Early nitrogen-deprivation responses in Arabidopsis roots reveal distinct differences on transcriptome and (phospho-) proteome levels between nitrate and ammonium nutrition

Plant J. 2016 Dec;88(5):717-734. doi: 10.1111/tpj.13272. Epub 2016 Sep 15.


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.

Keywords: Arabidopsis thaliana; microarray; nitrogen; nutrient signaling; primary nitrate response; shotgun phospho-proteomics.

MeSH terms

  • Ammonium Compounds / metabolism*
  • Arabidopsis / genetics
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / metabolism
  • Cell Membrane / metabolism
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / physiology
  • Nitrates / metabolism*
  • Nitrogen / metabolism*
  • Plant Roots / genetics
  • Plant Roots / metabolism*
  • Proteome / metabolism*
  • Proteomics / methods
  • Signal Transduction / genetics
  • Signal Transduction / physiology
  • Transcriptome / genetics


  • Ammonium Compounds
  • Arabidopsis Proteins
  • Nitrates
  • Proteome
  • Nitrogen

Associated data

  • GENBANK/GSE73903