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Proteomic analysis of plasmodesmata from Populus cell suspension cultures

ABSTRACT: 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.

INSTRUMENT(S): Q-Tof ultima

ORGANISM(S): Populus Trichocarpa (western Balsam Poplar) (populus Balsamifera Subsp. Trichocarpa)

TISSUE(S): Plant Cell, Primary Cell

SUBMITTER: Vaibhav Srivastava

LAB HEAD: Vaibhav Srivastava

PROVIDER: PXD010692 | Pride | 2018-12-31

REPOSITORIES: Pride

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			Action	DRS
	MIcrosomalBR2.prot.xml	Xml
	MicrosomalBR1.mgf	Mgf
	MicrosomalBR1.prot.xml	Xml
	MicrosomalBR1.rar	Other
	MicrosomalBR2.mgf	Mgf

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Publications

Proteomic Analysis of Plasmodesmata From Populus Cell Suspension Cultures in Relation With Callose Biosynthesis.

Leijon Felicia F Melzer Michael M Zhou Qi Q Srivastava Vaibhav V Bulone Vincent V

Frontiers in plant science 20181119

Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Here, we have isolated fractions enriched in plasmodesmata from cell suspension cultures of Populus trichocarpa and ...[more]

PMID: 30510561

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

Project description: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.

2019-07-05 | PXD006806 | Pride

Populus Palmitoylome - Proteomic Analysis of a Poplar Cell Suspension Culture Suggests a Major Role of Protein S-Acylation in Diverse Cellular Processes

Project description:The aim of this work was to identify S-acylated proteins in poplar. In order to achieve this, we have combined the acyl-biotin exchange method with a mass spectrometry based proteomic approach. To date, this is the only study on S-acylated proteins in a tree species. In total, we identified around 450 S-acylated proteins, the majority of which are involved in signal transduction, response to stress and transport.

2016-05-09 | PXD003735 | 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

Comparative proteomics of plasmodesmata

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.

2017-09-05 | PXD006880 | Pride

Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

Project description:Plasmodesmata (PD) are nanochannels that facilitate cell-to-cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)-bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein-tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M-BS wall interface than rice while the difference in M-M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co-expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD-associated genes and photosynthesis-related genes. PD-associated genes identified from our co-expression network analysis are related to cell wall expansion, translation and chloroplast signalling.

2024-11-21 | GSE260855 | GEO

Proteomic Analysis of Plasmodesmata From Populus Cell Suspension Cultures in Relation With Callose Biosynthesis.

Project description:Plasmodesmata are channels that link adjacent cells in plant tissues through which molecular exchanges take place. They are involved in multiple processes vital to plant cells, such as responses to hormonal signaling or environmental challenges including osmotic stress, wounding and pathogen attack. Despite the importance of plasmodesmata, their proteome is not well-defined. Here, we have isolated fractions enriched in plasmodesmata from cell suspension cultures of Populus trichocarpa and identified 201 proteins that are enriched in these fractions, thereby providing further insight on the multiple functions of plasmodesmata. Proteomics analysis revealed an enrichment of proteins specifically involved in responses to stress, transport, metabolism and signal transduction. Consistent with the role of callose deposition and turnover in the closure and aperture of the plasmodesmata and our proteomic analysis, we demonstrate the enrichment of callose synthase activity in the plasmodesmata represented by several gene products. A new form of calcium-independent callose synthase activity was detected, in addition to the typical calcium-dependent enzyme activity, suggesting a role of calcium in the regulation of plasmodesmata through two forms of callose synthase activities. Our report provides the first proteomic investigation of the plasmodesmata from a tree species and the direct biochemical evidence for the occurrence of several forms of active callose synthases in these structures. Data are available via ProteomeXchange with identifier PXD010692.

| S-EPMC6252348 | biostudies-literature

Assaying effector cell-to-cell mobility in plant tissues identifies hypermobility and indirect manipulation of plasmodesmata

Project description:In plants, plasmodesmata establish cytoplasmic continuity between cells to allow for communication and resource exchange across the cell wall. While plant pathogens use plasmodesmata as a pathway for both molecular and physical invasion, the benefits of molecular invasion (cell-to-cell movement of pathogen effectors) are poorly understood. To establish a methodology for identification and characterization of the cell-to-cell mobility of effectors, we performed a quantitative live imaging-based screen of candidate effectors of the fungal pathogen Colletotrichum higginsianum. We predicted C. higginsianum effectors by their expression profiles, the presence of a secretion signal, and their predicted and in planta localization when fused to GFP. We assayed for cell-to-cell mobility of nucleo-cytosolic effectors and identified 14 that are cell-to-cell mobile. We identified that 3 of these effectors are “hypermobile”, showing cell-to-cell mobility greater than expected for a protein of its size. To explore the mechanism of hypermobility we chose two hypermobile effectors and measured their impact on plasmodesmata function and found that even though they show no direct association with plasmodesmata, each increases the transport capacity of plasmodesmata. Thus, our methods for quantitative analysis of cell-to-cell mobility of candidate microbe-derived36effectors, or any suite of host proteins, can identify cell-to-cell hypermobility and offer greater understanding of how proteins affect plasmodesmal function and intercellular connectivity.

2023-11-27 | GSE248400 | GEO

Proteomics Analyses of Mycelium and Cysts of Phytophthora capsici

Project description:In this project, we have performed a comparative analysis of the proteomes of the mycelium and cysts of P. capsici. The identified proteins were functionally classified, which provides the basis for future research on these developmental stages of P. capsici and closely related species. Many of the proteins enriched in either the mycelium or cysts were found to contribute specific functions in these two life stages. Proteins enriched in mycelium were essentially associated with vegetative growth, whereas those enriched in cysts were primarily related to development-specific processes associated with the initiation of infection. The data provide a better understanding of the metabolic pathways underlying the mycelial and cyst developmental stages of P. capsici and point to potential targets of anti-oomycete compounds at each of these stages.

2016-08-02 | PXD002603 | Pride

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

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