title: Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination.
abstract: BACKGROUND
  Light plays an important role in plant growth and development. In this study, the impact of light on physiology of 20-d-old Arabidopsis leaves was examined through transcriptomic, proteomic and metabolomic analysis. Since the energy-generating electron transport chains in chloroplasts and mitochondria are encoded by both nuclear and organellar genomes, sequencing total RNA after removal of ribosomal RNAs provides essential information on transcription of organellar genomes. The changes in the levels of ADP, ATP, NADP(+), NADPH and 41 metabolites upon illumination were also quantified.
  
  
  RESULTS
  Upon illumination, while the transcription of the genes encoded by the plastid genome did not change significantly, the transcription of nuclear genes encoding different functional complexes in the photosystem are differentially regulated whereas members of the same complex are co-regulated with each other. The abundance of mRNAs and proteins encoded by all three genomes are, however, not always positively correlated. One such example is the negative correlation between mRNA and protein abundances of the photosystem components, which reflects the importance of post-transcriptional regulation in plant physiology.
  
  
  CONCLUSIONS
  This study provides systems-wide datasets which allow plant researchers to examine the changes in leaf transcriptomes, proteomes and key metabolites upon illumination and to determine whether there are any correlations between changes in transcript and protein abundances of a particular gene or pathway upon illumination. The integration of data of the organelles and the photosystems, Calvin-Benson cycle, carbohydrate metabolism, glycolysis, the tricarboxylic acid cycle and respiratory chain, thereby provides a more complete picture to the changes in plant physiology upon illumination than has been attained to date.
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. liangchao_1979@hotmail.com.
authors: Chao
authors: C
authors: Liang
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. chengshf@genomics.cn.
authors: Shifeng
authors: S
authors: Cheng
authors: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany. YOZhang@mpimp-golm.mpg.de.
authors: Youjun
authors: Y
authors: Zhang
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. yzsun@hku.hk.
authors: Yuzhe
authors: Y
authors: Sun
authors: Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany. Fernie@mpimp-golm.mpg.de.
authors: Alisdair R
authors: AR
authors: Fernie
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. kkang@connect.hku.hk.
authors: Kang
authors: K
authors: Kang
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. gipa@hku.hk.
authors: Gianni
authors: G
authors: Panagiotou
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. clivelo@hku.hk.
authors: Clive
authors: C
authors: Lo
authors: School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China. bllim@hku.hk.|State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China. bllim@hku.hk.
authors: Boon Leong
authors: BL
authors: Lim
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects*; D029681:Arabidopsis Proteins / Q000096:biosynthesis / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D008027:Light; D018515:Plant Leaves / Q000528:radiation effects*
chemical_list: D029681:Arabidopsis Proteins