“A weed is a plant whose virtues have not yet been discovered.”

Ralph Waldo Emerson

With the publication of its genome sequence, Arabidopsis now ranks among the elite of post-genomic organisms, alongside yeast, worms and flies. Being sessile organisms, it's not surprising that plants have evolved their own molecular peculiarities — Arabidopsis lacks stars of some well-known signal transduction pathways, such as Wnt and Notch, but has many unique protein families, especially among transcription factors. The complete sequence, the quality of which surpasses all other whole genome sequences published so far, will simplify forward-mutational analyses, although the frequent gene duplications raise the spectre of functional redundancy.

Surveying gene expression patterns provides another avenue for investigating gene function, and a recent microarray analysis of gene expression during the Arabidopsis immune defence response illustrates this point.

When challenged with a pathogen, plants mount both local, transient defence measures and a systemic, long-lasting disease resistance, known as systemic acquired resistance (SAR). One hallmark of the SAR response is the activation of pathogenesis-related (PR) genes that, along with other (unknown) factors, induce a concerted response to an immune challenge.

Maleck et al. examined the changes in gene activity that occur during the induction and maintenance of SAR. Using microarrays, the expression of about 7,000 genes was analysed in plants that had been subjected to fourteen different SAR-inducing or SAR-repressing treatments. 413 ESTs (1.5% of the genes in the genome) showed a minimum of 2.5-fold differential expression in at least two treated samples, which is the conservative criterion used by the authors to select the genes of interest. Plants that were given similar treatments yielded similar gene expression profiles, and these were used to define clusters of genes with co-regulated expression. The cluster that contains the PR-1 gene, the most robust marker for SAR, is the most likely to contain other genes involved in SAR, and so was studied in more detail. Backing the assumption that the 31 genes in the PR-1 cluster are co-regulated by similar control regions, the cis-elements of 26 genes were found to be highly enriched in W-boxes. These are the binding sites for plant-specific WRKY transcription factors, which the authors speculate might act to repress the SAR response.

This is the first transcriptional profile of the SAR response in Arabidopsis. Follow-up studies should reveal how it's possible to cope when you can't run or you can't hide.