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JXB Advance Access originally published online on April 29, 2007
Journal of Experimental Botany 2007 58(9):2359-2367; doi:10.1093/jxb/erm079
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© The Author [2007]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

RESEARCH PAPER

Insights into the genomic nitrate response using genetics and the Sungear Software System

Rodrigo A. Gutiérrez1,3, Miriam L. Gifford1, Chris Poultney2, Rongchen Wang4, Dennis E. Shasha2, Gloria M. Coruzzi1 and Nigel M. Crawford4,*

1Department of Biology, New York University, New York, NY 10003, USA
2Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA
3Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
4Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0116, USA

* To whom correspondence should be addressed. E-mail: ncrawford{at}ucsd.edu

Nitrate is both a nutrient and a potent signal that stimulates plant growth. Initial experiments in the late 1950s showing that nitrate enhances nitrate reductase (NR) activity after several hours of treatment have now progressed to transcriptome studies identifying over 1000 genes that respond to µM levels of nitrate within minutes. The use of an Arabidopsis NR-null mutant allowed the identification of genes that respond to nitrate when the production of downstream metabolites of nitrate is blocked. Further dissection of the nitrate response is now possible using new bioinformatic tools such as Sungear to perform comparative studies of multiple transcriptome responses across different laboratories and environmental conditions. These analyses have identified genes and pathways (e.g. nitrate assimilation, pentose phosphate pathway, and glycolysis) that respond to nitrate under a variety of conditions (context-independent). Most of these genes and pathways are ones that were identified using the NR-null mutant as responding directly to nitrate. By contrast, other processes such as protein synthesis respond only under a subset of conditions (context-dependent). Data from the NR-null mutant suggest these latter processes may be regulated by downstream nitrogen metabolites.

Key words: Genomics, microarray, nitrate, Sungear

Received 3 January 2007; Revised 16 March 2007 Accepted 20 March 2007


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