Genomic analysis of the response of Arabidopsis thaliana to trinitrotoluene as revealed by cDNA microarrays

2,4,6-trinitrotoluene (TNT) is a nitro-substituted xenobiotic explosive that is toxic to plants and animals. Plants absorb and metabolize TNT, but the pathways are uncertain and plant responses at the molecular level have not been adequately characterized. We analyzed gene expression in response to relatively long-term exposure to TNT at low and high concentration in Arabidopsis through the use of cDNA microarrays. Arabidopsis seedlings were grown on media containing 1 and 10 μM TNT, concentrations that were empirically determined by plant growth analysis. Microarray analysis revealed that a total of 52 genes were significantly upregulated, and 47 genes were downregulated in response to TNT at a 1.7-fold cut-off for differential gene expression. A substantial number of these genes have predicted functions in cell defense and detoxification. Conserved motifs were discovered in the promoter region of co-regulated genes, some of which are potentially novel cis-regulatory elements. With follow-up real time RT-PCR, we confirmed findings from the microarray experiments and examined the regulation of selected genes to two other xenobiotic substances: the explosive RDX and thiodiglycol. Results showed that increased transcription of At5g61600 encoding for a DNA-binding protein in shoots is specific to TNT and increased transcription of At5g42530 encoding for an unknown protein in shoots is specific to both TNT and RDX.