title: The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory of Plant and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
authors.forename: Jongchan
authors.initials: J
authors.lastname: Woo
authors.forename: Cameron Ross
authors.initials: CR
authors.lastname: MacPherson
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Huan
authors.initials: H
authors.lastname: Wang
authors.forename: Takatoshi
authors.initials: T
authors.lastname: Kiba
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Hannah
authors.forename: Xiu-Jie
authors.initials: XJ
authors.lastname: Wang
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics*; D003080:Cold Temperature; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D017343:Genes, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity / Q000187:drug effects / Q000235:genetics; D009997:Osmotic Pressure / Q000187:drug effects; D010710:Phosphates / Q000172:deficiency*; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics; D018520:Plant Shoots / Q000187:drug effects / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D012965:Sodium Chloride / Q000494:pharmacology; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*
chemical_list: D010710:Phosphates; D012965:Sodium Chloride; D000040:Abscisic Acid