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Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana

ABSTRACT: This research was undertaken to investigate the global role of inositol phosphorylceramide synthase (IPCS) activity in plants and reveal its potential as a herbicide target. The non-mammalian enzyme is a key component in the plant sphingolipid biosynthetic pathway and is shown here to be a possible herbicide target. RNA-Seq analyses demonstrated that over-expression of inositol phosphorylceramide synthase isoforms AtIPCS1, 2 or 3 in Arabidopsis thaliana resulted in the down-regulation of genes involved in plant response to pathogens. In addition, genes associated with the abiotic stress response to salinity, cold and drought were found to be similarly down-regulated. Detailed analyses of transgenic lines over-expressing AtIPCS1-3 at various levels revealed that the degree of down-regulation is specifically correlated with the level of IPCS expression. Singular enrichment analysis of these down-regulated genes showed that AtIPCS1-3 expression affects biological signaling pathways involved in plant response to biotic and abiotic stress. The up-regulation of genes involved in photosynthesis and lipid localization was also observed in the over-expressing lines.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE129016 | GEO | 2019/05/07

REPOSITORIES: GEO

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

2022-12-19 | GSE143427 | GEO

Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana

Project description:Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana

| PRJNA529715 | ENA

Transcriptome analysis indicates the involvement of herbicide-responsive and plant–pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti

Project description:Background: The continuous use of the herbicides contributes to the emergence of the resistant populations of numerous weed species that are tolerant to multiple herbicides with different modes of action (multiple resistance) which is provided by non-target-site resistance mechanisms. In this study, we addressed the question of rapid acquisition of herbicide resistance to pinoxaden (acetyl CoA carboxylase inhibitor) in Apera spica-venti, which endangers winter cereal crops and has high adaptation capabilities to inhabit many rural locations. To this end, de novo transcriptome of Apera spica-venti was assembled and RNA-sequencing analysis of plants resistant and susceptible to pinoxaden treated with this herbicide was performed. Results: The obtained data showed that the prime candidate genes responsible for herbicide resistance were those encoding 3-ketoacyl-CoA synthase 12-like, UDP-glycosyltransferases (UGT) including UGT75K6, UGT75E2, UGT83A1-like, and glutathione S-transferases (GSTs) such as GSTU1 and GSTU6. Also, such highly accelerated herbicide resistance emergence may result from the enhanced constitutive expression of a wide range of genes involved in detoxification already before herbicide treatment and may also influence response to biotic stresses, which was assumed by the detection of expression changes in genes encoding defence-related proteins, including receptor kinase-like Xa21. Moreover, alterations in the expression of genes associated with methylation in non-treated herbicide-resistant populations were identified. Conclusion: The obtained results indicated genes that may be involved in herbicide resistance. Moreover, they provide valuable insight into the possible effect of resistance on the weed interaction with the other stresses by indicating pathways associated with both abiotic and biotic stresses.

2023-04-22 | GSE204857 | GEO

Transcriptome analysis indicates the involvement of herbicide-responsive and plant-pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti

2023-04-22 | GSE204788 | GEO

Transcriptomic analysis of Bacteroides thetaiotaomicron inositol lipid knockout strains

Project description:We report next generation sequencing RNA-seq data of human gut commensal Bacteroides thetaiotaomicron strains deficient in inositol lipid synthesis, including dBT_1522 (phosphoinositol dihydroceramide synthase knockout) and its wild-type background strain, and iSPTdBT_1526 (myo-inositol-phosphate synthase) knockout with its background strain ("iSPT," inducible serine palmitoyltransferase).

2022-01-21 | GSE193734 | GEO

FPS down-regulation alters chloroplast development and triggers an sterol-dependent induction of JA-related and Fe deficiency transcriptional responses

Project description:In order to study the role of Farnesyl diphosphate synthase (FPS) in post-embryonic plant development, we generated Arabidopsis conditional knockdown mutants expressing amiRNAs devised to simultaneously silence both FPS (FPS1 and FPS2) genes. The expression of the amiRNAs is regulated by using a methoxyfenozide (MFZ) inducible promoter. An RNAseq analysis was made to compare the differentially expressed genes between control (not induced) and silenced (MFZ-induced) amiFPSa Arabidopsis seedlings. Differential gene expression analysis shows that a reduction in FPS activity levels triggers misregulation of genes involved in biotic and abiotic stress responses, the most prominent being the rapid induction of a set of genes related to the jasmonic acid (JA) pathway. Down-regulation of FPS also triggered a Fe-deficiency transcriptional response that is consistent with the Fe-deficient status observed in FPS silenced plants.

2016-11-08 | GSE79412 | GEO

Arabidopsis overexpressing DRB2 and DRB3 genes

Project description:The model plant Arabidopsis thaliana has five double-stranded RNA-binding proteins (DRB1-DRB5), two of which, DRB1 and DRB4, are well characterized. In contrast, the functions of DRB2, DRB3 and DRB5 have yet to be elucidated. In this study, we tried to uncover their functions using drb mutants and DRB-over-expressed lines. In over-expressed lines of all five DRB genes, the over-expression of DRB2 or DRB3 (DRB2ox or DRB3ox) conferred a downward-curled leaf phenotype, but the expression profiles of 10 small RNAs were similar to that of the wild-type (WT) plant. Phenotypes were examined in response to abiotic stresses. Both DRB2ox and DRB3ox plants exhibited salt-tolerance. When these plants were exposed to cold stress, drb2 and drb3 over-accumulated anthocyanin but DRB2ox and DRB3ox did not. Therefore, the over-expression of DRB2 or DRB3 had pleiotropic effects on host plants. Microarray and deep-sequencing analyses indicated that several genes encoding key enzymes for anthocyanin biosynthesis, including chalcone synthase (CHS), dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS), were down-regulated in DRB3ox plants. When DRB3ox was crossed with the pap1-D line, which is an activation-tagged transgenic line that over-expresses the key transcription factor PAP1 (Production of anthocyanin pigmentation1) for anthocyanin biosynthesis, over-expression of DRB3 suppressed the expression of PAP1, CHS, DFR and ANS genes. DRB3 negatively regulates anthocyanin biosynthesis by modulating the level of PAP1 transcript. Since two different small RNAs regulate PAP1 gene expression, a possible function of DRB3 for small RNA biogenesis is discussed.

2016-11-30 | GSE87780 | GEO

Comprehensive transcriptome analysis of the synthetic auxin herbicide response in the problematic weed species Erigeron canadensis

Project description:Background: The auxin herbicides 2,4-D and dicamba are commonly used for management of horseweed (Erigeron canadensis L, (syn: Conyza canadensis L)). Halauxifen-methyl is a new auxin herbicide and recently commercialized to control several broadleaf weed species under a range of sites and environmental conditions. While synthetic auxin herbicides have been used for over 70 years, the precise mode of action that leads to plant death has yet to be clearly characterized. As new chemical families are discovered and the use of these herbicides continues to increase, it is imperative to understand how synthetic auxin active ingredients work within the plant to cause an herbicidal effect. Results: At 1 hour after treatment (HAT), 48 genes were consistently upregulated across the three herbicides, many of which are involved in the auxin-activated signaling pathway and response to auxin. At 6 HAT, 735 genes were upregulated by all herbicide treatments including genes associated with hormone signaling, metabolism, transport, senescence, and gene expression. The GO terms representing the 501 genes downregulated in all herbicide treatments were broadly categorized under two major groups: ATP and photosynthesis. At 6 HAT, over 50% of the genes differential expressed among the three herbicide treatments were unique to a single active ingredient. Conclusion: This research presents a first look into the differential gene expression profiles in horseweed following a foliar application of synthetic auxin compounds that represent three unique chemical families. While there are an abundance of transcriptome similarities induced by each herbicide that accounts for the general auxin herbicide response, distinct gene expression changes exclusive to each compound cannot be ignored as a contributor to the mode of action.

2020-02-03 | GSE116958 | GEO

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