Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early phosphate-deficiency induced signal changes in Arabidopsis roots

ABSTRACT: A mutant previously isolated from a screen of EMS-mutagenized Arabidopsis lines, per1, showed normal root hair development under control conditions but displayed an inhibited root hair elongation phenotype upon Pi deficiency. Additionally, the per1 mutant exhibited a pleiotropic phenotype under control conditions, resembling Pi-deficient plants in several aspects. Under Pi deficiency, the accumulation of Pi and iron was increased in the mutant when compared to the wild-type. Inhibition of root hair elongation upon growth on low Pi media was reverted by treatment with the Pi analog phosphite, suggesting that the mutant phenotype is not the result of a defect in Pi sensing. Reciprocal grafting experiments revealed that the mutant rootstock is sufficient to cause the phenotype. Transcriptional profiling of per1 and wild-type plants subjected to short-term Pi starvation revealed genes that may be important for the signaling of Pi deficiency. We conclude that UBP14 function is crucial for adapting root development to the prevailing local availability of phosphate.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE15649 | GEO | 2009/04/14

SECONDARY ACCESSION(S): PRJNA116663

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Arabidopsis roots to investigate early phosphate-deficiency induced signal changes

Project description:A mutant previously isolated from a screen of EMS-mutagenized Arabidopsis lines, per1, showed normal root hair development under control conditions but displayed an inhibited root hair elongation phenotype upon Pi deficiency. Additionally, the per1 mutant exhibited a pleiotropic phenotype under control conditions, resembling Pi-deficient plants in several aspects. Under Pi deficiency, the accumulation of Pi and iron was increased in the mutant when compared to the wild-type. Inhibition of root hair elongation upon growth on low Pi media was reverted by treatment with the Pi analog phosphite, suggesting that the mutant phenotype is not the result of a defect in Pi sensing. Reciprocal grafting experiments revealed that the mutant rootstock is sufficient to cause the phenotype. Transcriptional profiling of per1 and wild-type plants subjected to short-term Pi starvation revealed genes that may be important for the signaling of Pi deficiency. We conclude that UBP14 function is crucial for adapting root development to the prevailing local availability of phosphate. Experiment Overall Design: Col-0 and per1 mutant plants were grown under control conditions or subjected to phosphate starvation for 10 h

2009-04-18 | E-GEOD-15649 | biostudies-arrayexpress

Blue light regulates phosphate deficiency-dependent primary root growth inhibition in Arabidopsis

Project description:Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that the ectopic expression of B-BOX32 (BBX32) and the mutation of ELONGATED HYPOCOTYL 5 (HY5), whose transcriptional activity is negatively regulated by BBX32, resulted in the tolerance to Pi deficiency in Arabidopsis. The primary root lengths of 35S:BBX32 and hy5 plants were only slightly inhibited under Pi deficient condition and the fresh weights were significantly higher than those of wild type. The Pi deficiency-tolerant root phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5 slr1, without lateral roots also showed a long primary root phenotype under phosphate deficiency, indicating that the root phenotype of hy5 does not result from increase of external Pi uptake. Moreover, we found that blue light may regulate Pi deficiency-dependent primary root growth inhibition through activating peroxidase gene expression, suggesting the Pi-deficiency tolerant root phenotype of hy5 may be due to blockage of blue-light responses. Altogether, this study points out light quality may play an important role in the regulation of Pi deficiency responses. It may contribute to regulate plant growth under Pi deficiency through a proper illumination.

2019-11-27 | GSE139100 | GEO

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

Project description:Phosphate (Pi) starvation induces a suite of adaptive responses aimed at recalibrating cellular Pi homeostasis. Plants harboring a mutation in OVARIAN TUMOR DOMAIN-CONTAINING DEUBIQUITINATING ENZYME5 (OTU5) showed altered DNA methylation of root hair-related genes and altered Pi-responsive root traits. Unlike the wild type, homozygous otu5 mutants did not respond to Pi starvation by increased lateral root formation and increased root hair length but formed very short root hairs when grown on low-Pi media. Under Pi-replete conditions, otu5 plants developed more root hairs than the wild type due to attenuated primary root growth, a phenotype that resembled that of Pi-deficient plants. Growth of plants on low-Pi media altered both H3K4 and H3K27 trimethylation levels at the transcriptional start site of a subset of genes encoding key players in Pi homeostasis, which was correlated with mRNA abundance changes of these genes. Pi starvation had a minor impact on DNA methylation. Differentially methylated regions were enriched in transposable elements, suggesting that DNA methylation associated with low Pi supply is required for maintaining genome integrity. It is concluded that DNA methylation and histone methylation constitute critical, interdependent regulatory components that orchestrate the activity of a subset of Pi-responsive genes.

2017-11-02 | GSE81407 | GEO

Arabidopsis thaliana Raw sequence reads

Project description:Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq.

2015-06-20 | E-MTAB-4396 | biostudies-arrayexpress

Role of cis-zeatin in root responses to phosphate starvation

Project description:In this work we show that root illumination influences Pi starvation responses, enhancing the root and shoot growth arrest and limiting the root/shoot ratio as well as root hair elongation. A comparative transcriptomic study using dark-grown roots (DGR) roots seedlings taht were grown with or without phosphate identifies several genes that respond to Pi deficiency that were not previously reported, likely by the negative effect of the root illumination.

2019-11-15 | GSE131096 | GEO

Arabidopsis thaliana strain:Col-0Transcriptome or Gene expression

Project description:When grown under phosphate (Pi) deficiency, plants adjust their developmental program and metabolic activity to cope with this nutritional stress. For Arabidopsis, the developmental responses include inhibition of primary root growth and enhanced formation of lateral roots and root hairs. Pi deficiency also inhibits photosynthesis by suppressing the expression of photosynthetic genes. Interestingly, early studies showed that photosynthetic gene expression was also suppressed in roots, a non-photosynthetic tissue. The biological relevance of this phenomenon, however, is not known. In this work, we characterized an Arabidopsis mutant, hps7, which is hypersensitive to Pi deficiency; the hypersensitivity includes an increased inhibition of root growth. HPS7 encodes a tyrosylprotein sulfotransferase (TPST). Accumulation of TPST proteins, but not mRNA, is induced by Pi deficiency. Comparative RNA-Seq analyses indicated that expression of many photosynthetic genes was activated in the roots of hps7. Under Pi deficiency, the expression of the photosynthetic genes in hps7 is further increased, which leads to the enhanced accumulation of chlorophyll, starch, and reactive oxygen species. The increased inhibition of root growth in hps7 under Pi deficiency was completely reversed by growing plants in the dark. Based on these results, we propose that suppression of photosynthetic gene expression in roots is required for sustained root growth under Pi deficiency.

2014-07-28 | E-MTAB-4405 | biostudies-arrayexpress

Chromatin enrichment for Proteomics in Plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in Jasmonate signaling

Project description:Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli.

2021-06-17 | PXD026541 | Pride

Role of cis-zeatin in root responses to phosphate starvation

Project description:In this work we show that root illumination influences Pi starvation response, enhancing the root and shoot growth arrest and limiting the root/shoot ratio as well as root hair elongation. A transcriptomic study in dark-grown roots (DGR) roots identifies several genes that respond to Pi deficiency that were not previously reported. Hormone profiling revealed that Pi starvation reduces the level of trans-Zeatin (tZ) but significantly increases the amount of cis-Zeatin (cZ) and cis-Zeatin Riboside (cZR). We have analyzed the transcriptomic response of Arabidopsis roots to phosphate starvation combined with cis- or trans-zeatin treatments for 8 hours.

2019-11-01 | GSE131056 | GEO

Comparative Morphophysiological Analyses and Molecular Profiling Reveal ‘Pi-Efficient Strategies’ of a Traditional Rice Genotypefor Low Phosphorus Tolerance in Traditional indica Rice

Project description:Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice cultivars are naturally compatible to low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes - Dular (low Pi tolerant) and PB1 (low Pi sensitive) - have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes raised under Pi deficient and sufficient conditions revealed the potential low Pi tolerance mechanisms of traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) are highly induced in traditional rice genotype, Dular. Higher reserve of phospholipid and greater accumulation of galactolipids under low Pi in Dular indicated its better internal Pi utilization. Furthermore, Dular also maintained better root growth than PB1 under low Pi resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.

2016-01-29 | GSE74795 | GEO

Gene expression pattern of Arabidopsis (WT and wrky6) colonized with Piriformospora indica under low and normal phosphate conditions

Project description:A whole cascade of genes involved in abiotic stress tolerance, starting from stress perception to transcriptional activation of downstream genes, leads to stress adaptation and tolerance responses in Arabidopsis. Understanding the function of their gene products is of critical importance for the development of transgenic strategies and to improve stress tolerance in crops. Pi limitation is one of the major abiotic stresses for plants used in agriculture. Using Arabidopsis as a model system, we provide evidence that WRKY6 functions as a repressor of several Pi-related processes in LP-exposed Arabidopsis roots, among them Pi transporter and metabolism genes. Inactivation of WRKY6 stimulates the Pi uptake and metabolism in LP-exposed WT roots. The Pi metabolism is further promoted by P. indica under Pi limitation conditions and the stimulatory effect of the fungus is much stronger in the wrky6 background when compared to the WT. Better performance of P. indica-colonized WT and mutant plants under Pi limitations is manifested by the healthy phenotype of the plants and growth promotion of their underground and aerial parts. In the wrky6 background, this results in larger roots with a bushy phenotype. It allows the identification of genes and mechanisms which trigger root growth and development as well as the alteration of the root architecture for optimal performance in the rhizospheric environment.

2015-11-28 | GSE63500 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data