PRJNA841829 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19372207_1.fastq.gz | Fastqsanger.gz | |||
| SRR19372207_2.fastq.gz | Fastqsanger.gz | |||
| SRR19372208_1.fastq.gz | Fastqsanger.gz | |||
| SRR19372208_2.fastq.gz | Fastqsanger.gz | |||
| SRR19372209_1.fastq.gz | Fastqsanger.gz |
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Project description:Gene expression was quantified in S. cerevisiae cells after 40 hours of LiCl treatment or control conditions. Cells expressing wild type (WT) Hcm1, a stable Hcm1 mutant (Hcm1-3N), or a consitutitvely active, phosphomimetic mutant (Hcm1-8E) were compared to allow the identification of genes whose expression depends upon dynamic phosphorylation of Hcm1. We found that dynamic phosphorylation of Hcm1 is required for expression of Hcm1 target genes in LiCl stress.
2024-09-18 | GSE276435 | GEO
Project description:The eukaryotic cell cycle is characterized by alternating oscillations in the activities of cyclin-dependent kinase (Cdk) and the anaphase-promoting complex (APC). Successful completion of the cell cycle is dependent on the precise, temporally ordered appearance of these activities. A modest level of Cdk activity is sufficient to initiate DNA replication, but mitosis and APC activation require an elevated Cdk activity. In present-day eukaryotes, this temporal order is provided by a complex network of regulatory proteins that control both Cdk and APC activities via sharp thresholds, bistability, and time delays. Using simple computational models, we show here that these dynamical features of cell-cycle organization could emerge in a control system driven by a single Cdk/cyclin complex and APC wired in a negative-feedback loop. We show that ordered phosphorylation of cellular proteins could be explained by multisite phosphorylation/dephosphorylation and competition of substrates for interconverting kinase (Cdk) and phosphatase. In addition, the competition of APC substrates for ubiquitylation can create and maintain sustained oscillations in cyclin levels. We propose a sequence of models that gets closer and closer to a realistic model of cell-cycle control in yeast. Since these models lack the elaborate control mechanisms characteristic of modern eukaryotes, they suggest that bistability and time delay
2024-09-02 | BIOMD0000000938 | BioModels
Project description:Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that pRB retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus independent of CDK phosphorylation. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide binding and expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists independent of CDK phosphorylation to establish regions of constitutive heterochromatin.
2016-10-31 | GSE85639 | GEO
Project description:Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that pRB retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus independent of CDK phosphorylation. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide binding and expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists independent of CDK phosphorylation to establish regions of constitutive heterochromatin
2016-10-31 | GSE85638 | GEO
Project description:Hyper-phosphorylation of RB controls its interaction with E2F and inhibits its tumor suppressor properties. However, during G1 active RB can be mono-phosphorylated on any one of 14 CDK phosphorylation sites. Here we used quantitative proteomics to profile protein complexes formed by each mono-phosphorylated RB isoform (mP-RB) and identified the associated transcriptional outputs. The results show that the 14 sites of mono-phosphorylation co-ordinate RB’s interactions and confer functional specificity. All 14 mP-RBs interact with E2F/DP proteins but they provide different shades of E2F regulation. RB mono-phosphorylation at S811, for example, alters RB transcriptional activity by promoting its association with NuRD complexes. The greatest functional differences between mP-RBs are evident beyond the cell cycle machinery. RB mono-phosphorylation at S811 or T826 stimulates the expression of oxidative phosphorylation genes, increasing cellular oxygen consumption. These results indicate that RB activation signals are integrated in a phosphorylation code that determines the diversity of RB activity.
2019-02-01 | GSE116346 | GEO
Project description:Genome stability requires complete DNA duplication exactly once before division. In eukaryotes, cyclin-dependent kinase (CDK) plays a dual role in this regulation by inhibiting helicase loading factors and activating origin firing. CDK drives initiation by phosphorylation of two substrates, Sld2 and Sld3, forming the transient and limiting intermediate called the pre-initiation complex (pre-IC). The importance and mechanism of dissociation of the pre-IC from origins is not understood. Here we show in the budding yeast Saccharomyces cerevisiae that CDK phosphorylations of Sld3 and Sld2 are specifically and rapidly turned-over during interphase by the PP2A and PP4 phosphatases. Inhibition of dephosphorylation of Sld3/Sld2 causes dramatic defects in replication initiation genome-wide, retention of the pre-IC at origins and cell death. These studies not only provide a mechanism to ensure that Sld3/Sld2 are dephosphorylated before helicase loading factors but also establish a novel positive role for phosphatases in eukaryotic origin firing.
2021-11-01 | GSE186490 | GEO
Project description:This model is from the article:
Downregulation of PP2A(Cdc55) phosphatase by separase initiates mitotic exit in budding yeast.
Queralt E, Lehane C, Novak B, Uhlmann F. Cell.
2006 May 19;125(4):719-32. 16713564
,
Abstract:
After anaphase, the high mitotic cyclin-dependent kinase (Cdk) activity is downregulated to promote exit from mitosis. To this end, in the budding yeast S. cerevisiae, the Cdk counteracting phosphatase Cdc14 is activated. In metaphase, Cdc14 is kept inactive in the nucleolus by its inhibitor Net1. During anaphase, Cdk- and Polo-dependent phosphorylation of Net1 is thought to release active Cdc14. How Net1 is phosphorylated specifically in anaphase, when mitotic kinase activity starts to decline, has remained unexplained. Here, we show that PP2A(Cdc55) phosphatase keeps Net1 underphosphorylated in metaphase. The sister chromatid-separating protease separase, activated at anaphase onset, interacts with and downregulates PP2A(Cdc55), thereby facilitating Cdk-dependent Net1 phosphorylation. PP2A(Cdc55) downregulation also promotes phosphorylation of Bfa1, contributing to activation of the "mitotic exit network" that sustains Cdc14 as Cdk activity declines. These findings allow us to present a new quantitative model for mitotic exit in budding yeast.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
For more information see the terms of use
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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000409 | BioModels
Project description:The cell division cycle culminates in mitosis when two daughter cells are born. As cyclin-dependent kinase (Cdk) activity reaches its peak, the Anaphase Promoting Complex (APC) is activated to trigger sister chromatid separation and mitotic spindle elongation, followed by spindle disassembly and cytokinesis. Degradation of mitotic cyclins and activation of Cdk-counteracting phosphatases are thought to cause protein dephosphorylation to control these sequential events. Here, we use budding yeast to analyze phosphorylation dynamics of 3456 phosphosites on 1101 proteins with high temporal resolution as cells progress synchronously through mitosis. This illustrates sequential protein dephosphorylation and reveals that the order arises from successive inactivation of S and M phase Cdks and of the mitotic kinase Polo. Unexpectedly, we detect as many new phosphorylation events as there are dephosphorylation events. These correlate with late mitotic kinase activation and identify numerous candidate targets of these kinases. Our findings revise our view of mitotic exit and portray it as a dynamic process in which a range of mitotic kinases instruct the order of both protein dephosphorylation as well as phosphorylation.
2018-10-15 | PXD008327 | Pride
Project description:In S. cerevisiae, the forkhead transcription factor Hcm1 has been involved in chromosome segregation, spindle pole dynamics and budding. We found that, in response to oxidative stress stimuli, Hcm1 shifts from cytoplasm to the nucleus, interacting with the histone deacetylase Sir2, which regulates Hcm1 localization. Hcm1-overexpressing cells showed increased resistance to oxidative stress which can be attributed to increased catalase and Sod2 activities. Microarray analysis revealed that genes corresponding to mitochondrial function and transition from exponential to stationary phase are clearly induced in these cells which consistently showed higher rates of oxygen consumption due to an increase in mitochondria – possibly triggered by higher amounts of Abf2, a protein involved in mitochondrial biogenesis. In wild-type cells, when glucose levels decreased by 50%, we observed Hcm1 translocation to the nucleus and increased Hcm1 levels. We conclude that Hcm1 may act as an early regulator to respond to nutrient limitation, increasing stress resistance and mitochondrial function and thereby allowing the cells to adapt to nutrient limitations by shifting from fermentative to respiratory metabolism.
2010-10-04 | GSE20420 | GEO