Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast AGC-kinases phospho-proteomics

ABSTRACT: Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take centre stage in regulating this process in S. cerevisiae. To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1.

INSTRUMENT(S): Orbitrap Fusion

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

SUBMITTER: Michael Plank

LAB HEAD: Robbie Loewith

PROVIDER: PXD015668 | Pride | 2020-02-27

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9.

Plank Michael M Perepelkina Mariya M Müller Markus M Vaga Stefania S Zou Xiaoming X Bourgoint Clélia C Berti Marina M Saarbach Jacques J Haesendonckx Steven S Winssinger Nicolas N Aebersold Ruedi R Loewith Robbie R

Molecular & cellular proteomics : MCP 20200226 4

Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take center stage in regulating this process in <i>S. cerevisiae</i> To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Sites hypo-phosphorylated upon PKA and Sch9 inhibition were preferentially located in RRxS/T-motifs su ...[more]

PMID: 32102971

Similar Datasets

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (ChIP-Seq data)

Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis. ChIP-Seq of 8 S. cerevisiae strains treated with 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.

2011-07-01 | E-GEOD-29124 | biostudies-arrayexpress

PRM of Nth1 phospho-peptides in response to AGC-kinase inhibition

Project description:Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take centre stage in regulating this process in S. cerevisiae. To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Reduced phosphorylation of Nth1 S83 upon PKA- and Ypk1-inhibition was validated by Western blotting and PRM.

2020-03-22 | PXD015760 | panorama

Comparing global transcriptional changes that resulted from loss of Ypk1 or Ypk2 activity

Project description:To identify genes regulated by the AGC kinases Ypk1 and Ypk2 Experiment is designed to identify genes regulated by the kinases Ypk1 and Ypk2. These are functionally redundant AGC kinases such that yeast cells can grow in the presence of either one but the absence of both is lethal. We used a chemical genetic approach to selectively inhibit engineered ATP analog sensitive alleles (AS alleles) of each kinase. Experimental design is such that wild type (WT) Ypk1 or Ypk2 or (AS) Ypk1 or Ypk2 genes are expressed individually on plasmids in a strain background that is deleted for both Ypk1 and Ypk2 (ypk1 delta ypk2 delta). Cultures expressing these plasmids are treated with an ATP analog that is specific for AS Ypk1 or AS Ypk2. Thus, cells expressing wild type Ypk1 or Ypk2 are not sensitive but cells expressing their AS counterparts are sensitive. Arrays typically compare expression patterns in WT versus AS expressing cells at the same time point following inhibitor treatment.

2011-10-28 | E-GEOD-33185 | biostudies-arrayexpress

PKA signaling network-quantitative proteomics and phosphoproteomics

Project description:Classically, connections within a complex network can be identified through systematically removing its components one at a time and observing the resulting functional changes throughout the network. We applied this concept to identify the signaling network downstream from protein kinase A (PKA) in epithelial cells expressing the Gs-coupled V2 vasopressin receptor. Both genes coding for PKA catalytic subunits (Prkaca and Prkacb) were modified using CRISPR-Cas9 to introduce indels resulting in the absence of detectable PKA catalytic subunit protein (immunoblotting and SILAC-based quantitative protein mass spectrometry). Analysis of multiple PKA double knockout (dKO) lines using SILAC-based quantitative phosphoproteomics showed that phosphorylation sites with decreased phospho-occupancy were dominated by the basophilic motif (R/K)-(R/K)-x-S, consistent with that seen for previously identified PKA targets. Overall, 233 PKA target sites were identified, the majority of which are not annotated as PKA sites in public databases. In addition, we identified a large number of sites with increased phospho-occupancy and the motif x-(S/T)-P, consistent with activation of one or more CMGC family kinases in response to PKA deletion. An unexpected finding was a complete, selective loss of expression of the Aqp2 gene (coding for a kidney-specific water channel) with PKA deletion observed both with quantitative proteomics and RNA-Seq based transcriptomics. Using large-scale data integration techniques, the quantitative proteomic, phosphoproteomic, and RNA-Seq datasets were integrated with prior data from the literature to identify a PKA signaling network that explains most of the cellular physiological responses to vasopressin in the target cells, including the regulation of Aqp2 gene transcription.

2017-11-23 | PXD005938 | Pride

Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L (mRNA-Seq data)

Project description:TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. Building on these data, we show here that Sch9, an AGC family kinase and direct substrate of TORC1, promotes ribosome biogenesis (ribi) and ribosomal protein (RP) gene expression via direct inhibitory phosphorylation of three transcription repressors, Stb3, Dot6 and Tod6. Dephosphorylation of these factors allows them to recruit the RPD3L histone deactelyase complex to ribi/RP gene promoters. Since rRNA and tRNA transcription are also under its control, Sch9 appears to be well positioned to coordinately regulate transcriptional aspects of ribosome biogenesis. mRNA-Seq of 8 S. cerevisiae strains treated with either DMSO alone or 1NM-PP1, a small molecule inhibitor for analog-sensitive kinases such as sch9-as.

2011-07-01 | E-GEOD-29122 | biostudies-arrayexpress

Bead-based kinase phosphorylation profiling identifies SRC as a therapeutic target in glioblastoma

Project description:Here we describe a bead-based method capable of profiling tyrosine kinase phosphorylations in a multiplexed, high-throughput and low-cost manner. This approach allows for the discovery of tyrosine kinase-activating events, even when the DNA sequence is wild-type. In an effort to pilot the establishment of a tyrosine kinase activation catalog, we profiled tyrosine phosphorylation levels of 62 tyrosine kinases in 130 human cancer lines, and followed-up on the frequent SRC phosphorylation in glioblastoma. Keywords: quantitative measurements of tyrosine phosphorylation levels on tyrosine kinases Total protein lysates were collected from 130 cancer cell lines. Tyrosine phosphorylation levels on 62 tyrosine kinases were measured with the bead assay.

2010-06-24 | E-GEOD-13808 | biostudies-arrayexpress

Transcription profiling of Candida albicans wild type and sch9 mutant grown under normoxia, hypoxia and hypoxia with CO2

Project description:sch9-mutant and wildtype grown under normoxi, hypoxia (four hours under 0,2% O2), or hypoxia with CO2 (0,2 % O2 and 6 % CO2)

2010-03-01 | E-MEXP-2407 | biostudies-arrayexpress

Bayesian Analysis of Dynamic Phosphoproteomic Data Identifies Protein Kinases Mediating Responses to a Galphas-Coupled GPCR

Project description:A major goal in the discovery of signaling networks is to identify regulated phosphorylation sites and map them to the protein kinases responsible for their phosphorylation. The V2 vasopressin receptor is a Galphas-coupled GPCR that is responsible for regulation of renal water excretion through control of osmotic water transport in kidney collecting duct cells. Genome editing experiments have demonstrated that virtually all vasopressin-triggered phosphorylation changes are dependent on PKA, but events downstream from PKA are obscure. Here we used: 1) TMT-based quantitative phosphoproteomics to track phosphorylation changes over time in native collecting duct cells isolated from rats; 2) a clustering algorithm to classify time course data; and 3) Bayes’ Theorem to integrate the dynamic phosphorylation data with multiple prior “omic” data sets to identify a set of protein kinases that are regulated secondary to PKA activation. The data establish three PKA-dependent protein kinase modules whose regulation mediate the physiological effects of vasopressin at a cellular level. The three modules are 1) a pathway involving several Rho/Rac/Cdc42-dependent protein kinases that control actin cytoskeleton dynamics; 2) MAP kinase and cyclin-dependent kinase pathways that control cell proliferation; and 3) calcium/calmodulin-dependent signaling. The findings provide a template for investigating signaling via other Galphas-coupled GPCRs.

2022-06-17 | PXD031332 | Pride

Transcriptional profiling of Neurospora crassa cells containing MAK2Q100G allele: Exposure to ATP-analog (1NM-PP1) vs control

Project description:To study the consequences of MAK-2 activity modulation during vegetative cell fusion, we took advantage of a previously constructed allele of MAK-2 (MAK-2Q100G) to specifically perturb kinase signaling during germling vegetative cell fusion (inhibition of MAK-2Q100G activity by addition of the ATP analog 1NM-PP1 results in a phenotype indistinguishable from mak-2 deletion strains). Whole genome microarrays of mak-2Q100G cells following 20 min 1NM-PP1 treatment were performed. Two-condition experiment, Neurospora crassa cells containing MAK2Q100G allele treated with 1NM-PP1 inhibitor vs untreated control. Cy3 and Cy5 dye swaps were performed.

2013-06-01 | E-GEOD-46912 | biostudies-arrayexpress

A PKA/PP2A AXIS DRIVES THE GROWTH OF NEUROENDOCRINE SCLC

Project description:Small cell lung cancer (SCLC) is an aggressive subtype of lung cancer whose biology is still poorly understood. Using a multiplexed inhibitor beads assay, we identified active kinases in SCLC. Among those, we found that PKA is critical for the expansion of SCLC in culture and in vivo. PKA promotes the neuroendocrine epithelial state associated with SCLC tumor-initiating cells. Phosphoproteomics analyses identify ~200 PKA substrates and show that PKA controls multiple facets of SCLC growth. Notably, the PP2A phosphatase counteracts the oncogenic effects of PKA, and PP2A activators inhibit SCLC as single agents and with chemotherapy. Our data uncover key signaling networks in SCLC and indicate that targeting the PKA/PP2A pathway may help inhibit this lethal neuroendocrine cancer.

2020-02-11 | GSE126353 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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