Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA559927 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13021800_1.fastq.gz | Fastqsanger.gz | |||
| SRR13021800_2.fastq.gz | Fastqsanger.gz | |||
| SRR13021801_1.fastq.gz | Fastqsanger.gz | |||
| SRR13021801_2.fastq.gz | Fastqsanger.gz | |||
| SRR13021802_1.fastq.gz | Fastqsanger.gz |
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Project description:Gene expression patterns of the plant colonizing bacterium,Pseudomonas putida KT2440 were evaluated as a function of growth in the Arabidopsis thaliana rhizosphere. Gene expression in rhizosphere grown P. putida cells was compared to gene expression in non-rhizosphere grown cells. Keywords: Gene expression
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Project description:Trichoderma spp. are filamentous fungi that colonize plant roots conferring beneficial effects to plants, indirectly through the induction of their defense systems or directly through the suppression of phytopathogens in the rhizosphere. Transcriptomic analyses of Trichoderma emerged as a powerful method for identifying the molecular events underlying the establishment of this beneficial relationship. Here, we focus on the transcriptomic response of Trichoderma virens during its interaction with Arabidopsis seedlings. The main response of T. virens to co-cultivation with Arabidopsis was the repression of gene expression. The biological processes of transport and metabolism of carbohydrates were downregulated, including a set of cell-wall-degrading enzymes putatively relevant for root-colonization. Repression of such genes reached their basal levels at later times of the interaction when genes belonging to the biological process of copper ion transport were induced, a necessary process providing copper as a cofactor for cell-wall degrading enzymes with auxiliary activities (AAs) class. RNA-Seq analysis showed the induction of a member of the SNF2 family of chromatin remodelers/helicase-related proteins, which was named IPA-1 (Increased Protection of Arabidopsis-1). Sequence analyses of IPA-1 showed as its closest relatives members of the Rad5/Rad16- and SNF2-subfamilies; however, it grouped into a different clade. Although deletion of ipa-1 in T. virens did not affect its growth, the antibiosis of Δipa-1 culture filtrates showed a diminished effect against Rhizoctonia solani but remained unaltered against Botrytis cinerea. Triggering of the plant defense genes in plants treated with Δipa-1 was higher, showing enhanced resistance against Pseudomonas syringae but not against B. cinerea as compared to wild type.
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2014-09-24 | E-MTAB-4449 | biostudies-arrayexpress
Project description:Microbes of the root-associated microbiome contribute to improve resilience and fitness of plants. In this study, the interaction between the salt stress tolerance-inducing beneficial bacterium Enterobacter sp. SA187 and Arabidopsis was investigated with a special focus on the plant immune system. Among the immune signalling mutants, the Lys-motif receptors LYK4 strongly affected the beneficial interaction. Overexpression of the chitin receptor components LYK4 compromised the beneficial effect of SA187 on Arabidopsis. Transcriptome analysis revealed that the role of LYK4 in immunity is intertwined with a function in remodeling defense responses. Overall, our data indicate that components of the plant immune system are key elements in mediating beneficial metabolite-induced plant abiotic stress tolerance.
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Project description:⢠Selected soil-borne rhizobacteria can trigger an induced systemic resistance (ISR) that is effective against a broad spectrum of pathogens. In Arabidopsis thaliana, the root-specific transcription factor MYB72 is required for the onset of ISR, but is also associated with plant survival under conditions of iron deficiency. Here we investigated the role of MYB72 in both processes. ⢠To identify MYB72 target genes, we analyzed the root transcriptomes of wild-type Col-0, mutant myb72, and complemented 35S:FLAG-MYB72/myb72 plants in response to ISR-inducing Pseudomonas fluorescens WCS417. ⢠Five WCS417-inducible genes were misregulated in myb72 and complemented in 35S:FLAG-MYB72/myb72. Amongst these, we uncovered β-glucosidase BGLU42 as a novel component of the ISR signaling pathway. Overexpression of BGLU42 resulted in constitutive disease resistance, whereas bglu42 was defective in ISR. Furthermore, we found 195 genes to be constitutively upregulated in MYB72-overexpressing roots in the absence of WCS417. Many of these encode enzymes involved in the production of iron-mobilizing phenolic metabolites under conditions of iron deficiency. We provide evidence that BGLU42 is required for their release into the rhizosphere. ⢠Together, this work highlights a thus far unidentified link between the ability of beneficial rhizobacteria to stimulate systemic immunity and mechanisms induced by iron deficiency in host plants. Total 18 samples of RNA extracted from Arabidopsis roots: Three genotypes: 1) Wild-type Arabidopsis thaliana accession Col-0, 2) mutant myb72-2 (Col-0 background), 3) Transgenic 35S:FLAG-MYB72 (oxMYB72) in the myb72-2 background; Two treatments: 1) non-treated control, 2) Roots colonized by beneficial Pseudomonas fluorescens WCS417 rhizobacteria; Replicates: three biological replicates per genotype/treatment combination
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Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
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Project description:Multi-species interactions are a major force in the evolution and dynamics of ecosystems. These interactions may occur either when species affect each other directly or when they interact indirectly via an intermediary species. Direct interactions between species are best understood, but indirect interactions may also often be strong enough to alter the evolutionary trajectories of the target species. Little is known about the genetic basis of direct interactions within an ecosystem and even less data is available for indirect interactions. This experiment uses a simple model ecosystem to build a view at the transcriptome level of how interactions between plants (Arabidopsis) and rhizosphere bacteria (Pseudomonas) are altered by biotic stressors (insect herbivores) and abiotic stressors (UV-B). Keywords: stress response
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Project description:• Selected soil-borne rhizobacteria can trigger an induced systemic resistance (ISR) that is effective against a broad spectrum of pathogens. In Arabidopsis thaliana, the root-specific transcription factor MYB72 is required for the onset of ISR, but is also associated with plant survival under conditions of iron deficiency. Here we investigated the role of MYB72 in both processes. • To identify MYB72 target genes, we analyzed the root transcriptomes of wild-type Col-0, mutant myb72, and complemented 35S:FLAG-MYB72/myb72 plants in response to ISR-inducing Pseudomonas fluorescens WCS417. • Five WCS417-inducible genes were misregulated in myb72 and complemented in 35S:FLAG-MYB72/myb72. Amongst these, we uncovered β-glucosidase BGLU42 as a novel component of the ISR signaling pathway. Overexpression of BGLU42 resulted in constitutive disease resistance, whereas bglu42 was defective in ISR. Furthermore, we found 195 genes to be constitutively upregulated in MYB72-overexpressing roots in the absence of WCS417. Many of these encode enzymes involved in the production of iron-mobilizing phenolic metabolites under conditions of iron deficiency. We provide evidence that BGLU42 is required for their release into the rhizosphere. • Together, this work highlights a thus far unidentified link between the ability of beneficial rhizobacteria to stimulate systemic immunity and mechanisms induced by iron deficiency in host plants.
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