Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative analysis of four- and seven-day-old Arabidopsis thaliana plasmodesmata fractions using label free method

ABSTRACT: To compare four- and seven-day-old Arabidopsis thaliana plasmodesmata proteome, the identification and the relative amount of proteins in plasmodesmata, cell wall and total cell extracts were performed using fractions purified from four- and seven-day-old liquid culture cells of A. thaliana. The relative amount for each protein was determined with a label-free quantification method. Four biological replicates of each fraction were used for quantification.

INSTRUMENT(S): Q Exactive

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

SUBMITTER: Stephane Claverol

LAB HEAD: Emmanuelle Bayer

PROVIDER: PXD006806 | Pride | 2019-07-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	eb151118_01.msf	Msf
	eb151118_01.raw	Raw
	eb151118_02.msf	Msf
	eb151118_02.raw	Raw
	eb151118_03.msf	Msf

Items per page:

1 - 5 of 48

Publications

Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata.

Brault Marie L ML Petit Jules D JD Immel Françoise F Nicolas William J WJ Glavier Marie M Brocard Lysiane L Gaston Amèlia A Fouché Mathieu M Hawkins Timothy J TJ Crowet Jean-Marc JM Grison Magali S MS Germain Véronique V Rocher Marion M Kraner Max M Alva Vikram V Claverol Stéphane S Paterlini Andrea A Helariutta Ykä Y Deleu Magali M Lins Laurence L Tilsner Jens J Bayer Emmanuelle M EM

EMBO reports 20190709 8

In eukaryotes, membrane contact sites (MCS) allow direct communication between organelles. Plants have evolved a unique type of MCS, inside intercellular pores, the plasmodesmata, where endoplasmic reticulum (ER)-plasma membrane (PM) contacts coincide with regulation of cell-to-cell signalling. The molecular mechanism and function of membrane tethering within plasmodesmata remain unknown. Here, we show that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of ...[more]

PMID: 31286648

Similar Datasets

Establishment of plasmodesmata core proteome using label free semi-quantitative proteomic analysis.

Project description:To establish the plasmodesmata core proteome, the identification and the relative amount of proteins in different cellular fractions, namely, the plasmodesmata, plasma membrane, total cell extract, microsomal and cell wall fractions, were determined using label-free quantification method. Four to six biological replicates for each fraction were used for quantification.

2019-07-05 | PXD006800 | Pride

Comparative phyloproteomics identifies conserved plasmodesmal proteins

Project description:Plasmodesmata are cytosolic bridges, lined by the plasma membrane and traversed by endoplasmic reticulum, connecting cells and tissues, and critical for many aspects of plant biology. While plasmodesmata are notoriously difficult to extract, tissue fractionation and proteomic analyses can yield valuable knowledge of their composition. Here we have generated two novel proteomes to expand tissue and taxonomic representation of plasmodesmata: one from mature Arabidopsis leaves and one from the moss Physcomitrium patens and leveraged these and existing data to perform a comparative analysis to identify evolutionarily conserved protein families that are associated with plasmodesmata. Thus, we identified b-1,3-glucanases, C2 lipid-binding proteins and tetraspanins as core plasmodesmal components that likely serve as essential structural or functional components. Our approach has not only identified elements of a conserved plasmodesmal proteome, but also demonstrated the added power offered by comparative analysis for recalcitrant samples. Conserved plasmodesmal proteins establish a basis upon which ancient plasmodesmal function can be further investigated to determine the essential roles these structures play in multicellular organism physiology in the green lineages.

2023-01-13 | PXD038964 | Pride

Proteomic analysis of plasmodesmata from Populus cell suspension cultures

Project description:In this project, we have investigated the proteome of the plasmodesmata (PD) enriched membrane fraction from poplar cell suspension cultures and quantitatively compared its protein composition with other membrane fractions. We build on the previously published literature on the PD proteome by using semiquantitative methods and, for the first time, demonstrate in vitro callose synthase activity from Populus PD proteins. To our knowledge, this study is the first proteomic investigation of the PD performed on a tree species.

2018-12-31 | PXD010692 | Pride

Transcription profiling of Arabidopsis seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA).

Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Three samples: Unimbibed seeds, untreated imbibed seeds, TSA-treated imbibed seeds.

2008-06-12 | E-GEOD-3784 | biostudies-arrayexpress

Transcription profiling of Arabidopsis treated with Trichostatin A (TSA) to inhibit of histone deacetylase in Arabiodopsis thaliana

Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Two samples (TSA-treated v.s. untreated). Two replicates for each sample.

2008-06-12 | E-GEOD-3783 | biostudies-arrayexpress

Transcription profiling of Arabidopsis treated with Histone acetylation during seed germination (GEO Super Series)

Project description:This SuperSeries is composed of the following subset Series:; GSE3783: Trichostatin A (TSA) inhibition of histone deacetylase in Arabiodopsis thaliana; GSE3784: Seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA). Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Refer to individual Series

2008-06-12 | E-GEOD-3799 | biostudies-arrayexpress

Expression profiles of embryo-defective Arabidopsis thaliana mutants increased size exclusion limit1 (ise1) and ise2

Project description:We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified ise1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, while ISE2 encodes a DEVH-type RNA helicase. Here we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function we performed whole genome expression analyses. The most significantly affected class of transcripts in both mutants encodes products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus crosstalk, add PD as a critical player in the plant cell communication network, and thereby illuminate a new signaling pathway, dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function. Three biological replicates each of either ise1 or ise2 mutant seeds vs. sister wild-type controls

2011-11-09 | E-GEOD-33558 | biostudies-arrayexpress

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

D. melanogaster gene expression profiling time course of Snail mutants

Project description:Expression profiling of Drosophila melanogaster halo[AJ] snail[Df(2L)TE116GW11] and halo[AJ] sna[V2] homozygous mutant embryos at two timepoints of embryogenesis. Embryos were manually sorted and assayed at cellularisation stage (stage 5 to early stage 6) and at gastrulation stage (late stage 6 to early stage 8). Homozygous mutant embryos were sorted based on their reduced transparency caused by the recessive mutation of halo[AJ]. Stage-matched halo[AJ] embryos served as wildtype control. Total RNA was extracted, amplified and hybridized to Affymetrix GeneChip Drosophila Genome array version 2. Three biological replicates at each condition were generated.

2014-01-10 | E-MTAB-1598 | biostudies-arrayexpress

AP-SWATH analysis reveals a direct involvement of VCP/p97 in integrated stress response signalling through CReP/PPP1R15B degradation

Project description:The ubiquitin-directed AAA-ATPase VCP/p97 facilitates degradation of misfolded proteins in diverse cellular stress response pathways. Resolving the complexity of dynamic interactions with hosts of accessory proteins and substrates has therefore been a major challenge. Here, we used affinity-purification SWATH mass spectrometry (AP-SWATH) to identify proteins that specifically interact with a p97 substrate-trapping mutant, p97-E578Q. AP-SWATH identified differential interactions over a large detection range from abundant cofactors to pathway-specific partners and individual ligases such as RNF185 and MUL1 that were trapped in p97-E578Q complexes. In addition, we identified substrate candidates including the PP1 regulator CReP/PPP1R15B that dephosphorylates eIF2α and thus counteracts attenuation of translation by stress-kinases. We demonstrate here that p97 with its Ufd1-Npl4 adapter ensures rapid turnover and balanced levels of CReP in unperturbed cells. Moreover, we show that p97 is essential for the quantitative stress-induced degradation of CReP and, consequently, robust eIF2α phosphorylation to enforce the stress response. Thus, p97 not only facilitates bulk degradation of misfolded proteins upon stress, but also has an unanticipated function in directly modulating the integrated stress response at the level of signalling.

2018-04-04 | PXD007876 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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