A comprehensive differential proteomic study of nitrate deprivation in Arabidopsis reveals complex regulatory networks of plant nitrogen responses

J Proteome Res. 2012 Apr 6;11(4):2301-15. doi: 10.1021/pr2010764. Epub 2012 Feb 29.


Nitrogen (N) is an important nutrient and signal for plant growth and development. However, to date, our knowledge of how plants sense and transduce the N signals is very limited. To better understand the molecular mechanisms of plant N responses, we took two-dimensional gel-based proteomic and phosphoproteomic approaches to profile the proteins with abundance and phosphorylation state changes during nitrate deprivation and recovery in the model plant Arabidopsis thaliana. After 7-day-old seedlings were N-deprived for up to 48 h followed by 24 h recovery, a total of 170 and 38 proteins were identified with significant changes in abundance and phosphorylation state, respectively. Bioinformatic analyses implicate these proteins in diverse cellular processes including N and protein metabolisms, photosynthesis, cytoskeleton, redox homeostasis, and signal transduction. Functional studies of the selected nitrate-responsive proteins indicate that the proteasome regulatory subunit RPT5a and the cytoskeleton protein Tubulin alpha-6 (TUA6) play important roles in plant nitrate responses by regulating plant N use efficiency (NUE) and low nitrate-induced anthocyanin biosynthesis, respectively. In conclusion, our study provides novel insights into plant responses to nitrate at the proteome level, which are expected to be highly useful for dissecting the N response pathways in higher plants and for improving plant NUE.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / anatomy & histology
  • Arabidopsis / chemistry
  • Arabidopsis / genetics
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / analysis
  • Arabidopsis Proteins / metabolism*
  • Cluster Analysis
  • Electrophoresis, Gel, Two-Dimensional
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks
  • Models, Biological
  • Mutation
  • Nitrates / metabolism*
  • Nitrogen / metabolism*
  • Phenotype
  • Phosphoproteins / analysis
  • Phosphoproteins / metabolism
  • Proteome / analysis
  • Proteome / metabolism*
  • Proteomics / methods
  • Reproducibility of Results
  • Stress, Physiological / physiology


  • Arabidopsis Proteins
  • Nitrates
  • Phosphoproteins
  • Proteome
  • Nitrogen