title: Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition.
abstract: Plant roots acquire nitrogen predominantly as ammonium and nitrate, which besides serving as nutrients, also have signaling roles. Re-addition of nitrate to starved plants rapidly re-programs the metabolism and gene expression, but the earliest responses to nitrogen deprivation are unknown. Here, the early transcriptional and (phospho)proteomic responses of roots to nitrate or ammonium deprivation were analyzed. The rapid transcriptional repression of known nitrate-induced genes proceeded the tissue NO3-concentration drop, with the transcription factor genes LBD37/38 and HRS1/HHO1 among those with earliest significant change. Similar rapid transcriptional repression occurred in loss-of-function mutants of the nitrate response factor NLP7 and some transcripts were stabilized by nitrate. In contrast, an early transcriptional response to ammonium deprivation was almost completely absent. However, ammonium deprivation induced a rapid and transient perturbation of the proteome and a differential phosphorylation pattern in proteins involved in adjusting the pH and cation homeostasis, plasma membrane H+, NH4+, K+and water fluxes. Fewer differential phosphorylation patterns in transporters, kinases and other proteins occurred with nitrate deprivation. The deprivation responses were not just opposite to the re-supply responses, but identified NO3-deprivation-induced mRNA decay and signaling candidates potentially reporting the external nitrate status to the cell.
authors.affiliation: Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Menz
authors.affiliation: Institute for Physiology and Biotechnology of Plants, Plant Systems Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Li
authors.affiliation: Institute for Physiology and Biotechnology of Plants, Plant Systems Biology, University of Hohenheim, Garbenstraße 30, 70593, Stuttgart, Germany.
authors.forename: Waltraud X
authors.initials: WX
authors.lastname: Schulze
authors.affiliation: Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Ludewig
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism*; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism; D002462:Cell Membrane / Q000378:metabolism; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D009566:Nitrates / Q000378:metabolism*; D009584:Nitrogen / Q000378:metabolism*; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D059467:Transcriptome / Q000235:genetics
chemical_list: D064751:Ammonium Compounds; D029681:Arabidopsis Proteins; D009566:Nitrates; D020543:Proteome; D009584:Nitrogen
keywords: 
  Arabidopsis thaliana
  ; microarray; nitrogen; nutrient signaling; primary nitrate response; shotgun phospho-proteomics