Rice cDNA microarray-based gene expression profiling of the response to flagellin perception in cultured rice cells.

Incompatible strains of Acidovorax avenae elicit an immune response in cultured rice cells, with immunity specifically induced by the flagellin of the incompatible strain. To identify genes regulated by flagellin perception signaling in cultured rice cells, gene expression patterns were analyzed with rice cDNA microarrays, including 3,353 independent rice cDNA clones. In all, 131 genes were differentially expressed between incompatible and compatible interactions. K-means clustering showed that 94 genes were upregulated and 32 genes were downregulated during incompatible interactions, whereas only 5 genes were upregulated during compatible interactions. Among the 126 genes that were up- or downregulated during incompatible interactions, expression of 46 genes was decreased when cultured rice cells were inoculated with a flagellin-deficient incompatible strain (delta fla1141-2), indicating that approximately 37% of the 126 genes were directly controlled by flagellin perception. Real-time reverse-transcription polymerase chain reaction analysis using flagellins purified from incompatible or compatible strains was performed to confirm flagellin-regulated expression of candidate genes selected by microarray analysis. Results showed that induction of some genes involved in the immune response is regulated not only by the flagellin perception pathway, but also by another recognition molecule-perception pathway.