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The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [At35b_MR]

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE33996 | GEO | 2012/06/18

SECONDARY ACCESSION(S): PRJNA156451

REPOSITORIES: GEO

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The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [At35b_MR]

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. 2 tissues X 3 treatments X 3 biological replicates

2012-06-17 | E-GEOD-33996 | biostudies-arrayexpress

The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [ATH1-121501]

2012-06-17 | E-GEOD-33790 | biostudies-arrayexpress

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SHORT-ROOT Stabilizes PHOSPHATE1 to Regulate Phosphate Allocation in Arabidopsis

Project description:Coordinated distribution of Pi between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHR (SHORT-ROOT) is well-characterized for its function in root radial patterning1-3. Here, we demonstrate a new role of SHR in controlling phosphate (Pi) allocation from roots to shoots by regulating PHOSPHATE1 (PHO1) in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis which accumulates much less Pi in the shoot and shows constitutive Pi starvation response (PSR) under Pi-sufficient condition. Besides, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP Ⅲ transcription factor PHB. PHB accumulates and directly binds the promoter of PHO2 to upregulate its transcription, resulting in PHO1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants repress Pi translocation from roots to shoots in response to Pi starvation.

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Oryza sativa Japonica Group transcriptome sequencing

Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.

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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.

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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

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [ChIP-Seq data]

Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks.

2013-01-02 | GSE39498 | GEO

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [gene expression data]

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