Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of Stress Granule interactor proteins in yeast S. cerevisiae

ABSTRACT: We investigated the sub-cellular architecture of Stress Granules in the context of glucose starvation. In order to uncover transient and peripheral Stress Granule interactors, we optimized the proximity-dependent biotinylation (BioID) approach for use in yeast. This approach allowed us to visualize Stress Granule formation while simultaneously inducing the biotinylation of SG components and nearby proteins in live cells. We used two independent Stress Granule components Pub1 and Pab1.

INSTRUMENT(S): Q Exactive

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

SUBMITTER: Triana Amen

LAB HEAD: Daniel Kaganovich

PROVIDER: PXD016988 | Pride | 2020-03-23

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Pab1andPub1proteomics_yeastS.cerevisiae_controlandglucosestarvation.xml	Xml
	Pab1andPub1proteomics_yeastS.cerevisiae_controlandglucosestarvation_rawdata.xml	Xml

Items per page:

1 - 2 of 2

Publications

Stress granules sense metabolic stress at the plasma membrane and potentiate recovery by storing active Pkc1.

Amen Triana T Kaganovich Daniel D

Science signaling 20200317 623

As the physical barrier between the cell and the outside environment, the plasma membrane is well-positioned to be the first responder to stress. The membrane is also highly vulnerable to many types of perturbation, including heat, force, osmotic pressure, lipid shortage, and starvation. To determine whether the structural changes in the plasma membrane of <i>Saccharomyces cerevisiae</i> brought about by nutrient stress can be communicated to regulatory networks within the cell, we identified pr ...[more]

PMID: 32184286

Similar Datasets

PABPC1 stress granule interactome identified by BioID

Project description:Identification of Stress Granule interacting proteins by BioID (Roux et al., 2012) using PABPC1-BirA(R118G)-GFP construct

2022-02-17 | PXD025334 | Pride

Fasnall induces atpically transient Stress Granules

Project description:Stress Granule formation has been linked to the resistance of some cancer cells to chemotherapeutic intervention. A number of studies have proposed that certain anti-tumor compounds promote cancer cell survival by inducing Stress Granules formation, leading to increased cellular fitness and apoptosis avoidance. Here we show that a potent fatty acid synthase inhibitor, fasnall, known for its anti-tumor capabilities, triggers the formation of non-canonical Stress Granules with a faster clearing and internal dynamics kinetics independently of fatty acid synthase inhibition. PABPC1 BioID interactomes in fasnall, and arsenite conditions were obtained.

2021-09-09 | PXD021229 | Pride

ECT2 and AURKB Modulate Formation of Stress Granules Containing Transcripts from Diverse Cellular Pathways in Astrocytoma Cells

Project description:Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins ECT2 and AurkB are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed utilizing high throughput fluorescent based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells and subsequent analysis revealed that astrocytoma stress granules harbour unique mRNAs for various cellular pathways including cellular migration, metabolism, translation and transcriptional regulation. Human astrocytoma cell stress granules contain mRNA that are known to be involved in glioma signaling and the mTOR pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptiblity to conventional therapy such as radiation and chemotherapy. Astrocytoma cells were either untreated or treated with arsenite to induce stress granule formation and RNA immunoprecipitates were analyzed by exon array analysis. RNA species that were enriched in TIAR RIPs and G3BP1 RIPS, respectively were compared to compared to TIAR and G3BP1 RIPs from untreated cells and input controls. Ingenuity pathway analysis was performed on the stress granule enriched mRNAs from the TIAR and G3BP1 RIPs to identify significant functional biology networks.

2016-02-29 | E-GEOD-76814 | biostudies-arrayexpress

Cardiac transcription factors in HL-1 cells: gene expression and genome binding profiling

Project description:[1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells. HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA. [2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells. We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq. We used a dox-inducible dual adenovirus system to express biotinylated Core Cardiac TFs in HL1. One adenovirus expressed the dox-activated reverse tet activator protein (rtTA) and the E. coli biotinylating enzyme BirA from the cardiac specific rat troponin T promoter. The second virus expressed a Core Cardiac TF fused to a C-terminal flag-bio epitope tag, where bio is the 15 amino acid substrate for BirA. This in vivo biotinylation approach permits pulldown of different factors to be performed under identical, stringent conditions, and circumvents limitations posed by available antibodies. We titrated adenovirus and dox doses to express GATA4flbio and MEF2Aflbio at near endogenous levels. The same conditions were then used to express SRFflbio, TBX5flbio, and NKX2-5flbio. Reference: 12. de Boer E, Rodriguez P, Bonte E, Krijgsveld J, Katsantoni E et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A 100: 7480-7485. [1] Gene expression profiling: Identify differentially expressed genes after siRNA Gata4 or Gata4_Mef2a double knockdown in HL-1 cells [2] Genome occupancy profiling: Identify cardiac active enhancers by identified 5 cardiac transcription factors and P300 peaks.

2011-03-02 | E-GEOD-21529 | biostudies-arrayexpress

Proximity-dependent biotinylation detects association between stress granule associated proteins and SARS coronavirus nonstructural protein 1

Project description:Severe acute respiratory syndrome coronavirus (SARS-CoV and SARS-CoV-2) nonstructural protein 1 (nsp1) is a critical viral protein that suppresses host gene expression by blocking the assembly of the ribosome on host messenger RNAs (mRNA). Using proximity-dependent biotinylation assay followed by proteomic analyses of biotinylated proteins, we captured multiple dynamic interactions of nsp1 with host cell proteins. In addition to ribosomal proteins, we have identified several mRNA processing proteins, including splicing factors and transcription termination proteins, exosomes- and stress granule (SG) associated proteins. The interactions with transcription termination factors are primarily governed by the C-terminal region of nsp1 and are disrupted by the mutation of K164 and H165 amino acids. We further show that nsp1 associates with SG protein G3BP and colocalizes with G3BP in SGs under sodium arsenite-induced stress for a short period of time. However, the presence of nsp1 disrupts the maturation of SGs over a long period.

2022-02-17 | PXD025980 | Pride

Norovirus infection results in assembly of virus-specific G3BP1 granules and evasion of eIF2 apha signaling

Project description:Proteomic analysis of murine stress granule and G3BP1 granulome in infected cells. BV2 GFP-G3BP1 cells were either treated with 0.1 mM arsenite for 1h to induce SG assembly or infected with MNV for 9h. G3BP1 granules were enriched by sequential centrifugation and purified by immunoprecipitation using antibodies to GFP (to trap GFP-G3BP1) or IgG (as a control) followed by pull down with Protein A-conjugated epoxy Dynabeads as previously described. To characterize the identity of G3BP1 partners within these, Mass Spectrometric analysis was performed.

2019-12-12 | PXD011956 | Pride

Gene expression profiling in dentate granule cells from patients with mesial temporal lobe epilepsy with or without hippocampal sclerosis

Project description:Hippocampal sclerosis (HS) is the most common neuropathological finding of medically intractable cases of mesial temporal lobe epilepsy (MTLE), the most common form of partial epilepsy. Within the dentate gyrus, HS may be associated with granule cell dispersion and aberrant mossy fiber sprouting, and these pathological changes are accompanied by a range of molecular changes. In this study, we analyzed the gene expression profiles of dentate granule cells of MTLE patients with and without HS to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations and to shed light on the transcriptional changes associated with HS. 12 samples of dentate granule cells from patients with mesial tempora lobe epilepsy, 5 with hippocampal sclerosis and 7 without hippocampal sclerosis. 10 samples had replicates.

2016-06-29 | E-GEOD-71058 | biostudies-arrayexpress

Identification of phasin PhaF interaction partners and proteomic analysis of polyhydroxyalkanoate granules in Pseudomonas putida

Project description:Phasin PhaF is a multifunctional protein associated with the surface of polyhydroxyalkanoate (PHA) granules (carbonosomes) that contributes significantly to PHA biogenesis in pseudomonads. PhaF participates in PHA granule stabilization and segregation and its deletion has a notable impact on overall transcriptome, PHA accumulation and cell physiology, suggesting a more extensive function than simply being a simply granule structural protein. We followed a systematic approach to detect potential interactions of PhaF with other components of the cell, which could pinpoint unexplored functions of PhaF in the regulation of PHA production. We determined the PhaF interactome in Pseudomonas putida KT2440 using pull-down-mass spectrometry (PD-MS), in which proteins interacting with PhaF were determined. We separately determined the PHA granule proteome (all proteins associated with PHA granules) in Pseudomonas putida KT2440 using two granule preparation methods.

2021-09-09 | PXD018787 | Pride

Dynamic transcriptome analysis of osmotic stress response

Project description:Dynamic transcriptome analysis of osmotic stress response. Unperturbed RNA synthesis and decay rates can be obtained via metabolic RNA labeling and kinetic modeling (Cleary et al, 2005; Kenzelmann et al, 2007; Dolken et al, 2008; Friedel and Dolken, 2009; Miller et al, 2009). The nucleoside analog 4-thiouridine (4sU) is taken up by eukaryotic cells and incorporated into mRNA during Pol II transcription (Melvin et al, 1978). The thiol-labeled newly transcribed RNA can then be isolated by affinity chromatography (Kenzelmann et al, 2007) or by biotinylation and purification with streptavidin-coated magnetic beads (Cleary et al, 2005; Dolken et al, 2008).

2013-01-08 | E-MTAB-1059 | biostudies-arrayexpress

Proximity-dependent biotinylation to elucidate the interactome of TNK2 non-receptor tyrosine kinase

Project description:Non-receptor tyrosine kinases represent an important class of signaling molecules which are involved in driving diverse cellular pathways. Although the large majority have been well-studied in terms of their protein binding partners, the interactomes of some important non-receptor tyrosine kinases such as TNK2 (also known as activated Cdc42-associated kinase 1 or ACK1) have not been systematically investigated. Aberrant expression and hyperphosphorylation of TNK2 have been implicated in a number of cancers, although the exact proteins and cellular events that mediate phenotypic changes downstream of TNK2 are unclear. Biological systems that employ proximity-dependent protein labeling methods, such as biotinylation identification (BioID), are being increasingly used to map protein-protein interactomes as they provide increased sensitivity in finding interaction partners. In the present study, we employ BioID coupled to a Biotinylation Site Identification Technology (BioSITe) method we recently developed to perform molecular mapping of intracellular protein interactors of TNK2. By performing a controlled comparative analysis between full-length TNK2 and its truncated counterpart, we were not only able to confidently identify site-level biotinylation of previously well-established TNK2 binders and substrates, but also several novel binders of TNK2 that may help explain its role in oncogenic signaling.

2021-08-25 | PXD010474 | 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