Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.

Like most organisms, plants have endogenous biological clocks that coordinate internal events with the external environment. We used high-density oligonucleotide microarrays to examine gene expression in Arabidopsis and found that 6% of the more than 8000 genes on the array exhibited circadian changes in steady-state messenger RNA levels. Clusters of circadian-regulated genes were found in pathways involved in plant responses to light and other key metabolic pathways. Computational analysis of cycling genes allowed the identification of a highly conserved promoter motif that we found to be required for circadian control of gene expression. Our study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.

[1]  D. E. Somers,et al.  ZEITLUPE Encodes a Novel Clock-Associated PAS Protein from Arabidopsis , 2000, Cell.

[2]  S. Kay,et al.  Coordination of Plant Metabolism and Development by the Circadian Clock. , 1997, The Plant cell.

[3]  D J Cosgrove,et al.  Assembly and enlargement of the primary cell wall in plants. , 1997, Annual review of cell and developmental biology.

[4]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[5]  G. Church,et al.  Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.

[6]  N. J. Chatterton,et al.  Photosynthate Partitioning into Starch in Soybean Leaves: I. Effects of Photoperiod versus Photosynthetic Period Duration. , 1979, Plant physiology.

[7]  S. J. Gilmour,et al.  Mode of action of the COR15a gene on the freezing tolerance of Arabidopsis thaliana. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  X. S. Zhang,et al.  Temporal and Spatial Regulation of 1-Aminocyclopropane-1-Carboxylate Oxidase in the Pollination-Induced Senescence of Orchid Flowers , 1993, Plant physiology.

[9]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[10]  K. V. Dun,et al.  Trehalose metabolism in plants. , 1999, Trends in plant science.

[11]  A. Millar,et al.  Circadian dysfunction causes aberrant hypocotyl elongation patterns in Arabidopsis. , 1999, The Plant journal : for cell and molecular biology.

[12]  G. Coupland,et al.  Time measurement and the control of flowering in plants. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  R. Last,et al.  Arabidopsis Mutants Lacking Phenolic Sunscreens Exhibit Enhanced Ultraviolet-B Injury and Oxidative Damage , 1995, Plant physiology.

[14]  J. Dunlap Molecular Bases for Circadian Clocks , 1999, Cell.

[15]  R. Last,et al.  Arabidopsis Flavonoid Mutants Are Hypersensitive to UV-B Irradiation. , 1993, The Plant cell.

[16]  D. E. Somers,et al.  Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. , 1998, Science.

[17]  L. Willmitzer,et al.  Inhibition of a starch-granule–bound protein leads to modified starch and repression of cold sweetening , 1998, Nature Biotechnology.

[18]  G. Coruzzi,et al.  THE MOLECULAR-GENETICS OF NITROGEN ASSIMILATION INTO AMINO ACIDS IN HIGHER PLANTS. , 1996, Annual review of plant physiology and plant molecular biology.

[19]  S. Kopriva,et al.  Regulation of sulfate assimilation by nitrogen in Arabidopsis. , 2000, Plant physiology.

[20]  J. Dillwith,et al.  Correlation between the Circadian Rhythm of Resistance to Extreme Temperatures and Changes in Fatty Acid Composition in Cotton Seedlings , 1993, Plant physiology.

[21]  K. Shinozaki,et al.  Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. , 2000, Current opinion in plant biology.

[22]  S. Kay,et al.  Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[23]  E. Grotewold,et al.  How genes paint flowers and seeds , 1998 .

[24]  T. Mirkov,et al.  Characterization of a new vacuolar membrane aquaporin sensitive to mercury at a unique site. , 1996, The Plant cell.

[25]  K. Kloppstech,et al.  Significance of circadian gene expression in higher plants. , 1996, Chronobiology international.

[26]  S. Golden,et al.  Resonating circadian clocks enhance fitness in cyanobacteria. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[27]  C. Darwin Power of Movement in Plants , 1880 .

[28]  Susan S. Golden,et al.  CYANOBACTERIAL CIRCADIAN RHYTHMS. , 1997, Annual review of plant physiology and plant molecular biology.

[29]  S. Cutler,et al.  Cellulose synthesis: Cloning in silico , 1997, Current Biology.

[30]  B. W. Shirley Flavonoid biosynthesis: ‘new’ functions for an ‘old’ pathway , 1996 .