Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling

J Proteome Res. 2008 Jul;7(7):2980-98. doi: 10.1021/pr800128q. Epub 2008 Jun 3.


Ozone (O(3)), a serious air pollutant, is known to significantly reduce photosynthesis, growth, and yield and to cause foliar injury and senescence. Here, integrated transcriptomics, proteomics, and metabolomics approaches were applied to investigate the molecular responses of O(3) in the leaves of 2-week-old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O(3) for a period of 24 h. On the basis of the morphological alteration of O(3)-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12, and 24 h using rice DNA microarray chip. A total of 1535 nonredundant genes showed altered expression of more than 5-fold over the control, representing 8 main functional categories. Genes involved in information storage and processing (10%) and cellular processing and signaling categories (24%) were highly represented within 1 h of O(3) treatment; transcriptional factor and signal transduction, respectively, were the main subcategories. Genes categorized into information storage and processing (17, 23%), cellular processing and signaling (20, 16%) and metabolism (18, 19%) were mainly regulated at 12 and 24 h; their main subcategories were ribosomal protein, post-translational modification, and signal transduction and secondary metabolites biosynthesis, respectively. Two-dimensional gel electrophoresis-based proteomics analyses in combination with tandem mass spectrometer identified 23 differentially expressed protein spots (21 nonredundant proteins) in leaves exposed to O(3) for 24 h compared to respective control. Identified proteins were found to be involved in cellular processing and signaling (32%), photosynthesis (19%), and defense (14%). Capillary electrophoresis-mass spectrometry-based metabolomic profiling revealed accumulation of amino acids, gamma-aminobutyric acid, and glutathione in O(3) exposed leaves until 24 h over control. This systematic survey showed that O(3) triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Air Pollutants / pharmacology*
  • Electrophoresis, Capillary
  • Electrophoresis, Gel, Two-Dimensional
  • Gene Expression Profiling
  • Mass Spectrometry
  • Oligonucleotide Array Sequence Analysis
  • Oryza / drug effects*
  • Oryza / metabolism
  • Ozone / pharmacology*
  • Plant Leaves / drug effects*
  • Plant Leaves / metabolism
  • Plant Proteins / genetics
  • Plant Proteins / metabolism*
  • Proteomics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Seedlings / drug effects
  • Seedlings / metabolism


  • Air Pollutants
  • Plant Proteins
  • Ozone