Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SILAC APEX2-GAL9 upon LLOMe or GPN treatment

ABSTRACT: Proximity proteomics of GAL9 upon lysosomal damage by LLOMe or GPN. Proximity labeling was performed in SILAC labelled HEK293T cells stably expressing APEX2-GAL9.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Early Embryonic Cell, Kidney

SUBMITTER: Christian Behrends

LAB HEAD: Christian Behrends

PROVIDER: PXD015779 | Pride | 2020-01-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20181106_LB_051.raw	Raw
	20181106_LB_052.raw	Raw
	20181106_LB_053.raw	Raw
	20181106_LB_054.raw	Raw
	20181106_LB_055.raw	Raw

Items per page:

1 - 5 of 8

Similar Datasets

VCP-dependent CNN2 proximity proteomics

Project description:Lysosomal membrane permeabilization (LMP) is an underlying feature of diverse conditions including neurodegeneration. Cells respond by extensive ubiquitylation of membrane-associated proteins for clearance of the organelle through lysophagy that is facilitated by the ubiquitin-directed AAA-ATPase VCP/p97. Here, we assessed the ubiquitylated proteome upon acute LMP and uncovered a large diversity of targets and lysophagy regulators. They include calponin-2 (CNN2) that, along with the Arp2/3 complex, translocates to damaged lysosomes and regulates actin filaments to drive phagophore formation. Importantly, CNN2 needs to be ubiquitylated during the process and eliminated by VCP/p97 and proteasome for efficient lysophagy. Moreover, we identified the small heat shock protein HSPB1 that assists VCP/p97 in extraction of CNN2, and show that other membrane regulators including SNAREs, PICALM, AGFG1 and ARL8B are ubiquitylated during lysophagy. Our data reveal a framework of how ubiquitylation and two effectors, VCP/p97 and HSPB1, cooperate to protect cells from the deleterious effects of LMP.

2022-06-23 | PXD032903 | Pride

UBE2QL1 prximity proteome in HeLa cells in response to lysosomal damage

Project description:SILAC-based proximity proteomics of UAPEX2-tagged UBE2QL1 in differential LLOMe-treated HeLa cells

2019-08-22 | PXD014521 | Pride

Lysosomal damage proteomics in HeLa cells

Project description:To identify ubiquitylation targets following lysosomal damage in HeLa cells treated with LLOMe we performed quantitative ubiquitin-remmnant (diGly) profilig coupled to mass spectrometry (MS). In addition, we performed APEX2-based proximity biotinylation followed by MS analysis to identify proximity partners of one of the ubiquitylation targets (CNN2).

2022-06-23 | PXD029926 | Pride

Autophagosome content profiling in TBK1-E696K knockin MEFs

Project description:To determine how the mutant TBK1-E696K protein impacts autophagosomes, we performed autophagosome content profiling using protease protection coupled APEX2 proximity proteomics of autophagosomes of homozygous TBK1-E696K knockin and wiltype mouse embryonic fibroblasts (MEFs) transfected with a APEX2-LC3 as previously described in Zellner et al. 2021 Molecular Cell.

2024-03-16 | PXD048795 | Pride

Mapping of the autophagosomal degradome identifies IL-7Rα as key 1 cargo in proliferating CD4+ T-cells

Project description:CD4+ T cells orchestrate both humoral and cytotoxic immune responses. While it is known that CD4+ T cell proliferation relies on autophagy, direct identification of the autophagosomal cargo involved is still missing. Here, we created a transgenic mouse model, which, for the first time, enables us to directly map the proteinaceous content of autophagosomes in any primary cell by LC3 proximity labelling. IL-7Rα, a cytokine receptor mostly found in naïve and memory T cells, was reproducibly detected in autophagosomes of activated CD4+ T cells. Consistently, CD4+ T cells lacking autophagy showed increased IL-7Rα surface expression, while no defect in internalisation was observed. Mechanistically, excessive surface IL-7Rα sequestrates the common gamma chain, impairing the IL-2R assembly and downstream signalling crucial for T cell proliferation. This study provides proof-of-principle that key autophagy substrates can be reliably identified with this model to help mechanistically unravel autophagy’s contribution to healthy physiology and disease.

2022-07-08 | PXD033733 | Pride

Dynamic Changes in the Proximitome of Neutral Sphingomyelinase-2 (NSM2) in TNFα Stimulated Jurkat Cells

Project description:Ceramides generated by the activity of the neutral sphingomyelinase 2 (NSM2) play a pivotal role in stress responses in mammalian cells. Dysregulation of sphingolipid metabolism has been implicated in numerous inflammation-related pathologies. However, its influence on inflammatory cytokine-induced signaling is yet incompletely understood. Here, we used proximity labeling to explore the plasma membrane proximal protein network of NSM2 and TNFα-induced changes thereof. We established Jurkat cells stably expressing NSM2 C-terminally fused to the engineered ascorbate peroxidase 2 (APEX2). Removal of excess biotin phenol substantially improved streptavidin-based affinity purification of biotinylated proteins. Using our optimized protocol, we determined NSM2-proximal biotinylated proteins and their changes within the first 5 min of TNFα stimulation by quantitative mass spectrometry. We observed significant dynamic changes in the NSM2 microenvironment in response to TNFαstimulation consistent with rapid remodeling of protein networks. Our data confirmed known NSM2 interactors and revealed that the recruitment of most proteins depended on NSM2 enzymatic activity. We measured significant enrichment of proteins related to vesicle-mediated transport, including proteins of recycling endosomes, trans-Golgi network, and exocytic vesicles in the proximitome of enzymatically active NSM2 within the first minutes of TNFα stimulation. Hence, the NSM2 proximal network and its TNFα-induced changes provide a valuable resource for further investigations into the involvement of NSM2 in the early signaling pathways triggered by TNFα.

2024-07-05 | PXD052930 | Pride

Autophagy content profiling in human cells

Project description:Identification of autophagy substrates by directing APEX2 to autophagosomes and immune isolation of lysosomes.

2021-01-27 | PXD020758 | Pride

Proximity labeling by a recombinant APEX2-FGF1 fusion protein reveals interaction of FGF1 with the proteoglycans CD44 and CSPG4

Project description:Fibroblast growth factor 1 (FGF1) binds to specific FGF receptors (FGFRs) at the surface of target cells to initiate intracellular signaling. In addition, FGF1 also binds to heparan sulfate proteoglycans (HSPG), which act as important co-receptors. Even if some interactions with HSPGs have been characterized, it is not entirely clear if FGF1 could interact with additional proteoglycans at the cell surface. We have devised and tested a method to identify novel binding sites for FGF1 at the cell surface, which may also be applicable for other protein ligands. First, we constructed an APEX2-FGF1 fusion protein to perform proximal biotin labeling of proteins after binding of the fusion protein to cells. After functional validation of the construct, we used this method to identify binding sites for FGF1 on living cells. We confirmed the feasibility of our approach by easy detection of FGFR4, a well-known and specific receptor for FGF1. We then performed a screen in RPE1 cells and among the top hits were the proteoglycans CSPG4 (NG2) and CD44. We found that FGF1 binds CD44 through its heparin-binding moiety. Moreover, we found that FGF1 co-localizes with both CSPG4 and CD44 at the cell surface suggesting that these receptors act as storage molecules creating a reservoir of FGF1. Importantly, our data demonstrate that recombinant ligand-APEX2 fusion proteins can be used to identify novel receptor interactions at the cell-surface.

2018-06-06 | PXD009302 | Pride

G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

Project description:Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into stress granules (SGs) reduces translation, but it remains unclear whether SGs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress-adaptation in cancer. Transcripts enriched in PSs, defined by polysome fractionation and RNAseq, were compared with mRNAs complexed with the SG-nucleator protein, G3BP1, defined by spatially-restricted enzymatic tagging. Short-term oxidative stress profoundly altered mRNA translation by promoting selective enrichment of transcripts within SGs or PSs. G3BP1 participates in this compartmentalisation by sequestering transcripts in SGs. Under stress, G3BP1-bound transcripts are PS-depleted and encode proteins involved in mRNA translation, pro-apoptosis, and mitochondrial function. In contrast, specific PS-enriched transcripts disassociate from G3BP1 under stress to encode proteins involved in diverse cellular cytoprotective pathways. Therefore, G3BP1 partitioning guides selective translation to support stress adaptation and cell survival.

2020-04-30 | PXD015491 | Pride

Proximity proteomics of phagophore-associated proteins using APEX2-LC3B in VPS37A KO U-2 OS cells

Project description:We utilized an APEX2-mediated proximity biotinylation approach to label proteins on LC3-positive membranes that accumulate in VPS37A-knockout (KO) U-2 OS cells. AP, APEX2 control; WT, APEX2-LC3B.

2024-12-03 | PXD057301 | 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