OuMV MP-interacting proteins in Arabidopsis
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress) Ourmia Melon Virus
TISSUE(S): Leaf
SUBMITTER: 
Natali Ozber
LAB HEAD: Cristina Rosa
PROVIDER: PXD035960 | Pride | 2022-09-04
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| MB-PC2.wiff | Wiff | |||
| MB-PC2.wiff.scan | Wiff | |||
| MBF1.group | Other | |||
| MBF1.wiff | Wiff | |||
| MBF1.wiff.scan | Wiff |
Items per page: 5 1 - 5 of 37 |
Similar Datasets
Project description:Cells of the vascular system release spherical vesicles, called microparticles (MP), in the size range of 0.1-1μm induced by a variety of stress factors resulting in variable MP concentrations between health and disease. Furthermore, MP have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today’s most used analytical technology for MP characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past. We propose the use of nano-liquid chromatography coupled to two-stage mass spectrometry as a non-biased tool for quantitative MP proteome analysis. Using aliquots of 250 μL platelet-free plasma (PFP) from one individual donor, we achieved excellent inter-assay CV’s of 2.7 ± 1.7% (mean ± 1 S.D.) on individual peptide intensities across 27 data-dependent nanoLC-MS/MS runs performed over a period of 3.5 months. With quantitative proteomics, we show that MP composition between twelve volunteers were remarkably stable. MP protein composition is clearly distinguishable from whole cell lysates and we propose that this trait should be used as a quality criterion of MP purity. Furthermore, MP were damaged by freezing PFP. The damage was articulated by a loss of cytoplasm proteins, encompassing a specific set of proteins involved in regulating dynamic structures of the cytoskeleton, and thrombin activation leading to MP clotting. On the other hand, plasma membrane protein composition (cell markers) was not affected. Finally, we show that multiplexed data-independent acquisition can be used for relative quantification of target proteins using Skyline software.
2016-10-18 | PXD003935 | Pride
Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing
2015-07-09 | E-GEOD-66183 | biostudies-arrayexpress
Project description:The goal of this experiment was to define gene expression patterns of two mouse retinal neuron subsets that express the Thy1-mitoCFP-P (MP) transgene. The two populations expressing the MP transgene are: 1) non-GABAergic, non-glycinergic amacrine cells; and 2) a subset of OFF-type bipolar cells. We used the VC1.1 monoclonal antibody, which labels amacrine cells (ACs) but not bipolar cells, to separately purify the AC and bipolar populations that express the MP transgene. Two biological replicates, originating from different litters, were collected for each sample. RNA was extracted from sorted cells and prepared for hybridization to Affymetrix microarrays.
2011-07-01 | E-GEOD-30324 | biostudies-arrayexpress
Project description:Analysis of the transcriptome of mononuclear side population (SP) and main population (MP) cells of human fetal skeletal muscle from 12 human subjects of gestational age 14-18 weeks. Total RNA was extracted and profiled from 12 human fetal skeletal muscle side population (SP) cells and 10 corresponding human skeletal muscle main population (MP) cells.
2011-01-26 | E-GEOD-26869 | biostudies-arrayexpress
Project description:The goal of this study is to characterize the expression profile of Epidermolysis bullosa simplex-mottled pigmentation (EBS-MP) patient compared with normal subjects using genomic expression analyses. Microarray analyses were performed with RNA isolated from skin biopsies. Robust multiarray analysis (RMA) normalization and Smyth’s moderated t test were used to select differentially expressed genes. Expression profiling comparisons show that 52 genes are differentially expressed in EBS-MP patients compared to control subjects. Difference of expression for three genes (TYR, CCL22 , and ACVR1C ) was validated using real-time reverse transcription–polymerase chain reaction. Twelve genes were related to lipid biosynthesis process, two to keratinisation and skin pigmentation, Nineteen to cell growth and apoptosis, five to immune response and fourteen to predicted or less known function cluster. To our knowledge, the distinctive pattern of gene expression that characterizes EBS-MP versus healthy skin tissue has never been reported. RNA used for the microarrays analysis was isolated from superficial 2mm punch biopsies composed of mainly epidermis with minimal dermis amounts of normal-appearing skin of one EBS-MP patient and seven healthy volunteers.
2012-03-10 | E-GEOD-36406 | biostudies-arrayexpress
Project description:Cerebral malaria (CM) is a severe complication of a Plasmodium falciparum infection and is still responsible for a high number of deaths and long term disabilities in children in sub-Saharan Africa. The pathogenesis of this syndrome remains incompletely understood but a number of mechanisms and effectors have been proposed, including plasma microparticles (MP). These submicron vesicles released by potentially all cells carry proteins and nucleic acids derived from the mother cell. In CM, their numbers are increased in patients’ circulation and, in the mouse model, they can be localised within inflamed vessels, suggesting their involvement in vascular damage. In the present work we define, for the first time, the protein cargo of MP during experimental cerebral malaria (ECM) with the overarching hypothesis that characterising this content could help in better understand CM pathogenesis. Using qualitative and quantitative high-throughput proteomics we compared MP proteins from non-infected mice and mice infected with P. berghei ANKA at two different stages of infection, i.e., pre-clinical phase and full blown syndrome. Overall, we identified 368 proteins, 60 of which were differentially expressed, as determined by quantitative comparison using the TMT® isobaric labelling. The analysis with Ingenuity® IPA highlighted important networks significantly represented among the proteins over-expressed (n=42) or identified only (n=21) in ECM, comprising mechanisms already proposed to be involved in CM, such as endothelial activation. Two proteins of interest, carbonic anhydrase I (CA-I) and S100A8, were verified by western blot on newly collected MP samples from DBA/1 (n=16) and C57BL/6 (n=8) mice, and confirmed to be associated with ECM MP. These results demonstrate that MP protein cargo represents a novel ECM pathogenic trait to consider in the understanding of CM pathogenesis. The identification of the cellular source of MP containing proteins associated to the disease state will contribute to further understanding their involvement in CM.
2016-12-13 | PXD003772 | Pride
Project description:Insulin (INS) synthesis and secretion from pancreatic M-NM-2 cells are tightly regulated; their deregulation causes diabetes. Here we map INS-associated loci in human pancreatic islets by 4C and 3C techniques and show that the INS gene physically interacts with the SYT8 gene, located over 300 kb away. This interaction is elevated by glucose and accompanied by increases in SYT8 expression. Inactivation of the INS promoter by promoter-targeting siRNA reduces SYT8 gene expression. SYT8-INS interaction and SYT8 transcription are attenuated by CTCF depletion. Furthermore, SYT8 knockdown decreases insulin secretion in islets. These results reveal a non-redundant role for SYT8 in insulin secretion and indicate that the INS promoter acts from a distance to stimulate SYT8 transcription. This suggests a function for the INS promoter in coordinating insulin transcription and secretion through long-range regulation of SYT8 expression in human islets. Circular Chromosome Conformation Capture (4C)-Seq experiments to profile interactions of INS promoter in human pancreatic islets isolated from two donors: donor 1 and donor 2.
2011-02-22 | E-GEOD-25862 | biostudies-arrayexpress
Project description:Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a cancer predisposition syndrome driven by mutation of the tumor suppressor fumarate hydratase (FH). Inactivation of FH causes accumulation of the electrophilic oncometabolite fumarate. In the absence of methods for reactivation, tumor suppressors can be targeted via identification of synthetic lethal interactions using genetic screens. Inspired by recent advances in chemoproteomic target identification, here we test the hypothesis that the electrophilicity of the HLRCC metabolome may produce unique susceptibilities to covalent small molecules, a phenomenon we term conditional covalent lethality. Screening a panel of chemically diverse electrophiles we identified a covalent ligand, MP-1, that exhibits FH-dependent cytotoxicity. Synthesis and structure-activity profiling identified key molecular determinants underlying the molecule’s effects. Chemoproteomic profiling of cysteine reactivity together with clickable probes validated the ability of MP-1 to engage an array of functional cysteines, including one lying in the Zn-finger domain of the tRNA methyltransferase enzyme TRMT1. TRMT1 overexpression rescues tRNA methylation from inhibition by MP-1 and partially attenuates the covalent ligand’s cytotoxicity. Our studies highlight the potential for covalent metabolites and small molecules to synergistically produce novel synthetic lethal interactions and raise the possibility of applying phenotypic screening with chemoproteomic target identification to identify new functional oncometabolite targets.
2024-01-26 | PXD033546 | Pride
Project description:Vascular formation in the leaves of higher plants begins with the selection of cells poised to become preprocambial cells, some of which eventually develop into procambial cells. The initiation of this process is accompanied by auxin-responsive and MONOPTEROS (MP) transcription factor-mediated modulations in gene expression. Here, we show that MP directly activates the expression of Dof5.8, which encodes a transcriptional repressor. Consistently, mutations within Dof5.8 enhanced the phenotype of a weak allele of mp, resulting in abnormal root and cotyledon development. However, although mp mutants showed reduced vascular patterns in cotyledons, the mp dof5.8 double mutants displayed both reduced and more complex vascular patterns in individual cotyledons. Thus, Dof5.8 appears to be associated with both positive and negative regulatory mechanisms for vascular network formation in leaves. Furthermore, both over-expression of Dof5.8 and expression of a Dof5.8 construct engineered to possess enhanced repressor activity in preprocambial cells prevented the formation of procambium for secondary and higher order veins, suggesting a predominantly negative regulatory role for Dof5.8. These results imply that proper vascular patterns in leaves are formed through the modulation of both positive and negative regulation by Dof5.8. MP may direct this fine-tuning mechanism by mediating the expression of Dof5.8. Gene expression in 4-day-old shoots was compared between the Dof5.8-overexpressing lines and control lines.
2013-06-11 | E-GEOD-47808 | biostudies-arrayexpress
Project description:Progesterone Receptor Membrane Component 1 (PGRMC1) is expressed in many cancer cells, where it is associated with detrimental patient outcomes. Multiple different functions and cellular locations have been attributed to PGRMC1 in a variety of contexts, however the mechanisms underlying PGRMC1 biology remain obscure. The protein contains several phosphorylated residues including tyrosines which were acquired early in animal evolution and could be involved with animal cell differentiation mechanisms. Here we demonstrate that mutagenic manipulation of PGRMC1phosphorylation status in MIA PaCa-2 (MP) pancreatic cells exerts broad pleiotropic effects, influencing cell plasticity and tumorigenicity, as assayed by cell biological and proteomics measurements. Relative to MP cells over-expressing hemagglutinin (HA)-tagged wild-type PGRMC1- HA (WT), cells expressing a PGRMC1-HA-S57A/S181A double mutant (DM) exhibited reduced levels of proteins involved in energy metabolism and mitochondrial function. This was associated with Rho-kinase inhibitor (ROCKI)-sensitive changes including altered cell shape, motility, increased PI3K/Akt and JNK activity, and fragmented mitochondrial morphology. An S57A/Y180F/S181A triple mutant (TM) reduced PI3K/Akt and JNK activation, indicating involvement of Y180. Both TM cells and Y180F single mutant cells exhibited attenuated mouse xenograft tumor growth. Tyrosine 180 phosphorylation status of PGRMC1 exerts dramatic influence over cancer cell biology.
2020-03-03 | PXD014716 | Pride