Browse
Submit Data
Databases
API
Help

Dataset Information

432 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative proteomics of plasmodesmata

ABSTRACT: Plants as multi cellular organisms are composed of various specialized cell types. Most of these cell types are symplasmically connected via plasmodesmata (PD) allowing exchange of nutrients and signal molecules. To date, the molecular composition of PD is not well understood. A comprehensive and comparative proteomic approach was followed to identify proteins providing new insights into the composition of these important regulatory structures.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Max Kraner

LAB HEAD: Uwe Sonnewald

PROVIDER: PXD006880 | Pride | 2017-09-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Comparative proteomic profiling of the choline transporter-like1 (CHER1) mutant provides insights into plasmodesmata composition of fully developed Arabidopsis thaliana leaves.

Kraner Max E ME Müller Carmen C Sonnewald Uwe U

The Plant journal : for cell and molecular biology 20171006 4

In plants, intercellular communication and exchange are highly dependent on cell wall bridging structures between adhering cells, so-called plasmodesmata (PD). In our previous genetic screen for PD-deficient Arabidopsis mutants, we described choline transporter-like 1 (CHER1) being important for PD genesis and maturation. Leaves of cher1 mutant plants have up to 10 times less PD, which do not develop to complex structures. Here we utilize the T-DNA insertion mutant cher1-4 and report a deep comp ...[more]

PMID: 28865150

Similar Datasets

Comparative proteomics of sink and source cell wall

Project description:Plants as multi cellular organisms are composed of various specialized cell types. Most of these cell types are symplasmically connected via plasmodesmata (PD) allowing exchange of nutrients and signal molecules. To date, the molecular composition of PD is not well understood. A comprehensive and comparative proteomic approach was followed to identify proteins providing new insights into the composition of these important regulatory structures.

2017-09-06 | PXD007282 | Pride

Multiple C2 domains and Transmembrane region Proteins (MCTPs) tether membranes at plasmodesmata

Project description:In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved unique MCS, the plasmodesmata intercellular pores, which combine organelle tethering with regulation of cell-to-cell signalling, the molecular mechanisms of which remains unknown. Here, we identify Multiple C2 domains and Transmembrane region Proteins (MCTPs) as tethers that link the endoplasmic reticulum (ER) to the plasma membrane (PM) within plasmodesmata. We report that MCTPs, including MCTP3 and 4 recently identified as modulators of SHOOTMERISTEMLESS trafficking, are ER-anchored proteins that cluster at plasmodesmata. MCTPs insert into the ER via their transmembrane region whilst their C2 domains dock to the PM through interaction with anionic phospholipids. A mctp3/4 loss-of function mutant induces plant developmental defects while MCTP4 expression in a yeast .tether mutant partially restores ER-PM tethering. Our data suggest that MCTPs are unique membrane tethers controlling both ER-PM contacts and cell-cell signalling.

2019-07-08 | PXD013999 | Pride

Label-free quantitative proteomics on Nicotiana benthamiana plasmodesmal proteome following viral infection

Project description:We analyzed the PD-enriched fraction from Turnip mosaic virus (TuMV)-infected Nicotiana benthmiana (N. benthamiana) by using label-free quantitative proteomics of which 100 and 48 were significantly increased and decreased respectively when compared with mock plants.

2017-10-19 | PXD006323 | Pride

A high confidence Physcomitrium patens plasmodesmata proteome

Project description:Cells of multicellular organisms exchange nutrients, building blocks and information. In animals this exchange happens via gap junctions, in plants via plasmodesmata (PD). PD have striking properties with a large range of molecules from ions, to metabolites and synthetic dyes, RNA and proteins up to 40 kDa being translocated, ranging. PD are hard to characterize due to deep embedding into cell walls and presence of several membranes. Previous studies of the protein composition of PD of angiosperms identified large lists of proteins, few were validated. Here, we developed a probabilistic scoring approach in iteration with systematic localization on a large scale to define a high-confidence PD proteome of Physcomitrium patens. Conservation of targeting allowed us to validate 100s of proteins in tobacco. We developed a PD Score based on protein enrichment during PD preparation and significantly enriched protein features of known PD proteins from literature. PD scoring was iteratively improved by extensive validation of PD candidate protein localizations. As a result we establish a high confidence PD proteome from Physcomitrium patens comprising close to 300 proteins which together with the bona fide PD proteins from literature are made available in the public PDDB database. Conservation in localization strengthens the reliability of plant proteome and provides a basis for exploring the evolution of this important organelle. Glycolyl hydrolase family 17 proteins are presented as example of an abundant PD protein family with representatives across an evolutionary scale.

2024-01-18 | PXD032820 | Pride

Comparison of gene expression profiles of Jurkat cells with or without PD-1 ligation

Project description:CD8+ T cells in chronic viral infections like HIV develop functional defects such as loss of IL-2 secretion and decreased proliferative potential that are collectively termed exhaustion1. Exhausted T cells express increased levels of multiple inhibitory receptors, such as Programmed Death 1 (PD-1). PD-1 inhibition contributes to impaired virus-specific T cell function in chronic infection because antibody-mediated blockade of its ligand, Programmed Death Ligand 1 (PD-L1) is sufficient to improve T cell function and reduce viral replication in animal models. Reversing PD-1 inhibition is therefore an attractive therapeutic target, but the cellular mechanisms by which PD-1 ligation results in T cell inhibition are not fully understood. PD-1 is thought to limit T cell activation by attenuating T cell receptor (TCR) signaling. It is not known whether PD-1 ligation also acts by upregulating genes in exhausted T cells that impair their function. Here, we analyzed gene-expression profiles from HIV-specific CD8+ T cells in patients with HIV and show that PD-1 coordinately upregulates a program of genes in exhausted CD8+ T cells from humans and mice. This program includes upregulation of basic leucine transcription factor, ATF-like (BATF), a transcription factor in the AP-1 family. Enforced expression of BATF was sufficient to impair T cell proliferation and cytokine secretion, while BATF knockdown reduced PD-1 inhibition. Silencing BATF in CD4+ and CD8+ T cells from chronic viremic patients rescued HIV-specific T cell function. Thus inhibitory receptors can cause T cell exhaustion by upregulating genes â such as BATF â that inhibit T cell function. PD-1 expressing Jurkat cells were cultured for 18 hours with beads coated with antibodies to CD3 and CD28, with our without an antibody to PD-1.

2010-10-03 | E-GEOD-24026 | biostudies-arrayexpress

The Requirement for Cyclin D Function in Tumor Maintenance

Project description:This SuperSeries is composed of the following subset Series: GSE40512: Gene expression profile of human T-ALL cell line KOPTK1 treated with vehicle or PD 0332991 GSE40513: Gene expression profile of mouse breast cancer V720 cells treated with vehicle or PD 0332991 Refer to individual Series

2012-10-16 | E-GEOD-40514 | biostudies-arrayexpress

Diagnosis of Parkinson's Disease Based on Disease-Specific Autoantibody Profiles

Project description:Parkinson's Disease (PD) and Non-Demented Control (NDC) human sera were probed onto human protein microarrays in order to identify differentially expressed autoantibody biomarkers that could be used as diagnostic indicators. In the study presented here, 29 PD and 40 NDC human serum samples were probed onto human protein microarrays in order to identify differentially expressed autoantibodies. Microarray data was analyzed using several statistical significance algorithms, and autoantibodies that demonstrated significant group prevelance were selected as biomarkers of disease. Prediction classification analysis tested the diagnostic efficacy of the identified biomarkers; and differentiation of PD samples from other neurodegeneratively-diseased and non-neurodegeneratively-diseased controls (Alzheimer's disease, multiple sclerosis, and breast cancer) confirmed their specificity.

2012-02-27 | E-GEOD-29654 | biostudies-arrayexpress

Restoring PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance

Project description:Immune checkpoint inhibitors (ICIs) are a type of cancer treatment that work by targeting molecules on immune cells that can inhibit the immune system's ability to attack cancer cells. One such checkpoint molecule is PD-1, which is found on the surface of T cells (a type of immune cell) and helps to prevent them from attacking healthy cells. When PD-1 binds to its ligand (a molecule on the surface of some cells), it sends a signal to the T cell to \\"turn off\\" and not attack the cell. This mechanism is important in preventing the immune system from attacking healthy cells, but it can also be exploited by cancer cells to avoid detection and destruction by the immune system. In this study YUMM2.1 mouse tumour cells were implanted subcutaneously. The effect of IFN-γ-pre-treatment, PARP14 inhibition and PD-1 antibody treatment are reported by RNA-seq.

2023-08-22 | E-MTAB-12872 | biostudies-arrayexpress

Analysis of mouse T cell transcription profile after co-culture with BaF3 cells with or without the oncogenic point mutation JAK2 V617F

Project description:The activation of PD-1 (Programmed Death receptor-1) on T cells can cause T cell exhaustion and immune tolerance. Some tumors up-regulate the expression of the ligand of PD-1, namely PD-L1 (Programmed Death Receptor-Ligand 1), thus preventing anti-tumor immune response and promoting immune-escape. Previous studies have shown that JAK2 (Janus Kinase 2) signaling can promote PD-L1 expression in Hodgkin Lymphoma. In Myeloproliferative Neoplasms (MPN), JAK2 is frequently characterized by the the presence of the point-mutation V617F, which leads to its constitutive activation and to uncontrolled cell proliferation and survival. Accordingly, tumor cell lines expressing JAK2 V617F express higher levels of PD-L1 as compared to tumor cell lines negative for such mutations. In this experiment, we transfected BaF3 cells with a vector (plasmid for Murine Stem Cell Virus) containing the gene for JAK2 with the point-mutation V617F. As control, we used BaF3 cells transfected with the same vector, but without the gene for JAK2 V617F (empty vector). Both the cell lines (with/without JAK2 V617F) were co-cultured with primary murine T cells. When co-cultured with BaF3 cells expressing JAK2 V617F, T cells upregulated genes connected to senescence pathways, showed increased apoptosis, less cytokine production, and displayed other forms of dysfunction which can be associated with the activation of PD-1.

2018-12-01 | E-MTAB-5028 | biostudies-arrayexpress

Evading immune evasion via reprograming of the tumor microenvironment by radiotherapy and simultaneous targeting of TGF-β/PD-L1

Project description:Single cell transcriptome showed TGF-β expression is confined to PD-L1+ endothelium and M2 /lipofibroblast-like cells. Hence, superior effects of BA could be attributed to its ability to trap TGF-β to relevant PD-L1+ compartments. Mice were irradiated (photon) and one group of mice was treated with Bintrafusp. Lungs were subsequently dissociated and processed with the 10x genomics 3 prime v2 kit.

2021-08-10 | E-MTAB-10633 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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