Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitomics and proteomics analysis of porcine articular cartilage post mechanical injury

ABSTRACT: We describe ubiquitomics and proteomics analysis of porcine articular cartilage post mechanical injury. Analysis showed ubiquitin peptides differentially enriched post injury compared to non injured controls.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Sus Scrofa Domesticus (domestic Pig)

TISSUE(S): Articular Cartilage, Articular Chondrocyte

SUBMITTER: Heba Ismail

LAB HEAD: Heba Ismail

PROVIDER: PXD030817 | Pride | 2022-12-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Cartilage_injury_ubiquitomics_and_proteomics_Ismail_PRIDE_submission.xlsx	Xlsx
	GlyGly__K_Sites.xlsx	Xlsx
	Oxidation__M_Sites.txt	Txt
	QE929_MSQ1321_20180329_Heba_s10_ctrl_P.raw	Raw
	QE929_MSQ1321_20180329_Heba_s11_ctrl_P.raw	Raw

Items per page:

1 - 5 of 33

Publications

The Mechano-Ubiquitinome of Articular Cartilage: Differential Ubiquitination and Activation of a Group of ER-Associated DUBs and ER Stress Regulators.

Kaokhum Nitchakarn N Pinto-Fernández Adán A Wilkinson Mark M Kessler Benedikt M BM Ismail Heba M HM

Molecular & cellular proteomics : MCP 20220928 12

Understanding how connective tissue cells respond to mechanical stimulation is important to human health and disease processes in musculoskeletal diseases. Injury to articular cartilage is a key risk factor in predisposition to tissue damage and degenerative osteoarthritis. Recently, we have discovered that mechanical injury to connective tissues including murine and porcine articular cartilage causes a significant increase in lysine-63 polyubiquitination. Here, we identified the ubiquitin signa ...[more]

PMID: 36182100

Similar Datasets

TCellXTalk enables the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells

Project description:Protein function is regulated by post-translational modifications (PTMs) that may act individually or interact with others in a phenomenon termed PTM cross-talk. Multiple databases have been dedicated to PTMs, including recent initiatives oriented to the in silico prediction of PTM interactions. The study of PTM cross-talk ultimately requires experimental evidence about whether certain PTMs co-exist in a single protein molecule. However, available resources do not assist researchers in the experimental detection of co-modified peptides. Here we present TCellXTalk, a comprehensive database of phosphorylation, ubiquitination and acetylation sites in human T cells that supports the experimental detection of co-modified peptides using targeted or directed mass spectrometry. We demonstrate the efficacy of TCellXTalk and the strategy presented here in a proof of concept experiment that enabled the identification and quantification of 15 co-modified (phosphorylated and ubiquitinated) peptides in CD3 proteins of the T-cell receptor complex. To our knowledge, these are the first co-modified peptide sequences described in this widely studied cell type. Furthermore, quantitative data showed distinct dynamics of co-modified peptides upon T cell activation, demonstrating differential regulation of co-occurring PTMs in this biological context. Overall, TCellXTalk enables the experimental detection of co-modified peptides in human T cells and puts forward a novel and generic strategy for the study of PTM cross-talk.

2018-09-19 | PXD010176 | Pride

Ubiquitin proteomics reveals critical targets of the Nse1 RING domain in rDNA and genome stability

Project description:Ubiquitination controls most cellular processes, and its deregulation is associated to many pathologies. The Nse1 subunit in the Smc5/6 complex contains a RING domain with ubiquitin E3 ligase activity and important functions in genome integrity. However, Nse1-dependent ubiquitin targets remain largely unknown. Here, we use label-free quantitative proteomics to analyse the nuclear ubiquitinome of nse1 RING mutant cells. Our results show that Nse1 impacts on the ubiquitination of several proteins involved in DNA damage tolerance, ribosome biogenesis and metabolism that, importantly, extend beyond canonical functions of the Smc5/6 complex in chromosome segregation. In addition, our analysis uncovers an unexpected connection between Nse1 and Pol I ubiquitination. Specifically, Nse1 promotes the ubiquitination of K408 and K410 in Rpa190, the largest subunit of Pol I, to induce its degradation. We propose that this mechanism contributes to Smc5/6-dependent rDNA disjunction in response to transcriptional elongation defects.

2023-05-05 | PXD028669 | Pride

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

Project description:Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double-membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated, and processed via the CHLORAD pathway: they are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically-derived chloroplasts, where it acts to regulate one of the most fundamental processes of life.

2022-12-06 | PXD031388 | Pride

Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition

Project description:mTOR is a central regulator of mammalian metabolism and physiology. Aberrant hyperactivation of this pathway promotes tumor growth and metastasis and drives tumor resistance to chemotherapy and cancer drugs, making mTOR an attractive cancer therapeutic target. mTOR inhibitors have been approved to treat cancer, however, the basis for drug sensitivity remains poorly understood. Here, whole exome sequencing of three chromophobe renal cell carcinoma (chRCC) patients with exceptional mTOR inhibitor sensitivity, uncovered USP9X deubiquitinase as the only mutated gene shared by the tumors. The clonal characteristics of the mutations, revealed by studying multiple patients’ primary and metastatic samples along the years, together with the low USP9X mutation rate in unselected chRCC series, reinforced a causal link between USP9X and mTOR inhibitor sensitivity. Rapamycin treatment of USP9X depleted HeLa and renal cancer 786-O cells and the pharmacological inhibition of USP9X, confirmed a crucial role of this protein in the patients’ sensitivity to mTOR inhibition. As no direct effect of USP9X in mTORC1 was detected, we performed ubiquitylome analyses that identified p62 as a direct USP9X target. Increased p62 ubiquitination and an augmented rapamycin effect upon bortezomib treatment, together with p62 and LC3 immunofluorescence assays, suggested that dysregulated autophagy in USP9X depleted cells can synergize with mTOR inhibitors. In summary, here we show that USP9X constitutes a potential novel marker of sensitivity to mTOR inhibitors in chRCC patients and represents a clinically exploitable strategy that could increase sensitivity to these drugs

2023-06-14 | PXD040496 | Pride

Ubiquitination in treated T. cruzi parasites

Project description:T. cruzi epimastigotes in the logarithmic growth phase (3×106 cells mL-1) were incubated for 12h with bortezomib (1.8 µM), GNF6702 (2.9 µM) or compound 1 (24 µM), equivalent to 8× the EC50 values of each compound. Controls were incubated in the presence of diluent (DMSO). Cells were harvested by centrifugation (1912g, 15 min, 4 °C) and washed with ice-cold PBS (1912g, 5 min, 4 °C), and finally, the cell pellets were resuspended in 1.5 mL of ice-cold lysis buffer (1 mM EDTA, 1 mM DTT, 100 μM TLCK, and 1× Roche EDTA-free cOmplete protease inhibitor cocktail in 50 mM potassium phosphate buffer, pH 7.4). Cell suspensions were submitted to 3 freeze–thaw cycles in a dry ice/ethanol bath to biologically inactivate the parasites and then lysed using the One ShotTM Cell disruptor (Constant Systems, UK) at 30 kpsi.

2022-02-17 | PXD027524 | Pride

Strigolactones positively regulate HY5-dependent autophagy and the degradation of ubiquitinated proteins in response to cold stress in tomato

Project description:Autophagy, involved in protein degradation and amino acid recycling, plays a key role in plant development and stress responses. However, the relationship between autophagy and phytohormones is unclear. We used diverse methods, including CRISPR/Cas9, UPLC-MS/MS, chromatin immunoprecipitation, electrophoretic mobility shift assays, and dual-luciferase assays to explore the molecular mechanism of strigolactones in regulating autophagy and the degradation of ubiquitinated proteins under cold stress in tomato. We show that cold stress induced the accumulation of ubiquitinated proteins. Mutants deficient in strigolactone biosynthesis were more sensitive to cold stress with a higher accumulation of ubiquitinated proteins, while treatment with the synthetic strigolactone analog GR245DS enhanced cold tolerance in tomato, with a higher accumulation of autophagosomes and transcripts of autophagy-related genes (ATGs), and a lower accumulation of ubiquitinated proteins. Meanwhile, cold stress induced ELONGATED HYPOCOTYL 5 (HY5) accumulation, which was triggered by strigolactones. HY5 further trans-activated ATG18a promoter, resulting in autophagy formation. Mutation of ATG18a compromised strigolactone-induced cold tolerance, followed by a decreased formation of autophagosomes and an increased accumulation of ubiquitinated proteins. These findings reveal that strigolactones positively regulate autophagy in an HY5-dependent manner and promote the degradation of ubiquitinated proteins under cold conditions in tomato.

2024-08-01 | PXD052107 | Pride

Proteome and Ubiquitome Changes during Rose Petal Senescence

Project description:Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were up-regulated and 726 were down-regulated during senescence. We identified 2208 ubiquitinated sites including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays important roles in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.

2020-05-27 | PXD016490 | Pride

Disruption of immune tolerance changes epididymal extracellular vesicle (EV) protein cargo

Project description:We characterized the protein-content profile of epididymal EVs after disruption of immune tolerance by performing mass spectrometry-based label-free quantitative proteomics. EVs were obtained from the proximal and distal epididymides of WT and Foxp3- DTR (diphtheria toxin receptor) mice 2 weeks after diphtheria toxin (DT) treatment.

2023-09-08 | PXD041223 | Pride

Quantitative K-GG site analysis

Project description:Post-translational modification of proteins by ubiquitin (UQ) and UQ-like modifiers is emerging as a central pathway in DNA replication. We previously showed that chromatin in the vicinity of replisomes is rich in SUMO and depleted in UQ, whereas an opposite pattern is observed in mature chromatin. How this SUMO-rich/UQ-low environment is maintained at replisomes is not known. Here we identify USP7 as a SUMO deubiquitinase that localizes to replication forks and is essential for DNA replication. By acting on SUMO and SUMOylated proteins, USP7 prevents their ubiquitination. Chemical inhibition or genetic deletion of USP7 leads to the accumulation of UQ on SUMOylated proteins, which are displaced from the replisomes. Our findings provide a model to explain the differential accumulation of SUMO and UQ in replication forks versus mature chromatin, and identify an essential role of USP7 that should be taken into account for the use of USP7 inhibitors as anticancer agents.

2016-01-13 | PXD002408 | Pride

Ubiquitination profile of polarized macrophages

Project description:Previous studies linked mac activation with the ubiquitination (ub) status of key proteins in inflammatory signal pathways. Lysine-48 ub (K48-ub) of the NF-κB inhibitor (IκB), the final checkpoint of the NFκB pathway, leads to IκB degradation and consequent NF-κB-associated inflammation. In contrast, TRAF6, an upstream positive regulator of the NF-κB pathway, is modulated by K63-ub, leading to its conformational change and activation. However, a comprehensive analysis of ub profiles of polarized macs has not been reported. If a unique ub signature is associated with individual mac subsets is not known.

2020-08-06 | PXD018743 | Pride