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The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation

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...

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Autores principales: Woo, Jongchan, MacPherson, Cameron Ross, Liu, Jun, Wang, Huan, Kiba, Takatoshi, Hannah, Matthew A, Wang, Xiu-Jie, Bajic, Vladimir B, Chua, Nam-Hai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520718/
https://www.ncbi.nlm.nih.gov/pubmed/22553952
http://dx.doi.org/10.1186/1471-2229-12-62
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author Woo, Jongchan
MacPherson, Cameron Ross
Liu, Jun
Wang, Huan
Kiba, Takatoshi
Hannah, Matthew A
Wang, Xiu-Jie
Bajic, Vladimir B
Chua, Nam-Hai
author_facet Woo, Jongchan
MacPherson, Cameron Ross
Liu, Jun
Wang, Huan
Kiba, Takatoshi
Hannah, Matthew A
Wang, Xiu-Jie
Bajic, Vladimir B
Chua, Nam-Hai
author_sort Woo, Jongchan
collection PubMed
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 a 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 by micro- and tiling-arrays (accessible from GEO: GSE34004) 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 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 specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7–9, SPX1-3, and PHO1;H1) display greater specificity to phosphate-starvation than their more generic counterparts. CONCLUSION: Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date.
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spelling pubmed-35207182012-12-13 The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation Woo, Jongchan MacPherson, Cameron Ross Liu, Jun Wang, Huan Kiba, Takatoshi Hannah, Matthew A Wang, Xiu-Jie Bajic, Vladimir B Chua, Nam-Hai BMC Plant Biol Research Article 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 a 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 by micro- and tiling-arrays (accessible from GEO: GSE34004) 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 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 specific versus generic members of closely related gene families with respect to phosphate-starvation. Thus, among others, we showed that PHR1-regulated members of closely related phosphate-responsive families (PHT1;1, PHT1;7–9, SPX1-3, and PHO1;H1) display greater specificity to phosphate-starvation than their more generic counterparts. CONCLUSION: Our results uncover much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the most complete genome-wide data on plant nutrient stress to-date. BioMed Central 2012-05-03 /pmc/articles/PMC3520718/ /pubmed/22553952 http://dx.doi.org/10.1186/1471-2229-12-62 Text en Copyright ©2012 Woo et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Woo, Jongchan
MacPherson, Cameron Ross
Liu, Jun
Wang, Huan
Kiba, Takatoshi
Hannah, Matthew A
Wang, Xiu-Jie
Bajic, Vladimir B
Chua, Nam-Hai
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title_full The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title_fullStr The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title_full_unstemmed The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title_short The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
title_sort response and recovery of the arabidopsis thaliana transcriptome to phosphate starvation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3520718/
https://www.ncbi.nlm.nih.gov/pubmed/22553952
http://dx.doi.org/10.1186/1471-2229-12-62
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