Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA144947 | ENA |
REPOSITORIES: ENA
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Project description:The objective of this project is to identify genes that are expressed in the Arabidopsis thaliana root tip and that are early induced (or repressed) by phoshate deficiency. Seedlings were germinated and grown (for 6 days) on phosphate rich medium and transfered to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800um) of the primary root was cut under a dissecting microscope. About 100 root tips per condition were harvested and there mRNA was analysed with the use of microarrays.
2011-09-09 | GSE31135 | GEO
Project description:Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root. Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date.
2012-06-18 | GSE33996 | GEO
Project description:Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root. Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date.
2012-06-18 | GSE33790 | GEO
Project description:Pi availability is a significant limiting factor for plant growth in both natural and agricultural systems. To cope with such limiting conditions, plants have adapted developmental and biochemical strategies to enhance Pi acquisition and to avoid starvation. A myriad of genes that are involved in the regulation and display of these strategies have been identified. However, the possible epigenetic components regulating the phosphate starvation responses have not been thoroughly investigated. DNA methylation is a major epigenetic mark involved in diverse biological processes and it may play a critical role in Pi starvation stress adaptation, also changes in DNA methylation can lead to a unique gene expression pattern in response to specific developmental and environmental conditions. Here in we demonstrate that non-CpG DNA methylation is required for proper expression of a number of Pi-limitation responsive genes in Arabidopsis thaliana and results in altered morphologic and physiologic phosphate starvation responses.Our data suggest that DNA methylation is involved in the modulation of Pi starvation responses via the transcriptional regulation of a set of phosphate-starvation responsive genes. Analysis of 8 different treatments, 2 different Organs (Root and Shoot), 2 different Phosphate treatments (High Pi, Low Pi), 2 different Times (Short Term, Long Term), 2 biological replicates for treatment
2015-12-31 | E-GEOD-72770 | biostudies-arrayexpress
Project description:Transcription profiling of Arabidopsis thaliana root tip region comparing argonaute1-101 (SALK_035319), scr-3 and wild-type Col-0.
2009-12-31 | GSE16460 | GEO
Project description:Phosphate is an essential macronutrient required for plant growth and development. However, it is present at suboptimal levels in many terrestrial ecosystems. To ameliorate this limitation, plants have evolved developmental and physiological mechanisms known as phosphate starvation responses (PSR). One of the main PSR in Arabidopsis thaliana is a deep restructuration of the root system architecture, which includes a reduction in primary root growth resulting in a shallower root system better adapted to explore the nutrient-rich topsoil. Intense research over the last years has shown that this developmental change is dependent on the accumulation and redistribution of iron (Fe) at the root tip, which in turn, participates in Fenton reactions and generates reactive oxygen species that affect meristem function and cell elongation. We have recently identified and characterized a cytochrome-containing protein in A. thaliana, named CRR, which is involved in the primary root growth response to phosphate starvation. Our results showed that CRR is an ascorbate-dependent ferric-reductase whose expression levels modulates iron distribution pattern in the root, affecting meristem function and cell elongation. Moreover, this activity also has shown to be critical for iron toxicity tolerance since CRR determines the transport rate of iron from root to shoot.
2023-10-25 | GSE235511 | GEO
Project description:Phosphate is an essential macronutrient required for plant growth and development. However, it is present at suboptimal levels in many terrestrial ecosystems. To ameliorate this limitation, plants have evolved developmental and physiological mechanisms known as phosphate starvation responses (PSR). One of the main PSR in Arabidopsis thaliana is a deep restructuration of the root system architecture, which includes a reduction in primary root growth resulting in a shallower root system better adapted to explore the nutrient-rich topsoil. Intense research over the last years has shown that this developmental change is dependent on the accumulation and redistribution of iron (Fe) at the root tip, which in turn, participates in Fenton reactions and generates reactive oxygen species that affect meristem function and cell elongation. We have recently identified and characterized a cytochrome-containing protein in A. thaliana, named CRR, which is involved in the primary root growth response to phosphate starvation. Our results showed that CRR is an ascorbate-dependent ferric-reductase whose expression levels modulates iron distribution pattern in the root, affecting meristem function and cell elongation. Moreover, this activity also has shown to be critical for iron toxicity tolerance since CRR determines the transport rate of iron from root to shoot.
2023-10-01 | GSE215755 | GEO
Project description:Sequence-specific transcription factor WRKY75 is highly responsive to reactive oxygen species on transcriptional level in the rosettes of Arabidopsis thaliana. In addition, it acts in developmental responses, acquisition of nutrients, and in stress responses. In the root, WRKY75 is a repressor of root hair formation, it regulates the phosphate starvation response, and the response to certain pathogens. In order to find the target genes of WRKY75, the effects of estradiol-inducible overexpression of WRKY75 on transcriptome was studied using RNA-seq.
2016-04-03 | GSE79856 | GEO
Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.
2010-12-09 | GSE16722 | GEO
Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation. The analysis was performed in wild-type plants grown for seven days in complete (+Pi) and Pi-lacking (-Pi) Johnson solid media and the single phr1 and double phr1-phl1 mutants grown for 7 days in –Pi medium. Three independent biological samples of total RNA from shoot and root were hybridized separately.
2010-12-09 | E-GEOD-16722 | biostudies-arrayexpress