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

Rodrigo A. Gutiérrez, Miriam L. Gifford, Chris Poultney, Rongchen Wang, Dennis E. Shasha, Gloria M. Coruzzi, Nigel M. Crawford

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2359-2367
Number of pages9
JournalJournal of Experimental Botany
Volume58
Issue number9
DOIs
StatePublished - Jul 2007

Fingerprint

Nitrates
Software
nitrates
genomics
Nitrate Reductase
nitrate reductase
Transcriptome
transcriptome
mutants
Genes
genes
metabolites
Pentose Phosphate Pathway
pentoses
glycolysis
Glycolysis
Computational Biology
Arabidopsis
bioinformatics
Dissection

Keywords

  • Genomics
  • Microarray
  • Nitrate
  • Sungear

ASJC Scopus subject areas

  • Plant Science

Cite this

Insights into the genomic nitrate response using genetics and the Sungear Software System. / Gutiérrez, Rodrigo A.; Gifford, Miriam L.; Poultney, Chris; Wang, Rongchen; Shasha, Dennis E.; Coruzzi, Gloria M.; Crawford, Nigel M.

In: Journal of Experimental Botany, Vol. 58, No. 9, 07.2007, p. 2359-2367.

Research output: Contribution to journalArticle

Gutiérrez, Rodrigo A. ; Gifford, Miriam L. ; Poultney, Chris ; Wang, Rongchen ; Shasha, Dennis E. ; Coruzzi, Gloria M. ; Crawford, Nigel M. / Insights into the genomic nitrate response using genetics and the Sungear Software System. In: Journal of Experimental Botany. 2007 ; Vol. 58, No. 9. pp. 2359-2367.
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