Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identifying the BACE1 interactome through BioID proximity assay

ABSTRACT: This study used the BioID proximity assay to establish the BACE1 interactome in healthy neuronal cells and identified interactions involved in BACE1 trafficking, post-translational modification and substrates.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Hippocampal Cell Line

SUBMITTER: Michele Tinti

LAB HEAD: Michael L.J. Ashford

PROVIDER: PXD021464 | Pride | 2021-12-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	JG_24hrs1.raw	Raw
	JG_24hrs2.raw	Raw
	JG_24hrs3.raw	Raw
	JG_48hrs1.raw	Raw
	JG_48hrs2.raw	Raw

Items per page:

1 - 5 of 12

Publications

Identifying the beta-site amyloid precursor protein cleaving enzyme 1 interactome through the proximity-dependent biotin identification assay.

Gabriel Jennie L JL Tinti Michele M Fuller William W Ashford Michael L J MLJ

Neuroscience letters 20211025

Beta-site amyloid precursor protein (APP) cleaving enzyme 1 (BACE1) is a key drug target against Alzheimer's Disease however, due to its promiscuous proteolytic activity, little is known about its physiological functions. Previous studies have analysed BACE1 cleavage products to examine BACE1 interactions and determine substrates, but these studies cannot establish non-enzymatic (and potentially functional) associations. This study used the biotin identification proximity assay to establish the ...[more]

PMID: 34710551

Similar Datasets

Define the interactome of IBTK by Affinity purification coupled with mass spectrometry (AP-MS) and proximity-dependent biotinylation identification (BioID) methods

Project description:Affinity purification coupled with mass spectrometry (AP-MS) and proximity-dependent biotinylation identification (BioID) methods are powerful tools to define the interactome for a specific protein bait. Whereas AP-MS results in the identification of proteins that are in a stable complex, BioID labels and identifies proteins that are in close proximity to the bait, resulting in overlapping yet distinct protein identifications. In order to comprehensively characterize the IBTK interactome networks in cells, we developed a tag workflow which allows for both AP-MS and BioID analysis with a single construct, pcDNA5/FRT vector containing FLAG-BirA-IBTK.

2024-05-10 | PXD038286 | Pride

Characterization of PARP-6 function in knock out mice and patients with developmental delay

Project description:PARP-6, a member of a family of enzymes (17 in humans) known as poly-ADP- ribose polymerases (PARPs), is a neuronally enriched PARP. While previous studies from our group show that PARP-6 is a regulator of dendrite morphogenesis in hippocampal neurons, its function in the nervous system in vivo is poorly understood. Here, we describe the generation of a PARP-6 loss-of-function mouse model for examining the function of PARP-6 during neurodevelopment in vivo. Using CRISPR-Cas9 mutagenesis, we generated a mouse line that expresses a PARP-6 truncated variant (PARP-6TR) in place of PARP-6WT. Unlike PARP-6WT, PARP-6TR is devoid of catalytic activity. Homozygous PARP-6TR do not exhibit obvious neuromorphological defects during development, but nevertheless die perinatally. This suggests that PARP-6 catalytic activity is important for postnatal survival. We also report PARP-6 mutations in six patients with several neurodevelopmental disorders, including microencephaly, intellectual disabilities, and epilepsy. The most severe mutation in PARP-6 (C563R) results in the loss of catalytic activity. Expression of the PARP-6C563R mutant in hippocampal neurons decreases dendrite morphogeneis. Taken together, these results suggest that PARP-6 is an essential gene in mice, and the loss of PARP-6 catalytic activity has detrimental effects on neuronal function in humans.

2021-07-21 | PXD025386 | Pride

Identification of the potential receptor of Musclin on C3H10T1/2 cell using BioID assay

Project description:To identify the potential receptor mediating the effect of Musclin on thermogenic adipocytes, we conducted a proximity-dependent biotin identification (BioID) assay to obtain the interactome of Musclin on the plasma membrane of beige adipocytes.

2023-06-13 | PXD041019 | Pride

A proximity interactome map of the VAC14-FIG4 complex using BioID

Project description:Conversion between phosphatidylinositol-3-phosphate and phosphatidylinositol-3,5-bisphosphate on endosomal membranes is critical for maturation of early endosomes to late endosomes/lysosomes, and is regulated by the PIKfyve-Vac14-Fig4 complex. In this study, we screened for the cellular interactome of Vac14 and Fig4 using proximity-dependent biotin labelling (BioID) in 293T cells.

2021-11-03 | PXD027917 | Pride

Cancer proteome and metabolite changes linked to SHMT2

Project description:To screen for proximate and interacting proteins of SHMT2 in HeLa cells, the BioID method was employed, which consists of biotinylation of proteins in the vicinity of FlagBirAR118G –SHMT2 followed by streptavidin-based affinity capture and mass spectrometry identification. Experimental procedures were carried out essentially as described previously.

2020-08-12 | PXD004629 | Pride

Definition of the fibroblast adhesome using multiplexed proximity biotinylation

Project description:Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry and topological organisation of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome. Integration of the interactomes of 16 IAC-associated baits revealed a network of 147 proteins with 361 proximity interactions. Candidates with underappreciated roles in adhesion were identified, in addition to established IAC components. Bioinformatic analysis revealed five clusters of IAC baits that link to common groups of prey, and which therefore may represent functional modules. The five clusters, and their spatial associations, are consistent with current models of IAC interaction networks and stratification. This study provides a resource to examine proximal relationships within IACs on a global level.

2020-06-01 | PXD017241 | Pride

Interactome of the long non-protein coding RNA (lncRNA) D4Z4 binding element-transcript (DBE-T)

Project description:Facioscapulohumeral muscular dystrophy (FSHD) is an inherited progressive neuromuscular disorder that afflicts both children and adults regardless of gender. FSHD is caused by aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover, targeting WDR5 rescues both cell viability and myogenic differentiation of FSHD patient cells. Notably, comparable results were obtained by pharmacological inhibition of WDR5. Importantly, WDR5 targeting was safe to healthy donor muscle cells. Our results support a pivotal role of WDR5 in the activation of DUX4 expression identifying a druggable target for an innovative therapeutic approach for FSHD.

2023-04-11 | PXD036038 | Pride

Identification of Cavin3-interacting proteins

Project description:Caveolae are specialized domains of the plasma membrane. Formation of these invaginations is dependent on the expression of Caveolin-1 or -3 and proteins of the cavin family. In response to stress, caveolae disassemble and cavins are released from caveolae, allowing cavins to potentially interact with intracellular targets. Here, we describe the intracellular (non-plasma membrane) cavin interactome using biotin affinity proteomics and mass spectrometry. We validate 47 potential cavin-interactor proteins using a cell-free expression system and protein-protein binding assays. These data, together with pathway analyses, revealed novel roles for cavin proteins in metabolism and stress signaling. We validated the interaction between one candidate interactor protein, protein phosphatase 1 alpha (PP1α), and Cavin-1 and -3 and show that UV treatment causes release of Cavin3 from caveolae allowing interaction with, and inhibition of, PP1α. This interaction increases H2AX phosphorylation to stimulate apoptosis, identifying a pro-apoptotic signaling pathway from surface caveolae to the nucleus.

2019-07-23 | PXD014081 | Pride

A proximity-labeling proteomic approach to investigate invadopodia molecular landscape in breast cancer cells

Project description:Invadopodia constitute a specialized machinery required for invasive tumor cells to travel through basement membranes and the interstitial matrix, and thus represent a key feature of metastatic cells. Therefore a better understanding of invadopodia biology and characteristics might permit the identification of markers of metastatic potential. Substantial efforts have been made to characterize invadopodia molecular composition, dynamics or triggering stimuli. However, the full molecular identity of these structures is still missing due to the fact that the isolation and purification of these structures has been challenging. To fill this gap, we developed a non-hypothesis driven proteomic approach based on the innovative BioID proximity biotinylation approach using the invadopodia-specific protein Tks5/FISH (its long form, Tks5) fused to the biotin ligase BirA as bait. As control, we also generated cells expressing the short form of Tks5 (Tks5) unable to localize to invadopodia. After validation of our cell models, Tks5 close neighbors were identified by label-free mass spectrometry after pulldown of biotinylated proteins. Known invadopodia components were identified revealing the pertinence of our strategy. Furthermore, this strategy allowed us to identify novel Tks5 in cellulo partners that appear as potential new invadopodia components/regulators and potential markers of metastasis.

2020-04-24 | PXD015847 | Pride

Chemical genetics and proteome-wide site mapping reveal cysteine MARylation by PARP-7 on immune-relevant protein targets

Project description:Poly (ADP-ribose) polymerase 7 (PARP-7) has emerged as a critically important member of a large enzyme family that catalyze ADP-ribosylation in mammalian cells. PARP-7 is a critical regulator of the innate immune response. What remains unclear is the mechanism by which PARP-7 regulates this process, namely because the protein targets of PARP-7 mono-ADP-ribosylation (MARylation) are largely unknown. Here, we combine chemical genetics, proximity labeling, and proteome-wide amino acid ADP- ribosylation site profiling for identifying the direct targets and sites of PARP-7-mediated MARylation in a cellular context. We found that the inactive PARP family member, PARP13 (a critical regulator of the antiviral innate immune response) is a major target of PARP-7. PARP-13 is preferentially MARylated on cysteine residues in its RNA binding zinc finger domain. Proteome-wide ADP-ribosylation analysis reveals cysteine as a major MARylation acceptor of PARP-7. This study provides insight into PARP-7 targeting and MARylation site preference.

2021-07-21 | PXD020323 | 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