Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Physical and functional interactome of human receptor tyrosine kinases

ABSTRACT: Much cell-to-cell communication is facilitated by cell surface receptor tyrosine kinases (RTKs). These proteins phosphorylate their downstream cytoplasmic substrates in response to stimuli such as growth factors. Despite their central roles, the functions of many RTKs are still poorly understood. To resolve the lack of systemic knowledge, we used three complementary methods to map the molecular context and substrate profiles of RTKs. We used affinity purification coupled to mass spectrometry (AP-MS) to characterize stable binding partners and RTK-protein complexes, proximity-dependent biotin identification (BioID) to identify transient and proximal interactions, and an in vitro kinase assay to identify RTK substrates. To identify how kinase interactions depend on kinase activity, we also used kinase-deficient mutants. Our data represent a comprehensive, systemic mapping of RTK interactions and substrates. This resource adds information regarding well-studied RTKs, offers insights into the functions of less well-studied RTKs, and highlights RTK-RTK interactions and shared signaling pathways

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Markku Varjosalo

PROVIDER: MSV000087816 | MassIVE | Wed Jul 14 00:02:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of PP1c-PPP1R12A Substrates Using K-BIPS (Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates)

Project description:Protein phosphatase 1 regulatory subunit 12A (PPP1R12A) interacts with the catalytic subunit of protein phosphatase 1 (PP1c) to form one of the many protein phosphatase 1 complexes, PP1c-PPP1R12A (or myosin phosphatase). In addition to a well-documented role in muscle contraction, the PP1c-PPP1R12A complex is associated with cytoskeleton organization, cell migration, adhesion, cell division, and insulin signaling. Despite the variety of biological functions, only a few substrates of the PP1c-PPP1R12A complex are characterized, which limits a full understanding of PP1c-PPP1R12A activities. Here, the chemoproteomics method K-BIPS (Kinase-catalyzed Biotinylation to Identify Phosphatase Substrates) was used to identify substrates of the PP1c-PPP1R12A complex in L6 skeletal muscle cells. K-BIPS enriched 136 candidate substrates with 14 high confidence hits. Two high confidence hits, AKT1 kinase and COPS4 signalosome proteins, were studied as novel PP1c-PPP1R12A substrates. Interestingly, both AKT1 and COPS4 were previously documented to regulate PP1c-PPP1R12A phosphatase activity. Therefore, the data suggest that PP1c-PPP1R12A influences its own phosphatase activity through substrate-dependent feedback mechanisms

2023-10-24 | PXD035211 | Pride

Identification of PP1c-PPP1R12A Substrates Using K-BIPS (Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates)

2023-10-24 | PXD035213 | Pride

Identification of PP1c-PPP1R12A Substrates Using K-BIPS (Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates)

2023-10-24 | PXD035212 | Pride

Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-Protein interactions

Project description:Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.

2024-04-04 | PXD048869 | Pride

3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and nuclear exosome mutant strains

Project description:The nuclear exosome performs critical functions in non-coding RNA processing, and in diverse surveillance functions including the quality control of mRNP formation, and in the removal of pervasive transcripts. Most non-coding RNAs and pervasive nascent transcripts are targeted by the Nrd1p-Nab3p-Sen1p (NNS) complex to terminate Pol II transcription coupled to nuclear exosome degradation or 3´-end trimming. Prior to nuclear exosome activity, the Trf4p-Air2p-Mtr4p polyadenylation complex adds an oligo-A tail to exosome substrates. Inactivating exosome activity stabilizes and lengthens these A-tails. We utilized high-throughput 3´-end poly(A)+ sequencing to identify at nucleotide resolution the 3´ ends targeted by the nuclear exosome, and determine the sites of NNS-dependent termination genome-wide.

2016-08-12 | GSE75586 | GEO

3´-end sequencing of poly(A)+ RNA in wild-type Saccharomyces cerevisiae and a strain carrying a deletion of the RRP6 nuclear exosome catalytic component

2016-08-12 | GSE75584 | GEO

A genome-wide genetic interaction screen reveals metabolic roles of human histone deacetylase 1

Project description:Dynamic acetylation of metabolic proteins has emerged as a ubiquitous post-translational modification of human metabolic proteins. However, the corresponding modifying enzymes and the functions of the modification await exploration. Using a genome-wide synthetic lethality screen, we constructed a genetic interaction network of human histone deacetylases (HDACs) and discovered many metabolic substrates of these enzymes. We further confirmed that the adenosine monophosphate-activated protein kinase (AMPK) catalytic subunit is acetylated and deacetylated by EP300 and HDAC1, respectively. Deacetylation of AMPK catalytic subunit enhances physical interaction with the upstream kinase LKB1, and leads to AMPK phosphorylation and activation. These findings highlight the importance of genetic interaction profiling to identify specific substrates of individual HDACs and elucidate how cells use protein (de)acetylation to coordinate nutrient availability and cellular energy status.

2012-02-10 | GSE29662 | GEO

Phosphoproteomics analysis identifies novel candidate substrates of the non-receptor tyrosine kinase, SRMS

Project description:SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites) or PTK 70 (Protein tyrosine kinase 70) is a non-receptor tyrosine kinase that belongs to the BRK family kinases (BFKs). The gene encoding SRMS was first discovered in 1994. Yet to date less is known about the cellular role of SRMS primarily due to the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS. Our analyses led to the identification of 1259 tyrosine-phosphorylated peptides which mapped to 663 phosphoproteins, exclusively from SRMS-expressing cells. Dok1, a previously characterized SRMS substrate, was also identified in our analyses. Functional enrichment analyses revealed that the candidate SRMS substrates represented various biological processes typically linked to cell growth and RNA metabolism. Analyses of the sequence surrounding the phospho-sites in these proteins led us to identify novel candidate SRMS consensus substrate motifs. We utilized customized high-throughput peptide arrays to validate a subset of the candidate SRMS substrates and motifs identified in our MS-based analyses. Finally, we independently validated Vimentin and Sam68, as bonafide SRMS substrates through in vitro and in vivo assays. Overall, our study led to the identification of a significant number of novel and biologically relevant SRMS candidate substrates, which suggests the involvement of the kinase in a vast array of unexplored cellular functions.

2018-03-08 | PXD006809 | Pride

Phosphoproteomic analysis identifies supervillin as a new ERK3 substrate regulating cytokinesis and ploidy of breast cancer cells

Project description:Extracellular signal-regulated kinase 3 (ERK3) is a poorly characterized member of the mitogen-activated protein (MAP) kinase family. Functional analysis of the ERK3 signaling pathway has been hampered by a lack of knowledge about the substrates and downstream effectors of the kinase. Here, we used large-scale quantitative phosphoproteomics and targeted gene silencing to identify direct ERK3 substrates and gain insight into its potential cellular functions. Detailed validation of one candidate substrate identified the gelsolin/villin family member supervillin (SVIL) as a bona fide ERK3 substrate. We show that ERK3 phosphorylates SVIL on Ser245 to regulate myosin II activation and cytokinetic furrowing in dividing cells. Depletion of SVIL or ERK3 leads to cytokinesis failure and multinucleation, a phenotype rescued by wild type SVIL but not by the non-phosphorylatable S245A mutant. Our results unveil a new function of the atypical MAP kinase ERK3 in cell division and the regulation of cell ploidy

2023-02-21 | PXD028061 | Pride

In vitro kinase assay to detect STX17 phosphorylation by ULK1

Project description:To identify the specific site of STX17 phosphorylated by ULK, in vitro kinase assays were performed with ULK1 immunoprecipitated from 293T cells and STX17 purified from E. coli. Purified GST-STX17 proteins were used for kinase assay as substrates to determine phosphorylation sites.

2023-06-27 | PXD039362 |

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