RNA-seq of enriched barley stomatal complexes versus total leaves
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 3000
ORGANISM(S): Hordeum vulgare
SUBMITTER: Peter Ache
PROVIDER: E-MTAB-5877 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We prepared RNA from total leaves and epidermal peels, containing living guard cells (GC) and subsidiary cells (SC) only. In the third sample we blended epidermal peels to mechanically destroy the SC, leading to a pure guard cells fraction. By RNAseq and substraction of GC from SC transcripts, we were able to reliably assign transcripts to the barley SCs and GCs.
2023-12-31 | E-MTAB-10534 | biostudies-arrayexpress
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. We isolated guard cell protoplasts from 4-week-old WT(Col-0) and scap1 mutant plants and extracted RNA independently. Four biological replicates were performed for each experiment.
2013-02-28 | E-GEOD-43964 | biostudies-arrayexpress
Project description:Soil salinity is a major environmental constraint affecting crop growth and threatening global food security. Plants adapt to salinity by optimizing performance of stomata, the microscopic sphincters inserted into the wax-covered epidermis of the shoot, which balance CO2 intake for photosynthetic carbon gain and concomitant water loss. Stomata are formed by two guard cells (GCs) that are morphologically and functionally distinct from the other leaf cells. In order to better understand the molecular mechanisms underlying stomatal function under saline conditions we used proteomics approach to study isolated GCs from the salt-tolerant sugar beet species.
2020-05-27 | PXD017583 | Pride
Project description:Plant salt glands are nature’s desalination devices that harbour potentially useful information pertaining to salt and water transport during secretion. As part of the program toward deciphering secretion mechanisms in salt glands, we adopted a shotgun approach to look into the proteome of salt-gland enriched tissues of the mangrove tree species Avicennia officinalis. To achieve this, we isolated the adaxial epidermal peels (which harbour the salt glands), and separated them from the mesophyll tissues of the leaves. Three biological replicates were prepared and total proteins were extracted from these tissues. Proteins that were found to be unique in salt gland-enriched tissues were obtained by eliminating proteins found in the mesophyll tissues. The proteins that are uniquely present in salt gland-enriched tissues were then selected and categorized by GO analysis.
2015-07-22 | PXD000771 | Pride
Project description:Investigation of the interaction between barley and B. graminis. Individual resistant and infected epidermal cells of the susceptible barley line Pallas were easily distinguished by microscopy, and their contents collected in micro-capillaries. We hybridized 12 arrays with radioactively labeled material from these cell specific samples; 3 with material from resistant cells, 3 with material from infected cells, 3 with material from non-inoculated control cells, and 3 identical samples for technical replication. Pooling equal amounts of material from the 3 infected samples made these last 3 samples.
2005-11-13 | E-MEXP-457 | biostudies-arrayexpress
Project description:In this experiment the transcriptome reprogramming in barley during host and nonhost interaction with Magnaporthe sp. was analyzed in a time-series approach. Seven days old barley plants of cv. Vada were mock-inoculated or inoculated with adapted Magnaporthe isolate TH6772 from rice or non-adapted isolate CD180 from Pennisetum. After 6, 12, 24 and 48 hours the abaxial epidermis was sampled. Total RNA was extracted using the RNeasy Plant Mini Kit with on-column DNase digestion (Qiagen, Hilden, Germany), and hybridized to Agilent 44k oligonucleotide arrays.
2017-12-02 | E-MTAB-5634 | biostudies-arrayexpress
Project description:Quinoa, like a large fraction of halophytes, use so-called bladder cells to detoxify excess salt. These leaf exterior structures are formed by specialized trichomes and consist of a leaf epidermal cell, a stalk cell and the bladder cell itself. Under salt stress, Na+ and Cl- as well as K+ and metabolites are imported from leaf sources and stored in the bladder. During this process the stalk cell simultaneously operates as both a selectivity filter and a flux controller. We submerged detached leaves in buffer, then lightly brushed the abaxial surface with a fine paintbrush to remove only the EBCs. The abaxial epidermis was then removed using tweezers and sampled in buffer for RNA extraction and RNA sequencing to separate the gene expression profiles of stalk cells from bladders and leaves.
2022-04-01 | E-MTAB-10363 | biostudies-arrayexpress
Project description:Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity.
2014-11-24 | E-MTAB-3063 | biostudies-arrayexpress
Project description:Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at transcription levels in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme (NADP-ME) and pyruvate dehydrogenase (PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase (CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase (ALDH), ascorbate-dependant oxidoreductase (ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8 (HSP17.8) and dehydrin 3 (DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were likely constitutively expressed in drought-tolerant genotypes. Among them, 7 known annotated genes might enhance drought tolerance through signaling (such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP), anti-senescence (G2 pea dark accumulated protein GDA2) and detoxification (glutathione S-transferase (GST) pathways. In addition, 18 genes, including those encoding Δl-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C) and several chaperones, were differentially expressed in all genotypes under drought; thus, they were more likely general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley. Seven flag leaves of a replication for each genotype were harvested at 0 d, 1 d, 3 d and 5 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany). A table of the average, log2 RMA signal intensity values of three biological replicates for each Sample is linked below as a supplementary file.
2009-05-13 | E-GEOD-15970 | biostudies-arrayexpress
Project description:Leaf-to-leaf, systemic immune signaling known as systemic acquired resistance (SAR) is poorly understood in monocotyledonous plants. Here, we characterize systemic immunity in barley (Hordeum vulgare) triggered after primary leaf infection with either Pseudomonas syringae pathovar japonica (Psj) or Xanthomonas translucens pathovar cerealis (Xtc). Both pathogens induced resistance in systemic, uninfected leaves against a subsequent challenge infection with Xtc. In contrast to SAR in Arabidopsis thaliana, systemic immunity in barley was not associated with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 or the local or systemic accumulation of salicylic acid (SA). Instead, we documented a moderate local but not systemic induction of abscisic acid (ABA) after infection of leaves with Psj. In contrast to SA or its functional analog benzothiadiazole, local applications of the jasmonic acid methyl ester or ABA triggered systemic immunity to Xtc. RNA-seq analysis of local and systemic transcript accumulation revealed unique gene expression changes in response to both Psj and Xtc and a clear separation of local from systemic responses. The systemic response appeared relatively modest and quantitative RT-PCR associated systemic immunity with the local and systemic induction of two WRKY and two ETHYLENE RESPONSIVE FACTOR-like transcription factors. Systemic immunity against Xtc was further associated with transcriptional changes after a secondary/systemic Xtc challenge infection; these changes were dependent on the primary treatment. Taken together, bacteria-induced systemic immunity in barley may be mediated in part by WRKY and ERF-like transcription factors possibly facilitating transcriptional reprogramming to potentiate immunity.
2014-11-24 | E-MTAB-3056 | biostudies-arrayexpress