Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A cell-sorting based nano-scale pipeline for cell type-specific multi-omics in plants

ABSTRACT: Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the characteristics of each type of cells will reveal specific cell functions and enhance understanding of how an organism organizes and works. Here we report a high-sensitive and efficient cell-type-specific multi-omics pipeline, combining simplified flow cytometry-based fluorescent cell-sorting for fluorescent protoplasts and optimized nano-scale proteomics and metabolomics methods, which allow us to in-depth analyze the proteomics and metabolomics of a particular type of cells. By this method, we quantitatively compared the proteomics and metabolomics between guard cells and mesophyll cells and revealed that the enrichment of signal transduction-related proteins enables guard cells to respond to various environmental stimuli quickly. We uncovered a guard-cell-specific kinase cascade consisting of RAF15 and OST1 mediates the ABA-induced stomatal closure in guard cells. This pipeline is applicable to various types of cells in plant or non-plant systems to acquire systemic knowledge of how cells work specifically and in highly organized multiple cell organisms.

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

SUBMITTER: Pengcheng Wang

PROVIDER: PXD030489 | JPOST Repository | Sat Dec 17 00:00:00 GMT 2022

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20200204-WPC-SS%2010000_E4_1_4694.d.xlsx	Xlsx
	20200204-WPC-SS%205000_E5_1_4696.d.xlsx	Xlsx
	20200204-WPC-SS10000_E4_1_4694_5.3.236.mgf	Mgf
	20200204-WPC-SS5000_E5_1_4696_5.3.236.mgf	Mgf
	20200217-WPC-Gd%2010000_F2_1_4937.d.xlsx	Xlsx

Items per page:

1 - 5 of 20

Similar Datasets

A cell-sorting based nano-scale pipeline for cell type-specific multi-omics in plants

Project description:Multicellular organisms such as plants contain different types of cells with specialized functions. Analyzing the characteristics of each type of cells will reveal specific cell functions and enhance understanding of how an organism organizes and works. Here we report a high-sensitive and efficient cell-type-specific multi-omics pipeline, combining simplified flow cytometry-based fluorescent cell-sorting for fluorescent protoplasts and optimized nano-scale proteomics and metabolomics methods, which allow us to in-depth analyze the proteomics and metabolomics of a particular type of cells. By this method, we quantitatively compared the proteomics and metabolomics between guard cells and mesophyll cells and revealed that the enrichment of signal transduction-related proteins enables guard cells to respond to various environmental stimuli quickly. We uncovered a guard-cell-specific kinase cascade consisting of RAF15 and OST1 mediates the ABA-induced stomatal closure in guard cells. This pipeline is applicable to various types of cells in plant or non-plant systems to acquire systemic knowledge of how cells work specifically and in highly organized multiple cell organisms.

2022-12-18 | PXD030511 | JPOST Repository

A cell type-specific proteomics uncovers a guard cell-specific RAF15-SnRK2.6/OST1 kinase cascade

2023-05-23 | PXD034026 | JPOST Repository

Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells

Project description:Multicellular organisms such as plants contain different cell types with specialized functions. Analyzing the characteristics of each cell type reveals specific cell functions and enhances understanding of organization and function at the organismal level. Guard cells are specialized epidermal cells that play an important role in gaseous exchange in and out of plant leaves by regulating the opening and closing of the stomata, and provide a model genetic system for analyzing cell fate, signaling and function. Several proteomics analyses of guard cells are available, but these are limited in depth. Here we used enzymatic isolation and flow cytometry to enrich for guard cell and mesophyll cell protoplasts and acquire in-depth proteomics in these two major cell types in Arabidopsis leaves. We identified ~3,000 proteins not previously found in the guard cell proteome and more than 500 proteins that may be specific to guard cells. The depth of our proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf-like kinase15(RAF15) and Snf1-related kinase2.6(SnRK2.6)/OST1(open stomata 1) mediate abscisic acid (ABA)-induced stomatal closure. RAF15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the dephosphorylated inactive form of SnRK2.6/OST1. ABA-triggered SnRK2.6/OST1 activation and stomatal closure was impaired in raf15 mutants. Our study answers the long-standing question of how ABA activates SnRK2.6/OST1 in guard cells and represents a resource potentially providing many more insights into the molecular basis of guard cell and mesophyll cell development, structure, and function.

2024-02-04 | PXD039858 | JPOST Repository

Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells

2023-02-04 | PXD039857 | JPOST Repository

Cell type-specific proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells

Project description:Multicellular organisms such as plants contain different cell types with specialized functions. Analyzing the characteristics of each cell type reveals specific cell functions and enhances understanding of organization and function at the organismal level. Guard cells are specialized epidermal cells that play an important role in gaseous exchange in and out of plant leaves by regulating the opening and closing of the stomata, and provide a model genetic system for analyzing cell fate, signaling and function. Several proteomics analyses of guard cells are available, but these are limited in depth. Here we used enzymatic isolation and flow cytometry to enrich for guard cell and mesophyll cell protoplasts and acquire in-depth proteomics in these two major cell types in Arabidopsis leaves. We identified ~3,000 proteins not previously found in the guard cell proteome and more than 600 proteins that may be specific to guard cells. The depth of our proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf-like kinase15(RAF15) and Snf1-related kinase2.6(SnRK2.6)/OST1(open stomata 1) mediate abscisic acid (ABA)-induced stomatal closure. RAF15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the dephosphorylated inactive form of SnRK2.6/OST1. ABA-triggered SnRK2.6/OST1 activation and stomatal closure was impaired in raf15 mutants. We also showed that enrichment of enzymes and in flavone metabolism in GCP, and consistently, dramatically highly accumulation of flavone metabolites. Our study answers the long-standing question of how ABA activates SnRK2.6/OST1 in guard cells and represents a resource potentially providing many more insights into the molecular basis of guard cell and mesophyll cell development, metabolism, structure, and function.

2024-04-05 | PXD041345 | JPOST Repository

A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

Project description:Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

2023-10-02 | PXD045840 | Pride

Distinct guard cell specific remodeling of chromatin accessibility during abscisic acid and CO2 dependent stomatal regulation (RNA-Seq)

Project description:In plants, epidermal guard cells integrate and respond to numerous environmental signals to control stomatal pore apertures thereby regulating gas exchange. Chromatin structure controls transcription factor access to the genome, but whether large-scale chromatin remodeling occurs in guard cells during stomatal movements, and in response to the hormone abscisic acid (ABA) in general, remain unknown. Here we isolate guard cell nuclei from Arabidopsis thaliana plants to examine whether the physiological signals, ABA and CO2, regulate guard cell chromatin during stomatal movements. Our cell type specific analyses uncover patterns of chromatin accessibility specific to guard cells and define novel cis-regulatory sequences supporting guard cell specific gene expression. We find that ABA triggers extensive and dynamic chromatin remodeling in guard cells, roots, and mesophyll cells with clear patterns of cell-type specificity. DNA motif analyses uncover binding sites for distinct transcription factors enriched in ABA-induced and ABA-repressed chromatin. We identify the ABF/AREB bZIP-type transcription factors that are required for ABA-triggered chromatin opening in guard cells and implicate the inhibition of a set of bHLH-type transcription factors in controlling ABA-repressed chromatin. Moreover, we demonstrate that ABA and CO2 induce distinct programs of chromatin remodeling. We provide insight into the control of guard cell chromatin dynamics and propose that ABA-induced chromatin remodeling primes the genome for abiotic stress resistance.

2023-12-19 | GSE243472 | GEO

Distinct guard cell specific remodeling of chromatin accessibility during abscisic acid and CO2 dependent stomatal regulation (ATAC-Seq)

2023-12-19 | GSE243470 | GEO

Microarray analysis of scap1 mutant and wild type in Arabidopsis thaliana guard cell protoplast

Project description:Stomata are highly specialized organs which consist of pairs of guard cells and regulate gas and water vapor exchange in plants. While early stages of guard cell differentiation have been described and were interpreted in analogy to processes of cell type differentiation in animals, the downstream development of functional stomatal guard cells remains poorly understood. We have isolated an Arabidopsis mutant, scap1 (stomatal carpenter 1), that develops irregularly shaped guard cells and lacks the ability to control stomatal aperture, including CO2-induced stomatal closing and light-induced stomatal opening. SCAP1 was identified as a plant-specific Dof-type transcription factor expressed in maturing guard cells but not in guard mother cells. SCAP1 regulates the expression of genes encoding key elements of stomatal functioning and morphogenesis, such as a K+ channel protein, MYB60 transcription factor, and pectin methyl esterase. Consequently, ion homeostasis was disturbed in scap1 guard cells, and esterification of extracellular pectins was impaired so that the cell walls lining the pores did not mature normally. We conclude that SCAP1 regulates essential processes of stomatal guard cell maturation and functions as a key transcription factor regulating the final stages of guard cell differentiation.

2013-02-28 | GSE43964 | GEO

Microarray analysis of scap1 mutant and wild type in Arabidopsis thaliana guard cell protoplast

2013-02-28 | E-GEOD-43964 | biostudies-arrayexpress