Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA311601 | ENA |
REPOSITORIES: ENA
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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
2016-02-11 | E-GEOD-77806 | biostudies-arrayexpress
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.
2016-02-11 | GSE77806 | GEO
Project description:To optimize access to nitrogen under limiting conditions, root systems must continuously sense and respond to local or temporal fluctuations in nitrogen availability. In Arabidopsis thaliana and several other species, external N levels that induce only mild deficiency stimulate the emergence of lateral roots and especially the elongation of primary and lateral roots. However, the identity of the genes involved in this coordination remains still largely elusive. In order to identify novel genes and mechanisms underlying nitrogen-dependent root morphological changes, we investigated time-dependent changes in the root transcriptome of Arabidopsis thaliana plants grown under sufficient nitrogen or under conditions that induced mild nitrogen deficiency.
2023-09-12 | GSE216293 | GEO
Project description:This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
J Theor Biol.2011 Aug 21;283(1):152-67.
PMID: 21640126,
Abstract:
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.
2012-04-10 | BIOMD0000000416 | BioModels
Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.
2023-12-31 | GSE225299 | GEO
Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.
2020-09-22 | GSE158273 | GEO
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
2020-11-01 | GSE151376 | GEO
Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.
2013-07-17 | E-GEOD-43162 | biostudies-arrayexpress
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
2021-11-03 | GSE169629 | GEO
Project description:E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana. The role of BTS in root tissues has been well established. However, its role in shoot tissues has been scarcely studied. Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. Moreover, in shoot tissues of bts-1 plants, levels of ADP and ATP and the ratio of ADP/ATP were greatly increased with a concomitant decrease in levels of soluble sugar and starch. The decreased starch level inbts-1 shoot tissues was restored to the level of shoot tissues of wild-type plants upon vanadate treatment. Through this study, we expand the role of BTS to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots.
2022-04-19 | GSE189090 | GEO