Exploring plant–microbe interactions using DNA microarrays

Abstract

Functional genomics, facilitated by DNA microarray technology, has vast potential for our understanding of plant–microbe systems. But how useful are the data when there is limited genomic information and the organisms cannot yet be genetically manipulated? During the 10th New Phytologist Symposium in Nancy, France, the potential and the problems associated with using DNA microarray technology for studying the molecular background of plant–microbe interactions were discussed. ‘There is a danger that microarray experiments will lead to a vast accumulation of data that cannot be meaningfully interpreted’ Since their introduction in the mid-1990s, DNA microarrays (Box 1 Box 1 The DNA array technique The DNA array technique is in principle very simple. Thousands of DNA sequences (typically presynthesized oligonucleotides or inserts from cDNA libraries) are printed onto glass slides or nylon sheets using a robotic arrayer. To compare the abundance of these genes in a sample, RNA or DNA is extracted (the ‘target’), labelled and hybridized to the arrayed DNA (the ‘probe’). After washing, the probe is detected by fluorescence scanning or phosphor imaging. The primary data in microarray experiments consist of scans of the array (images). The spots on the images are quantified and the intensities are normalized. The final step is to identify genes that are significantly up- or down-regulated and to identify clusters of coregulated genes (regulons). The rationale behind the approach is that genes displaying similarity in expression pattern might be functionally related and governed by the same genetic control mechanism (Brown & Botstein, 1999). ) have become one of the major tools in functional genomics for exploring the genome-wide patterns of gene expression in an organism (Colebatch et al., 2002a). The main application of the DNA microarray technique has so far been in the analysis of gene expression in model organisms such as Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and Caenorhabiditis elegans, simply because their complete genome sequences are available. However, DNA microarray technology is now rapidly being applied to studies of other organisms, including plant pathogens and symbionts (Martin, 2001). Complete genome sequences are available for a number of important bacterial pathogens and symbionts and genome sequencing of several fungi is under way. In the absence of fully sequenced genomes, information from large sets of expressed sequence tags (ESTs) is well suited for constructing cDNA arrays. Genome sequences are also becoming available for several plant hosts including rice, legumes and poplar. There is, clearly, great potential in applying DNA microarray technology to examining plant–microbe systems, as this will substantially increase our knowledge of the genetic background behind these interactions. However, concerns have been raised about the usefulness of the data obtained from microarray experiments in organisms for which there is limited genomic information and that cannot be genetically manipulated. To what extent can the complex and large data sets generated from microarray experiments in nonmodel organisms be meaningfully interpreted and validated? How can microarray data from different experiments and labs be compared? The first demonstrations of the applicability of the DNA array technique for monitoring the gene expression of plant–microbe interactions originate from studies on defence reactions in Arabidopsis. Schenk et al. (2000) analysed the expression of genes in Arabidopsis either infected by the incompatible fungal pathogen Alternaria brassicicola or treated with the defence-related signalling molecules salicylic acid (SA), methyl jasmonate (MJ), or ethylene. Analysis of the expression data obtained indicated the existence of a considerable network of regulatory interactions and coordination of signalling pathways, which had not been observed previously when analysing a few ge