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Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock

ABSTRACT: The importance of oligogalacturonides for plant defence and growth has been described extensively in litterature. However, much of previous global transcriptome analyses for plants treated with oligogalacturonides have focused on long (>10 galacturonosyl residues) oligogalacturonides. This study focuses on the transcriptomic impact that trimeric oligogalacturonides and a mixture of oligogalacturonides have on plant transcriptomes and overall biology.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE69538 | GEO | 2015/06/05

SECONDARY ACCESSION(S): PRJNA285810

REPOSITORIES: GEO

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Comparative transcriptomic analysis of Arabidopsis plants treated with short oligogalacturonides and mock

Project description:The importance of oligogalacturonides for plant defence and growth has been described extensively in litterature. However, much of previous global transcriptome analyses for plants treated with oligogalacturonides have focused on long (>10 galacturonosyl residues) oligogalacturonides. This study focuses on the transcriptomic impact that short (<10 galacturonosyl residues) oligogalacturonides have on plant transcriptomes and overall biology. Arabidopsis seedling were grown on liquid 1/2 MS medium in 12-well culture plates in vitro for 12 days. 12 seedlings were cultured per well, and three wells were combined per biological replicate. The seedling plants were treated either with 1/2 MS medium (mock), 1/2 MS with trimeric oligogalacturonides (trimers) and a mixture of 1/2 MS and oligogalacturonides (short OG-mix) containing 2-9 residues for 3 hours. RNA was extracted from the seedlings, three biological replicates per treatment, and sequenced using the SOLiD 5500XL platform.

2015-06-05 | E-GEOD-69538 | biostudies-arrayexpress

DNA hypomethylation confers enhanced immunity against parasitic nematodes in plants

Project description:Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes. Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context. Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.

2020-07-07 | GSE130064 | GEO

Ascorbate oxidation primes rice plants for enhanced defence against root-knot nematode Meloidogyne graminicola through jasmonate/ethylene-activation

Project description:Ascorbic acid (AA) is known to play a vital role in plant growth and detoxification of reactive oxygen species, however little is known about the significance of AA oxidation in plant defence against pathogens. • The role of ascorbate oxidation in rice defence against root-knot nematodes, Meloidogyne graminicola, was tested with application of AA, ascorbate oxidase (AO), dehydroascorbic acid (DHA), biosynthesis inhibitors and use of mutants. Transcriptome analysis was done on AO treated plants, and hormone measurements were executed to confirm the results. Biochemical analyses were used to study oxidative stress markers, including accumulation of H2O2, , malondialdehyde and AA/DHA.

2020-01-22 | GSE125427 | GEO

Gene expression in rice roots after Pythium arrhenomsnes infection versus mock infection

Project description:Next to their essential roles in plant growth and development, phytohormones play a central role in plant immunity against pathogens. In this study we examined the role of hormones in the antagonism of the plant-pathogenic oomycete Pythium arrhenomanes against the root-knot nematode Meloidogyne graminicola in rice roots. Hormone measurements and gene expression analyses showed that the jasmonate (JA) pathway is induced early upon P. arrhenomanes infection. Exogenous application of methyl-jasmonate (MeJA) on the plant confirmed that JA is needed for basal defence against both P. arrhenomanes and M. graminicola in rice. Whereas M. graminicola suppresses root JA levels to increase host susceptibility, Pythium inoculation boosts JA accumulation up to levels that can no longer be repressed by the nematode in double-inoculated plants. Exogenous MeJA supply phenocopied the defence-inducing capacity of P. arrhenomanes against the root-knot nematode, whereas the antagonism was weakened in JA-insensitive mutants. Transcriptome analysis confirmed upregulation of JA biosynthesis and signalling genes upon P. arrhenomanes infection, and additionally revealed induction of genes involved in biosynthesis of diterpenoid phytoalexins, consistent with strong activation of the gene encoding the JA-inducible transcriptional regulator DITERPENOID PHYTOALEXIN FACTOR. Next to that, our results provide evidence for induced expression of genes encoding ERF83, and related PR proteins, as well as auxin depletion in P. arrhenomanes infected rice roots, which potentially further contributes to the reduced nematode susceptibility seen in double-infected plants.

2019-10-21 | GSE133268 | GEO

RNAseq of Arabidopsis seedlings of either wt or hsl3-1, in response to a 30 minute treatment of 100 nM CTNIP4 relative to mock

Project description:In order to identify novel stress-induced signalling peptides, we searched for Arabidopsis thaliana transcripts encoding short proteins (<150 amino acids) with a predicted signal peptide, which were induced upon biotic elicitor treatment (Bjornson et al., 2021). Through this analysis, we identified an uncharacterised family of peptides with 5 predicted members, which we named CTNIP1 to 5 (pronounced catnip) based on relatively conserved residues within the peptides. CTNIP4 is perceived by Arabidopsis, inducing some hallmark outputs of defence (Pattern-Triggered Immunity) signalling. Mass spectrometric analyses indicated that HSL3 may be the receptor mediating CTNIP recognition. Through assaying transcriptomic responses in wild type and hsl3-1 mutants, we were able to confirm similarity of CTNIP and defence responses at the transcriptional level, and the dependence of these responses on HSL3.

2022-06-13 | E-MTAB-11093 | biostudies-arrayexpress

Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid

Project description:Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid.

2013-07-22 | GSE34899 | GEO

Adenovirus vs Mock Infection

Project description:human bronchial smooth muscle cells were either infected with empty adenoviral type 5 vector at 40 MOI for 4 days, or Mock infected. Each sample set was then stimulated with a mixture of 10ng/mL IL-1beta, TNF-alfa, and gamma-IFN for 20 hours prior to RNA harvest. RNA samples were split, and the series consists of 3 slides, 2 of which are dye flipped. Keywords: parallel sample

2004-04-09 | GSE1291 | GEO

Expression analysis of Arabidopsis plants infected with Pseudomonas syringae pv. tomato DC3000 (Pto) strains

Project description:Effector-Triggered Immunity (ETI) and Pattern-Triggered Immunity (PTI) are well-defined modes of plant immunity triggered by recognition of pathogen effector proteins and microbe-associated molecular patterns, respectively. While ETI and PTI network extensively share signaling components, the shared components are used in different ways, resulting in distinct network properties in the model plant Arabidopsis: immunity is highly robust against network perturbations in ETI but relatively sensitive in PTI. However, the molecular mechanism how the shared network leads to the different properties is not known. Here we show that salicylic acid (SA) reponsive genes can respond in the absense of SA during ETI.

2014-07-29 | GSE40544 | GEO

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Pleiotropic expression of endogenous genes upon fungus infection of wheat plants containing anti-fungal transgenes

Project description:Recent attempts to increase endogenous disease resistance of plants by overexpression of anti-fungal transgenes have shown a potential of this method. However, it has also been shown that such improvements are usually small. One of the obvious reasons for this low anti-fungal effect might be the regulation of endogenous genes in parallel. In this project, we will study the effect of anti-fungal transgenes on the endogenous gene expression. Such effects might relate to substantial equivalence which is a biosafety issue of concern to the public. The GeneChip Wheat Genome Array will be used to detect expression of defence response genes and key genes of metabolic pathways. We will use wheat plants transformed with anti-fungal gene of specific effect against a small group of seed transmitted, pathogenic fungi (KP4 against smuts and bunts). Transformed spring wheat line will be challenged by stinking smut (inhibited by KP4). The effect on the endogenous gene expression will be tested for plants grown in the field in collaboration with the USDA Department. This work will contribute to our understanding of plant defence responses in general and may allow improving strategies to strengthen these responses.

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