Research

Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants

Peter M Palenchar¹ , Andrei Kouranov² , Laurence V Lejay³ and Gloria M Coruzzi⁴

¹Department of Chemistry, Rutgers University, Camden, NJ 10003, USA

²Center for Bioinformatics, University of Pennsylvania, 423 Guardian Drive, Philadelphia, PA 19104, USA

³Laboratoire de Biochimie et physiologie moleculaire des plantes, 2 Place Viala, 34060 Montpellier Cedex 1, France

⁴Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA

author email corresponding author email

Genome Biology 2004, 5:R91doi:10.1186/gb-2004-5-11-r91

Published:	29 October 2004

Subject areas: Plant biology, Bioinformatics, Genetics, Genome studies

Abstract

Background

Carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known about which genes are regulated by interactions between carbon and nitrogen signaling or the mechanisms by which the different pathways interact.

Results

Microarray analysis was used to study global changes in mRNA levels due to carbon and nitrogen in Arabidopsis thaliana. An informatic analysis using InterAct Class enabled us to classify genes on the basis of their responses to carbon or nitrogen treatments. This analysis provides in vivo evidence supporting the hypothesis that plants have a carbon/nitrogen (CN)-sensing/regulatory mechanism, as we have identified over 300 genes whose response to combined CN treatment is different from that expected from expression values due to carbon and nitrogen treatments separately. Metabolism, energy and protein synthesis were found to be significantly affected by interactions between carbon and nitrogen signaling. Identified putative cis-acting regulatory elements involved in mediating CN-responsive gene expression suggest multiple mechanisms for CN responsiveness. One mechanism invokes the existence of a single CN-responsive cis element, while another invokes the existence of cis elements that promote nitrogen-responsive gene expression only when present in combination with a carbon-responsive cis element.

Conclusion

This study has allowed us to identify genes and processes regulated by interactions between carbon and nitrogen signaling and take a first step in uncovering how carbon- and nitrogen-signaling pathways interact to regulate transcription.