Abstract
Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR) is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor) fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able to control NPR1-dependent transcription and identify direct transcriptional targets of NPR1. We show that NPR1 directly upregulates the expression of eight WRKY transcription factor genes. This large family of 74 transcription factors has been implicated in various defense responses, but no specific WRKY factor has been placed in the SAR network. Identification of NPR1-regulated WRKY factors allowed us to perform in-depth genetic analysis on a small number of WRKY factors and test well-defined phenotypes of single and double mutants associated with NPR1. Among these WRKY factors we found both positive and negative regulators of SAR. This genomics-directed approach unambiguously positioned five WRKY factors in the complex transcriptional regulatory network of SAR. Our work not only discovered new transcription regulatory components in the signaling network of SAR but also demonstrated that functional studies of large gene families have to take into consideration sequence similarity as well as the expression patterns of the candidates.
Highlights
Systemic acquired resistance (SAR) is an inducible plant defense response against pathogens
Using p, 0.001 as a cutoff, we found 64 genes differentially expressed between NPR1-glucocorticoid receptor (GR) and npr1–3 (Table S1)
Among the 64 genes, we found that the expression of WRKY54, WRKY38, WRKY59, WRKY18, WRKY70, WRKY66, and WRKY53 was reproducibly induced in two biological replicates
Summary
Systemic acquired resistance (SAR) is an inducible plant defense response against pathogens. A microarray experiment showed that NPR1 directly upregulates the protein secretory pathway This is essential for SAR since disrupting this pathway diminished the secretion of PR proteins and resulted in reduced resistance [6]. NPR1 likely regulates these secretion-related genes through a novel transcription factor [6]. In addition to this unknown transcription factor and the TGAs, WRKY transcription factors have been implicated in regulating the response against pathogen infection. Likewise, overexpressing WRKY18 resulted in gain of PR gene expression and resistance in a developmentally regulated manner [14]. Since ectopically expressing several WRKY genes all resulted in a similar range of phenotypes, it is difficult to conclude functional specificity from these studies
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