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

• Published in: Journal of experimental botany 2008-02, Vol.59 (2), p.177-186
• Main Authors: Palmieri, M. Cristina, Sell, Simone, Huang, Xi, Scherf, Matthias, Werner, Thomas, Durner, Jörg, Lindermayr, Christian
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis thaliana; Binding Sites; Bioinformatics; Biological and medical sciences; Cell culture techniques; Computational Biology; DNA; FOCUS REVIEW; Fundamental and applied biological sciences. Psychology; gene expression; Gene Expression Profiling; Gene expression regulation; Gene Expression Regulation, Plant; Genes; Genes, Plant; Genes. Genome; microarray; Molecular and cellular biology; Molecular genetics; nitric oxide; Nitric Oxide - metabolism; Oligonucleotide Array Sequence Analysis; Oxides; Plant cells; Plants; Promoter regions; Promoter Regions, Genetic; signal transduction; Transcription factors; Transcription Factors - metabolism; Transcriptional regulatory elements
• ISSN: 0022-0957; 1460-2431
• DOI: 10.1093/jxb/erm345

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.