Quantitative mass spectrometric analysis of UBE2S auto-ubiquitination throughout the cell cycle.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture
SUBMITTER: 
James Wright
LAB HEAD: Jyoti Choudhary
PROVIDER: PXD012643 | Pride | 2022-03-23
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Fusion_UBE2SIP_TMT6plexB_10.raw | Raw | |||
| Fusion_UBE2SIP_TMT6plexB_15.raw | Raw | |||
| Fusion_UBE2SIP_TMT6plexB_20.raw | Raw | |||
| Fusion_UBE2SIP_TMT6plexB_50.raw | Raw | |||
| Fusion_UBE2S_IP_gel1_TMTcheck.pep.xml | Pepxml |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:In this project we aimed to explore the effect of Dscc1 gene loss on the proteome. Embyros from wildtype and aged matched Dssc1 null embryos were profiled.
2023-11-17 | PXD034902 | Pride
Project description:Toxoplasma gondii encodes three Protein Kinase A catalytic (PKAc1-3) and one regulatory (PKAr) subunits to integrate cAMP-dependent signals. Here, we show that inactive PKAc1 is maintained at the parasite pellicle by interacting with dually acylated PKAr. Either a conditional knockdown of PKAr or the overexpression of PKAc1 results in a block in parasite division. In contrast, conditional expression of a dominant negative PKAr isoform unable to bind cAMP, triggers premature egress of parasites from infected cells. This untimely egress critically depends on parasite density and host cell acidification. A comparative phosphoproteome analysis reveals that PKA genetic inhibition significantly changed the phosphorylation profile of a putative cGMP-phosphodiesterase, PDE2. Consistently, the phenotype of PKA genetic inhibition is alleviated by chemical inhibition of the cGMP-dependent protein kinase G (PKG). A phosphodiesterase inhibitor is able to circumvent egress repression by PKA or pH neutralisation, indicating that environmental acidification and PKA signalling act as balancing regulators of cGMP degradation to control PKG-mediated egress. Collectively, these results reveal a cross-talk between PKA and PKG pathways to govern egress in T. gondii.
2017-10-12 | PXD006045 | Pride
Project description:Covalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to most, if not all biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we have developed an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2 conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracto. This enables purification and identification of modified proteins by mass spectrometry under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of the APC/C in human cells. Finally, performing E2~dID with SUMO in S. cerevisiae we show that E2-dID can be easily adapted to other ubiquitin-like modifiers and experimental models.
2019-04-03 | PXD008624 | Pride
Project description:Resistance is a major problem with effective cancer treatment and the stroma forms a significant portion of the tumor mass but traditional drug screens involve cancer cells alone. Cancer-associated fibroblasts (CAFs) are a major tumor stroma component and its secreted proteins may influence the function of cancer cells. The majority of secretome studies compare different cancer or CAF cell lines exclusively. Here, we present the direct characterization of the secreted protein profiles between CAFs and KRAS mutant-cancer cell lines from colorectal, lung, and pancreatic tissues using multiplexed mass spectrometry. 2573 secreted proteins were annotated, and differential analysis highlighted understudied CAF-enriched secreted proteins, including Wnt family member 5B (WNT5B), in addition to established CAF markers, such as collagens. The functional role of CAF secreted proteins was explored by assessing its effect on the response to 97 anticancer drugs since stromal cells may cause a differing cancer drug response, which may be missed on routine drug screening using cancer cells alone. CAF secreted proteins caused specific effects on each of the cancer cell lines, which highlights the complexity and challenges in cancer treatment and so the importance to consider stromal elements.
2024-05-29 | PXD048307 | Pride
Project description:An overall goal of functional genomics has been to measure the impact of variants on molecular endophenotypes (e.g. gene expression levels or the degree of TF binding) and relate this to organismal traits and disease phenotypes. However, all the experiments to date have been described relative to a generic reference genome, significantly hobbling their interpretation. Here, we describe a strategy for finding significant relationships between disease variation and genomic annotation via personal functional genomics, by performing personal genome sequencing and paired functional genomics experiments, on the same individual.
2024-05-22 | PXD022787 | Pride
Project description:In this study we combined previous transcriptomics and immunopeptidomics data with new proteomics data from untreated and IFNg-treated CRC PDOs to dissect mechanisms that lead to remodeling of the immunopeptidome through IFNg treatment (this is from the paper introduction, let me know if it needs any stylistic changes). · Experiment description: The cells were grown in DMEM/F12 media with 20% fetal bovine serum, 1X Glutamax, 100 units/ml penicillin/streptomycin and 2% matrigel, and treated with 600ng/mL IFNg for 48 hours before harvesting. Cells were washed twice with ice-cold PBS then snap-frozen.
2023-09-29 | PXD031634 | Pride
Project description:How the cell rapidly and completely reorganises its architecture when it divides is a problem that has fascinated for almost 150 years. We now know that the core regulatory machinery is highly conserved in eukaryotes but how these multiple protein kinases, protein phosphatases, and ubiquitin ligases are coordinated in space and time to remodel the cell in a matter of minutes remains a major question. Cyclin B-Cdk is the primary kinase that drives mitotic remodelling and here we show that it is targeted to the nuclear pore complex (NPC) by binding an acidic face of the kinetochore checkpoint protein, MAD1, where it coordinates NPC disassembly with kinetochore assembly. This localised Cyclin B1-Cdk1 activity is needed for the proper release of MAD1 from the embrace of TPR at the nuclear pore so that it can be recruited to kinetochores before nuclear envelope breakdown to maintain genomic stability.
2020-06-29 | PXD017202 | Pride
Project description:Genomic instability due to defective DNA damage response or arising from mitotic chromosomal imbalance can lead to sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of genomic instability associated diseases and ageing, the catalogue of genetic players that regulate their generation remains to be determined. Here analysed 996 mouse mutant lines, revealing 143 factors whose loss significantly increases (71) or decreases (72) MN formation. Most such genes, including the Dscc1 (DNA replication and sister chromatid cohesion 1) gene, have never been studied in mouse models. We found that Dscc1 defective mice were sub-viable and displayed phenotypes like the clinical characteristics of cohesinopathy patients. After validating the DSCC1-MN phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define its synthetic lethal and synthetic viable interactors. Perhaps surprisingly, we found that loss of Sirtuin 1 (SIRT1) can rebalance/rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of SMC3 (structural maintenance of chromosomes protein 3) protein acetylation. Our study provides a resource of novel factors involved in maintenance of genomic stability and shows how this information can be used to uncover mechanisms relevant to better understand disease biology.
2023-11-17 | PXD030499 | Pride
Project description:Purpose Cancer-associated fibroblasts (CAFs) are a key component of tumors. We aimed to profile the proteome of cancer cell lines representing three common cancer types (lung, colorectal and pancreatic) and a representative CAF cell line from each tumor type to gain insight into CAF function and identify new CAF biomarkers. Experimental Design We used isobaric labeling, liquid chromatography and mass spectrometry to evaluate the proteome of 9 cancer and 3 CAF cell lines. Functions of selected differentially expressed proteins in CAF cell lines were further investigated using siRNA and the expression levels of candidate novel CAF biomarkers were evaluated by immunohistochemistry in 30 human tumor specimens. Results Of the 9460 proteins evaluated, functional enrichment analysis revealed N-glycan biosynthesis and extracellular membrane proteins to be upregulated in CAFs and not in cancer cells. 85 proteins had 16-fold higher expression in CAFs compared to cancer cells. These included previously known CAF markers like ACTA2, FAP and SDC2. Novel biomarkers overexpressed in CAFs were noted, including HSPB6 and PTGS1. SiRNA knockdown of these genes encoding these proteins did not reduce contractility in lung CAFs, suggesting they were not crucial to this function despite high expression. Immunohistochemical analysis of 30 tumor samples (10 lung, 10 colorectal and 10 pancreatic) showed HSPB6 and PTGS1 expression were restricted to the stroma. Conclusions An unbiased analysis of the differences in the proteome of cancer cells compared to CAFs revealed increased expression of HSPB6 and PTGS1 in CAFs.
2023-08-21 | PXD040360 | Pride
Project description:EROS (Essential for Reactive Oxygen Species) protein (CYBC1) is indispensable for expression of the gp91phox-p22phox heterodimer of the phagocyte NADPH oxidase. EROS deficiency in humans is a novel cause of chronic granulomatous disease (CGD) but its mechanism of action remains unclear. Our work describes how EROS regulates protein abundance and describes novel roles for EROS in innate and adaptive immunity. EROS acts very early in gp91phox maturation, binding the translated 58kDa precursor directly in the endoplasmic reticulum prior to glycosylation and heme incorporation, thus preventing its degradation. Its actions are distinct from that of p22phox, which is required much later in gp91phox biosynthesis. Further, EROS’s ability to regulate p22phox abundance is entirely secondary to its effect on gp91phox. EROS also regulates the expression of other proteins, including the purine receptors P2X7 and P2X1 through direct interactions.
2023-03-11 | PXD024659 | Pride