Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination

Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7251-6. doi: 10.1073/pnas.0900952106. Epub 2009 Apr 9.


In higher plants, the circadian clock controls a wide range of cellular processes such as photosynthesis and stress responses. Understanding metabolic changes in arrhythmic plants and determining output-related function of clock genes would help in elucidating circadian-clock mechanisms underlying plant growth and development. In this work, we investigated physiological relevance of PSEUDO-RESPONSE REGULATORS (PRR 9, 7, and 5) in Arabidopsis thaliana by transcriptomic and metabolomic analyses. Metabolite profiling using gas chromatography-time-of-flight mass spectrometry demonstrated well-differentiated metabolite phenotypes of seven mutants, including two arrhythmic plants with similar morphology, a PRR 9, 7, and 5 triple mutant and a CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1)-overexpressor line. Despite different light and time conditions, the triple mutant exhibited a dramatic increase in intermediates in the tricarboxylic acid cycle. This suggests that proteins PRR 9, 7, and 5 are involved in maintaining mitochondrial homeostasis. Integrated analysis of transcriptomics and metabolomics revealed that PRR 9, 7, and 5 negatively regulate the biosynthetic pathways of chlorophyll, carotenoid and abscisic acid, and alpha-tocopherol, highlighting them as additional outputs of pseudo-response regulators. These findings indicated that mitochondrial functions are coupled with the circadian system in plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscisic Acid / biosynthesis
  • Arabidopsis / genetics
  • Arabidopsis / growth & development
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Biological Clocks*
  • Carotenoids / biosynthesis
  • Chlorophyll / biosynthesis
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genome, Plant / genetics
  • Multigene Family / genetics
  • Mutation / genetics
  • Phenotype
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • alpha-Tocopherol / metabolism


  • Arabidopsis Proteins
  • CCA1 protein, Arabidopsis
  • Transcription Factors
  • Chlorophyll
  • Carotenoids
  • Abscisic Acid
  • alpha-Tocopherol