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

Handle URI:
http://hdl.handle.net/10754/325252
Title:
The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation
Authors:
Woo, Jongchan; MacPherson, Cameron Ross; Liu, Jun; Wang, Huan; Kiba, Takatoshi; Hannah, Matthew A; Wang, Xiu-Jie; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Chua, Nam-Hai
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 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. 2012 Woo et al.; licensee BioMed Central Ltd.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Woo J, MacPherson C, Liu J, Wang H, Kiba T, et al. (2012) The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biol 12: 62. doi:10.1186/1471-2229-12-62.
Publisher:
Springer Nature
Journal:
BMC Plant Biology
Issue Date:
3-May-2012
DOI:
10.1186/1471-2229-12-62
PubMed ID:
22553952
PubMed Central ID:
PMC3520718
Type:
Article
ISSN:
14712229
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorWoo, Jongchanen
dc.contributor.authorMacPherson, Cameron Rossen
dc.contributor.authorLiu, Junen
dc.contributor.authorWang, Huanen
dc.contributor.authorKiba, Takatoshien
dc.contributor.authorHannah, Matthew Aen
dc.contributor.authorWang, Xiu-Jieen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorChua, Nam-Haien
dc.date.accessioned2014-08-27T09:42:37Z-
dc.date.available2014-08-27T09:42:37Z-
dc.date.issued2012-05-03en
dc.identifier.citationWoo J, MacPherson C, Liu J, Wang H, Kiba T, et al. (2012) The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation. BMC Plant Biol 12: 62. doi:10.1186/1471-2229-12-62.en
dc.identifier.issn14712229en
dc.identifier.pmid22553952en
dc.identifier.doi10.1186/1471-2229-12-62en
dc.identifier.urihttp://hdl.handle.net/10754/325252en
dc.description.abstractBackground: 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. 2012 Woo et al.; licensee BioMed Central Ltd.en
dc.language.isoenen
dc.publisherSpringer Natureen
dc.rightsThis 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.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectComparative analysis with AtGenExpressen
dc.subjectFunctional analysisen
dc.subjectHydroponic cultureen
dc.subjectInitial, Persistent, and Latent expression patternsen
dc.subjectMicro-array and tiling-arrayen
dc.subjectOrgan specificen
dc.subjectPhosphate starvationen
dc.subjectResponse and recoveryen
dc.subjectRoots and shootsen
dc.subjectWhole seedlingen
dc.subjectArabidopsisen
dc.subjectArabidopsis thalianaen
dc.subjectabscisic aciden
dc.subjectphosphateen
dc.subjectsodium chlorideen
dc.subjecttranscriptomeen
dc.subjectantibody specificityen
dc.subjectArabidopsisen
dc.subjectcolden
dc.subjectDNA microarrayen
dc.subjectdrug effecten
dc.subjectgene expression profilingen
dc.subjectgene expression regulationen
dc.subjectgene locusen
dc.subjectgeneticsen
dc.subjectosmotic pressureen
dc.subjectplanten
dc.subjectplant geneen
dc.subjectplant rooten
dc.subjectreverse transcription polymerase chain reactionen
dc.subjectsignal transductionen
dc.subjectAbscisic Aciden
dc.subjectArabidopsisen
dc.subjectCold Temperatureen
dc.subjectGene Expression Profilingen
dc.subjectGene Expression Regulation, Planten
dc.subjectGenes, Planten
dc.subjectGenetic Locien
dc.subjectOligonucleotide Array Sequence Analysisen
dc.subjectOrgan Specificityen
dc.subjectOsmotic Pressureen
dc.subjectPhosphatesen
dc.subjectPlant Rootsen
dc.subjectPlant Shootsen
dc.subjectReverse Transcriptase Polymerase Chain Reactionen
dc.subjectSignal Transductionen
dc.subjectSodium Chlorideen
dc.subjectTranscriptomeen
dc.titleThe response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvationen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalBMC Plant Biologyen
dc.identifier.pmcidPMC3520718en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionLaboratory of Plant and Molecular Biology, The Rockefeller University, New York, 10065, NY, United Statesen
dc.contributor.institutionBayer Crop Science, Technologiepark 38, 9052, Ghent, Belgiumen
dc.contributor.institutionState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, Chinaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorMacPherson, Cameron R.en
kaust.authorBajic, Vladimir B.en
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