Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle 3344

ABSTRACT: The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. To compare phosphorylation and dephosphorylation dynamics we arrest cells in mitosis when most Cdk substrates are fully phosphorylated. Then, we acutely, and chemically inhibit Cdk. The rate of Cdk substrate dephosphorylation will be measured, which will be an indication of the efficiency of Cdk counteracting phosphatases on each substrate.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Helen Flynn

LAB HEAD: Frank Uhlmann

PROVIDER: PXD054870 | Pride | 2025-04-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	3344_takacsl_10pc_FeNTA.raw	Raw
	3344_takacsl_10pc_TiO2.raw	Raw
	3344_takacsl_45pc_FeNTA_HCD.raw	Raw
	3344_takacsl_45pc_FeNTA_MSA.raw	Raw
	3344_takacsl_45pc_TiO2_HCD.raw	Raw

Items per page:

1 - 5 of 24

Similar Datasets

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle1757

Project description:The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. To compare phosphorylation and dephosphorylation dynamics we arrest cells in mitosis when most Cdk substrates are fully phosphorylated. Then, we acutely, and chemically inhibit Cdk. The rate of Cdk substrate dephosphorylation will be measured, which will be an indication of the efficiency of Cdk counteracting phosphatases on each substrate.

2025-04-10 | PXD054832 | Pride

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle 3270

Project description:The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. As a reference dataset, I would like to know when the different proteins (and phosphosites) get phosphorylated as the cells go from G1 to metaphase during undisturbed cell cycle progression. This will allow me to compare phosphorylation kinetics with phosphorylation timing.

2025-04-10 | PXD054772 | Pride

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle 2305

Project description:The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. As a reference dataset, I would like to know when the different proteins (and phosphosites) get phosphorylated as the cells go from G1 to metaphase during undisturbed cell cycle progression. This will allow me to compare phosphorylation kinetics with phosphorylation timing.

2025-04-10 | PXD054725 | Pride

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle 2522

Project description:The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. We want to compare unperturbed phosphorylation and rephosphorylation from an artificially low phosphorylation state in metaphase arrest. To do that, we arrest cells in metaphase, inhibit Cdk until substrates get dephosphorylated, and reactivate Cdk and record the time and kinetics of the substrate rephosphorylation.

2025-04-10 | PXD054974 | Pride

Evidence for substrate control of Cdk phosphorylation timing during the budding yeast cell cycle 3174

Project description:The main intention of this project is to investigate how Cdk substrate phosphorylation is ordered during the cell cycle. We want to understand what makes a ‘good’ Cdk substrate that is phosphorylated early during the cell cycle, e. g. to promote S phase, as compared to a ‘bad’ Cdk substrate that is phosphorylated much later, e. g. when cells enter mitosis. This could be because a late substrate is indeed a poor Cdk substrate, or it could be that the late substrate is a good substrate for Cdk counteracting phosphatases. The two possibilities are not mutually exclusive. We want to compare unperturbed phosphorylation and rephosphorylation from an artificially low phosphorylation state in metaphase arrest. To do that, we arrest cells in metaphase, inhibit Cdk until substrates get dephosphorylated, and reactivate Cdk and record the time and kinetics of the substrate rephosphorylation.

2025-04-10 | PXD055238 | Pride

PP21Cdc55 phosphatase imposes phosphothreonine-specific ordering of cell cycle phosphorylation

Project description:In the quantitative model for cell cycle control, progression from G1 through S phase and into mitosis is ordered by thresholds of increasing cyclin-dependent kinase (Cdk) activity. How such thresholds are read out by substrates, that respond with the correct phosphorylation timing, if not known. In budding yeast, Cdk phosphorylates its many substrates with widely varying efficiencies, but there is no obvious correlation between phosphorylation efficiency and timing. Instead, we explore here whether Cdk-counteracting phosphatases impose Cdk thresholds. We find that the abundant PP2ACdc55 phosphatase counteracts Cdk phosphorylation in interphase and delays phosphorylation of late Cdk substrates, an effect that is independent of its known impact on the Cdk tyrosine phosphorylation status. Strikingly, PP2ACdc55 specifically counteracts phosphorylation of threonine residues. Consequently, we find that threonine-directed phosphorylation occurs late in the cell cycle, compared to serine phosphorylation. Late phosphorylation of Ndd1, a model substrate, depends on threonine identity. Our results support a model in which phosphatases contribute to ordering cell cycle progression by directly counteracting Cdk phosphorylation and unveil a principle of cell cycle control based on the phosphoacceptor amino acid.

2017-01-23 | PXD004461 | Pride

Kinases orchestrate phospho-proteome dynamics during mitotic exit

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

Human Cdc14A is phosphorylated by Cdk1 at early mitosis

Project description:Cdc14 enzymes compose a family of highly conserved phosphatases that are present in a wide range of organisms, including yeast and humans, and that preferentially reverse the phosphorylation of Cyclin-Dependent Kinase (Cdk) substrates. The budding yeast Cdc14 orthologue has essential functions in the control of late mitosis and cytokinesis. In mammals, however, the two Cdc14 homologues, Cdc14A and Cdc14B, do not play a prominent role in controlling late mitotic events, suggesting that some Cdc14 functions are not conserved across species. Moreover, in yeast, Cdc14 is regulated by changes in its subcellular location and by phosphorylation events. In contrast, little is known about the regulation of human Cdc14 phosphatases. Here, we have studied how the human Cdc14A orthologue is regulated during the cell cycle. We found that Cdc14A is phosphorylated on Ser411, Ser453 and Ser549 by Cdk1 early in mitosis and becomes dephosphorylated during late mitotic stages. Interestingly, in vivo and in vitro experiments revealed that, unlike in yeast, Cdk1-mediated phosphorylation of human Cdc14A did not control its catalytic activity but likely modulated its interaction with other proteins in early mitosis. These findings point to differences in Cdk1-mediated mechanisms of regulation between human and yeast Cdc14 orthologues.

2018-08-13 | PXD009481 | Pride

TOX4 Facilitates Promoter-Proximal Pausing and C-Terminal Domain Dephosphorylation of RNA Polymerase II in Human Cells

Project description:TOX4 is one of the regulatory proteins of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation.

2022-03-29 | GSE164277 | GEO

Cdc14 and PP2A Phosphatases Cooperate to Shape Phosphoproteome Dynamics during Mitotic Exit

Project description:Temporal control over protein phosphorylation and dephosphorylation is crucial for accurate chromosome segregation and for completion of the cell division cycle during exit from mitosis. In budding yeast, the Cdc14 phosphatase is thought to be a major regulator at this time, while in higher eukaryotes PP2A phosphatases take a dominant role. Here, we use time-resolved phosphoproteome analysis in budding yeast to evaluate the respective contributions of Cdc14 and the two main PP2A isoforms, PP2A(Cdc55) and PP2A(Rts1). This reveals an overlapping requirement for all three phosphatases during mitotic progression. Cdc14 instructs the sequential pattern of phosphorylation changes, in part through its preferential recognition of serine-based cyclin-dependent kinase (Cdk) substrates. PP2A(Cdc55) and PP2A(Rts1) in turn exhibit a broad substrate spectrum with some selectivity for phospho-threonines and a role for PP2A(Rts1) in sustaining Aurora kinase activity. Our results illustrate synergy and coordination between phosphatases as they orchestrate phosphoproteome dynamics during mitotic progression.

2019-11-12 | PXD012860 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data