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Ecd protein interactome in Drosophila melanogaster S2 cells

ABSTRACT: Identification of the interaction partners of the protein ecdysoneless (Ecd) in Drosophila melanogaster S2 cells as well as profiling of the changes in binding for mutant, truncated Ecd del34 protein.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Drosophila Melanogaster Drosophila Melanogaster (fruit Fly)

SUBMITTER: Steffen Erkelenz

LAB HEAD: Mirka Uhlirova

PROVIDER: PXD019838 | Pride | 2021-09-09

REPOSITORIES: Pride

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			Action	DRS
	20171201_Q1_AWH_ColID_471_PojID_923_Uhlirova_sample_1.raw	Raw
	20171201_Q1_AWH_ColID_471_PojID_923_Uhlirova_sample_10.raw	Raw
	20171201_Q1_AWH_ColID_471_PojID_923_Uhlirova_sample_11.raw	Raw
	20171201_Q1_AWH_ColID_471_PojID_923_Uhlirova_sample_12.raw	Raw
	20171201_Q1_AWH_ColID_471_PojID_923_Uhlirova_sample_2.raw	Raw

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Publications

Ecd promotes U5 snRNP maturation and Prp8 stability.

Erkelenz Steffen S Stanković Dimitrije D Mundorf Juliane J Bresser Tina T Claudius Ann-Katrin AK Boehm Volker V Gehring Niels H NH Uhlirova Mirka M

Nucleic acids research 20210201 3

Pre-mRNA splicing catalyzed by the spliceosome represents a critical step in the regulation of gene expression contributing to transcriptome and proteome diversity. The spliceosome consists of five small nuclear ribonucleoprotein particles (snRNPs), the biogenesis of which remains only partially understood. Here we define the evolutionarily conserved protein Ecdysoneless (Ecd) as a critical regulator of U5 snRNP assembly and Prp8 stability. Combining Drosophila genetics with proteomic approaches ...[more]

PMID: 33444449

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SmD3 protein interactome in Drosophila melanogaster wing imaginal discs

Project description:Screening for binding partners of the splicing factor SmD3 and changes in interaction upon depletion of the protein Ecdysoneless (Ecd) in the nubbin domain of third-instar larval wing imaginal discs.

2021-09-09 | PXD019761 | Pride

Pancreatic Cancer HPAF/CD18 cells: Ecd knockdown vs Scrambled

Project description:Purpose: To study the expression and function of a novel cell cycle regulatory protein, human ecdysoneless (Ecd), during pancreatic cancer (PC) pathogenesis. Experimental Design: Immunohistochemical expression profiling of Ecd was done in non-neoplastic normal pancreatic tissues and pancreatic ductal adenocarcinoma lesions (from tissue microarray and Rapid Autopsy program) as well as precancerous PanIN lesions and metastatic organs. To analyze the biological significance of Ecd in PC progression, Ecd was stably knocked down in PC cell line followed by in vitro and in vivo functional assays. Results: Normal pancreatic ducts show very weak to no Ecd expression compared to significant positive expression in PC tissues (mean±SE composite score: 0.3±0.2 and 3.8±0.2 respectively, p<0.0001) as well as in PanIN precursor lesions with a progressive increase in Ecd expression with increasing dysplasia (PanIN-1 to PanIN-3). Analysis of matched primary tumors and metastases from PC patients revealed that Ecd is highly expressed in both primary pancreatic tumor and in distant metastatic sites. Further, knockdown of Ecd suppressed cell proliferation in vitro and tumorigenicity of PC cells in mice orthotopic tumors. Microarray study revealed that Ecd regulates expression of glucose transporter GLUT4 in PC cells and was subsequently shown to modulate glucose uptake, lactate production and ATP generation by PC cells. Finally, knockdown of Ecd also reduced level of pAkt, key signaling molecule known to regulate aerobic glycolysis in cancer cells. Conclusion: Ecd is a novel tumor promoting factor that is differentially expressed in pancreatic cancer and potentially regulates glucose metabolism within cancer cells. Two-condition experiment, Ecd knockdown vs Scrambled cells. Biological replicates: 3 Ecd knockdownl, 3 Scrambled, independently grown and harvested. One replicate per array

2012-08-09 | E-GEOD-39988 | biostudies-arrayexpress

Comparative circadian proteomes in mouse liver under normal versus ECD conditions

Project description:Exam change in the whole-cell and nuclear proteome circadian proteome in response to environmental circadian disruption (ECD) in mouse liver

2024-06-12 | PXD052085 | Pride

Characterization of the redox proteome of Drosophila melanogaster S2 cells and w1118 fly eyes.

Project description:Reactive oxygen species (ROS) serve as intracellular signaling molecules; however, in excess ROS molecules are damaging to biomacromolecules such as DNA, lipids, and proteins. The excess accumulation of ROS leads to oxidative stress, disrupting redox homeostasis in the cell and has been linked with aging and neurodegenerative disease. The eye is particularly vulnerable to oxidative stress due to the tissue’s high energy demand and generation of ROS by products. In proteins, the thiol group on cysteine residues is susceptible to oxidation. Cysteine residues have multiple oxidation states that can be classified into two categories—reversible and irreversible. Irreversible oxidation states include sulfinic and sulfonic acids, which may alter or impair the activity of the protein depending on the position of the cysteine residue. In contrast, reversible oxidation states include sulfenic acid or inter- and intramolecular disulfides, and can often function as redox sensors in the cell. Here, we sought to evaluate how increasing amounts of oxidative stress alters the redox proteome landscape in Drosophila. To characterize the redox proteome, we developed an iodoTMT-multiplex isolation, labeling, and enrichment method to identify cysteine availability and potential oxidation in both S2 cells and w1118 fly eyes. To do this, we exposed S2 cells to 20mM H2O2 relative to control (untreated), and w1118 flies to prolonged blue light versus an untreated control, followed by redox proteome profiling with iodoTMT-sixplex reagents.

2023-04-27 | PXD034050 | Pride

Caspr2 interacts with type 1 inositol 1,4,5-trisphosphate receptor in the developing cerebellum and regulates Purkinje cell morphology

Project description:Contactin-associated protein-like 2 (Caspr2) is a neurexin-like protein that has been associated with numerous neurological conditions. However, the mechanisms underlying Caspr2 function in the central nervous system remain incompletely understood. Here, we report on a functional role for Caspr2 in the developing cerebellum. Loss of Caspr2 impairs Purkinje cell dendritic development, alters cell signaling and results in motor coordination deficits. Caspr2 is highly enriched at synaptic specializations in the cerebellum. Using a proteomic approach, we identify type 1 inositol 1,4,5-trisphosphate receptor (IP3R1) as a specific synaptic interaction partner of the Caspr2 extracellular domain (ECD) in the molecular layer (ML) of the developing cerebellum. The interaction of Caspr2 ECD with IP3R1 inhibits IP3R1-mediated changes in cellular morphology. Together, our work defines a mechanism by which Caspr2 controls the development and function of the cerebellum, and advances our understanding of how Caspr2 dysfunction might lead to specific brain disorders.

2020-07-13 | PXD018972 | Pride

Verification of utORFs in Drosophila melanogaster

Project description:To verify unannotated translated open reading frames (utORFs) identified from Drosophila melanogaster, we collected data to target them.

2022-04-06 | PXD032197 | Pride

Transcription profiling of human CD4 positive T cell subsets

Project description:Peripheral Blood Mononuclear Cells (PBMCs) were isolated from a buffy coat (Australian Blood Bank) using Ficoll methodology. CD4+ T cells were isolated using Dynal Beads kit. Pure CD4+ T cells were then stained using a cocktail of monoclonal antobodies (mAbs), including: anti-CD4PE, CD45RO ECD, CD62L APC-Cy7, CD25 APC, CD127 Pacific Blue. After incubation, cells were washed twice in PBS/FCS (0.2%), and sorted into five different cell subsets: CD4+CD25+CD127low CD62L+CD45RO- (naive regulatory T cells), CD4+CD25+CD127low CD62L+/- CD45RO+ (activated regulatory T cells), CD4+CD25+CD127hi CD62L+/- CD45RO+ (memory T cells), CD4+CD25-CD127low CD62L+/- CD45RO+ (effector T cells) and CD4+CD25-CD127hi CD62L+ CD45RO- (naive T cells).

2011-02-10 | E-MEXP-2578 | biostudies-arrayexpress

Exploring Top-Down Mass Spectrometric Approaches To Probe Forest Cobra (Naja melanoleuca) Venom Proteoforms

Project description:Three main top-down mass spectrometry methodologies were employed in a proof-of-concept study to characterise selected three finger toxins and phospholipase A2 toxins from the forest cobra (Naja melanoleuca) venom. The novel utility of data-independent acquisition, alternative hybrid ECD-CID fragmentation and the incorporation of cyclic ion mobility separation in a top-down proteomic workflow were explored for snake venom proteins.

2024-09-05 | PXD052561 | Pride

Copper homoeostasis in Drosophila melanogaster S2 cells.

Project description:Copper homoeostasis was investigated in the Drosophila melanogaster S2 cell line to develop an insect model for the study of copper regulation. Real-time PCR studies have demonstrated expression in S2 cells of putative orthologues of human Cu regulatory genes involved in the uptake, transport, sequestration and efflux of Cu. Drosophila orthologues of the mammalian Cu chaperones, ATOX1 (a human orthologue of yeast ATX1), CCS (copper chaperone for superoxide dismutase), COX17 (a human orthologue of yeast COX17), and SCO1 and SCO2, did not significantly respond transcriptionally to increased Cu levels, whereas MtnA, MtnB and MtnD (Drosophila orthologues of human metallothioneins) were up-regulated by Cu in a time- and dose-dependent manner. To examine the effect on Cu homoeostasis, expression of several key copper homoeostasis genes was suppressed using double-stranded RNA interference. Suppression of the MTF-1 (metal-regulatory transcription factor 1), reduced both basal and Cu-induced gene expressions of MtnA, MtnB and MtnD, significantly reducing the tolerance of these cells to increased Cu. Suppression of either Ctr1A (a Drosophila orthologue of yeast CTR1) or Ctr1B significantly reduced Cu uptake from media, demonstrating that both these proteins function to transport Cu into S2 cells. Significantly, Cu induced Ctr1B gene expression, and this could be prevented by suppressing MTF-1, suggesting that Ctr1B might be involved in Cu detoxification. Suppression of DmATP7, the putative homologue of human Cu transporter genes ATP7A and ATP7B, significantly increased Cu accumulation, demonstrating that DmATP7 is essential for efflux of excess Cu. This work is consistent with previous studies in mammalian cells, validating S2 cells as a model system for studying Cu transport and identifying novel Cu regulatory mechanisms.

| S-EPMC1134071 | biostudies-literature

Electron Capture vs. Transfer Dissociation for Site Determination of Tryptic Peptide Tyrosine Sulfation: Direct Detection of Fibrinogen Sulfation Sites and Identification of Novel Isobaric Interferences

Project description:Tyrosine sulfation is an understudied posttranslational modification (PTM) of crucial biological significance. Conventional liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods are unable to directly identify sulfation sites due to the high lability of the sulfate PTM. In this study, we were able to directly detect and localize tyrosine sulfation sites in a proteomics workflow. To meet that objective, we combined bottom-up nanoflow LC-beam-type CID (nanoLC-HCD) with conventional “MSFragger-Labile” analysis, nanoLC-electron transfer with supplemental HCD (EThcD) MS/MS, and LC-electron capture dissociation (ECD) MS/MS for the characterization of bovine fibrinogen sulfopeptide candidates from both purified protein and from plasma.

2024-06-21 | PXD048811 | Pride

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