Plant Physiology Preview
Published on November 3, 2006; 10.1104/pp.106.090167
Received September 21, 2006
Accepted October 17, 2006
Genome-wide Analysis of the Arabidopsis Leaf Transcriptome Reveals Interaction of Phosphate and Sugar Metabolism
Renate Müller , Marc Morant , Hanne Jarmer , Lena Nilsson , and Tom Hamborg Nielsen *
Plant Biochemistry Laboratory, Department of Plant Biology, Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark; Department of Agricultural Sciences, Crop Science, Royal Veterinary and Agricultural University, Højbakkegård Allé 13, 2630 Taastrup, Denmark
Plant Biochemistry Laboratory, Department of Plant Biology, Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Denmark
Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Kemitorvet, DK-2800 Lyngby, Denmark
* Corresponding author; email: thni{at}kvl.dk.
Global gene expression was analyzed in Arabidopsis thaliana by microarrays comprising 21,500 genes. Leaf segments derived from P-starved and P-replenished plants were incubated with or without Suc to obtain tissues with contrasting combinations of P and carbohydrate levels. Transcript profiling revealed the influence of the two factors individually and the interactions between P- and sugar-dependent gene regulation. A large number of gene transcripts changed more than 2-fold: In response to P-starvation 171 genes were induced and 16 repressed, while Suc incubation resulted in 337 induced and 307 repressed genes. A number of new candidate genes involved in P-acquisition were discovered. In addition, several putative transcription factors and signaling proteins of P-sensing were disclosed. Several genes previously identified to be sugar responsive were also regulated by P-starvation, and known P-responsive genes were sugar inducible. Nearly 150 genes were synergistically or antagonistically regulated by the two factors. These genes exhibit more prominent or contrasting regulation in response to Suc and P in combination than expected from the effect of the two factors individually. The genes exhibiting interactions form three main clusters with different response patterns and functionality of genes. One cluster (cluster 1) most likely represents a regulatory program to support increased growth and development when both P and carbohydrates are ample. Another cluster (cluster 3) represents genes induced to alleviate P-starvation and these are further induced by carbohydrate accumulation. Thus, interactions between P and Suc reveal two different signaling programs, and novel interactions in gene regulation in response to environmental factors. Cis-regulatory elements were analyzed for each factor and for interaction clusters. PHR1 binding sites were more frequent in promoters of P-regulated genes as compared to the entire Arabidopsis genome, and E2F and PHR1 binding sites were more frequent in interaction clusters 1 and 3, respectively.
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