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Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [bacteria RNA-seq]

ABSTRACT: Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [bacteria RNA-seq]

PROVIDER: PRJNA600498 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10869418_1.fastq.gz	Fastqsanger.gz
	SRR10869418_2.fastq.gz	Fastqsanger.gz
	SRR10869419_1.fastq.gz	Fastqsanger.gz
	SRR10869419_2.fastq.gz	Fastqsanger.gz
	SRR10869420_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [BS-seq]

Project description:Plants develop mutualistic association with beneficial rhizobacteria. To understand this important phenomenon, early mechanisms for establishing the mutualism are critical. Here we report that active DNA demethylation in plants controls root secretion of myo-inositol, which triggers and further facilitates colonization of the beneficial rhizobacteria Bacillus megaterium strain YC4, thereby allowing for plant growth-promotion. YC4 promotes plant growth but the beneficial effects were lost in the Arabidopsis mutant rdd that is defective in active DNA demethylation. Roots of rdd failed to associate with YC4, meanwhile the level of myo-inositol in root exudates was drastically reduced in rdd. Supplementation of myo-inositol to rdd restored YC4 colonization and plant growth-promotion, while plants with defective myo-inositol monophosphatase also failed in establishing mutualism with YC4. myo-Inositol not only induced chemotaxis of YC4 but also increased YC4 biofilm production, consistent with the transcriptional regulation of YC4 by myo-inositol. In addition, myo-inositol preferentially attracts Bacillus megaterium among the examined bacteria species. Regardless of YC4 inoculation, myo-inositol biosynthesis and catabolism genes are down- and up-regulated, respectively, in rdd compared to wild type plants. The differential expression of myo-inositol homeostasis genes is correlated with local DNA hypermethylation, whereas genetic disruption of the RNA-directed DNA methylation pathway abolished these epigenetic marks and reset the corresponding gene expression patterns, resulting in restored YC4 colonization and plant growth-promotion. Importantly, that active DNA demethylation controls myo-inositol-mediated mutualism between YC4 and plants was also demonstrated in Solanum lycopersicum. Our results uncover an important function of myo-inositol in plant-microbe interactions and its dependence on plant epigenetic regulation.

2022-12-19 | GSE143427 | GEO

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [bacteria RNA-seq]

2022-12-19 | GSE143434 | GEO

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [TAIR-RNA-seq]

2022-12-19 | GSE143433 | GEO

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

Project description:Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

| PRJNA600495 | ENA

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [BS-seq]

Project description:Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [BS-seq]

| PRJNA600485 | ENA

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [TAIR-RNA-seq]

Project description:Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria [TAIR-RNA-seq]

| PRJNA600493 | ENA

Active DNA demethylation regulates myo-inositol-mediated mutualism between plants and beneficial rhizobacteria

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-19 | GSE143436 | GEO

Airway epithelial cells from smokers treated with myo-inositol or placebo

Project description:Samples were obtained as part of a randomized, double blind, placebo-controlled, phase IIb study to determine the effects of myo-inositol in smokers with bronchial dysplasia. Smokers with greater than 1 site of dysplasia identified by autofluorescence bronchoscopy-directed biopsy were randomly assigned to receive oral placebo or myo-inositol, 9 g once/day for two weeks and then twice/day for 6 months. Cytologically normal airway epithelial cells were obtained via bronchoscopy from the right or left mainstem bronchus at baseline and 6 months post-treatment with myo-inositol or placebo from 69 study participants (n=138 samples). The RNA from these samples was isolated and used to prepare libraries for mRNA sequencing. Subjects were classified by response according to their change in dysplasia rate after 6-months. Among subjects with a complete response in the myo-inositol arm, there was a significant decrease in a gene expression signature reflective of PI3K activation.

2016-09-26 | GSE86422 | GEO

Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol

Project description:E. histolytica is believed to be devoid of peroxisomes, like most anaerobic protists. In this work, we provided the first evidence that peroxisomes are present in E. histolytica, although the set of proteins (peroxins) responsible for peroxisome biogenesis was reduced to only seven members (Pex1, Pex6, Pex5, Pex11, Pex14, Pex16, and Pex19). Targeting matrix proteins to peroxisomes is reduced to the PTS1-dependent pathway mediated via the soluble Pex5 receptor, while the PTS2 receptor Pex7 is absent. Immunofluorescence microscopy showed that peroxisomal markers (Pex5, Pex14, Pex16, Pex19) are present in vesicles distinct from mitosomes, the endoplasmic reticulum and the endosome/phagosome system, except Pex11, which has dual localization in peroxisomes and mitosomes. Immunoelectron microscopy revealed that Pex14 localized to vesicles of approximately 90-100 nm in diameter. Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets, including myo-inositol dehydrogenase (myo-IDH). Peroxisomal NAD-dependent myo-IDH appeared to be a dimeric enzyme with high affinity to myo-inositol (Km 0,044 mM) and can utilize also scyllo-inositol, D-glucose and D-xylose as substrates. Phylogenetic analyses revealed that orthologs of myo-IDH with PTS1 are present in E. dispar, E. nutalli and E. moshkovskii but not in E. invadens, and form a monophyletic clade of mostly peroxisomal orthologs with free-living M. balamuthi and P. schiedti. The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs.

2021-10-29 | PXD026653 | Pride

Transcription profiling of Rhizobium leguminosarum biovar viciae strain 3841grown in AMS minimal salts on either glucose ammonia or myo-inositol ammonia

Project description:Rhizobium leguminosarum biovar viciae strain 3841 was grown in AMS minimal salts on either glucose ammonia or myo-inositol ammonia and gene expression compared.

2008-12-18 | E-MEXP-1961 | biostudies-arrayexpress

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