Transcript and metabolite profiling during cold acclimation of Arabidopsis reveals an intricate relationship of cold-regulated gene expression with modifications in metabolite content

Plant J. 2007 Jun;50(6):967-81. doi: 10.1111/j.1365-313X.2007.03100.x. Epub 2007 Apr 25.


Exposure of Arabidopsis to low temperatures results in cold acclimation where freezing tolerance is enhanced. To achieve a wider view of the role of transcriptome to biochemical changes that occur during cold acclimation, analyses of concurrent transcript and metabolite changes during cold acclimation was performed revealing the dynamics of selected gene-metabolite relationships. Exposure to low temperature resulted in broad transcriptional and metabolite responses. Principal component analysis revealed sequentially progressive, global changes in both gene expression and metabolite profiles during cold acclimation. Changes in transcript abundance for many metabolic processes, including protein amino acid biosynthetic pathways and soluble carbohydrates, during cold acclimation were observed. For some metabolic processes, changes in transcript abundance temporally correlated with changes in metabolite levels. For other metabolic processes, changes in transcript levels were not correlated with changes in metabolite levels. The present findings demonstrate that regulatory processes independent of transcript abundance represent a key part of the metabolic adjustments that occur during cold acclimation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acclimatization / physiology*
  • Amino Acids / metabolism
  • Arabidopsis / metabolism*
  • Arabidopsis / physiology
  • Carbohydrate Metabolism / physiology
  • Cold Temperature*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Principal Component Analysis
  • Raffinose / metabolism
  • Sucrose / metabolism
  • Time Factors
  • gamma-Aminobutyric Acid / metabolism


  • Amino Acids
  • gamma-Aminobutyric Acid
  • Sucrose
  • Raffinose