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JXB Advance Access published online on February 13, 2008
Journal of Experimental Botany, doi:10.1093/jxb/erm345
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© The Author [2008]. 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

FOCUS REVIEW

Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach

M. Cristina Palmieri1, Simone Sell1, Xi Huang1 *, Matthias Scherf2, Thomas Werner2, Jörg Durner1,{dagger} and Christian Lindermayr1

1Institute for Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
2Genomatix Software GmbH, Munich, Germany

{dagger} To whom correspondence should be addressed. E-mail: durner{at}gsf.de

Due to its high reactivity and its ability to diffuse and permeate the cell membrane, nitric oxide (NO) and its exchangeable redox-activated species are unique biological messengers in animals and in plants. Although an increasing number of reports indicate that NO is an essential molecule in several physiological processes, there is not a clear picture of its method of action. Studies on the transcriptional changes induced by NO permitted identification of genes involved in different functional processes such as signal transduction, defence and cell death, transport, basic metabolism, and reactive oxygen species (ROS) production and degradation. The co-expression of these genes can be explained by the co-operation of a set of transcription factors that bind a common region in the promoter of the regulated genes. The present report describes the search for a common transcription factor-binding site (TFBS) in promoter regions of NO-regulated genes, based on microarray analyses. Using Genomatix Gene2Promotor and MatInspector, eight families of TFBSs were found to occur at least 15% more often in the promoter regions of the responsive genes in comparison with the promoter regions of 28 447 Arabidopsis control genes. Most of these TFBSs, such as ocs element-like sequences and WRKY, have already been reported to be involved in particular stress responses. Furthermore, the promoter regions of genes involved in jasmonic acid (JA) biosynthesis were analysed for a common TFBS module, since some genes responsible for JA biosynthesis are induced by NO, and an interaction between NO and JA signalling has already been described.

Key words: Arabidopsis, gene expression, microarray, nitric oxide, signal transduction

* Present address: Institute of Biological Science and Technology, Hainan University, Haikou, PR China.

Received 19 June 2007; Revised 19 November 2007 Accepted 10 December 2007


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