Microarray analysis of Psm-induced transcriptome changes in the systemic leaves of Arabidopsis plants

The goal of the microarray was to compare the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326 (Psm)-induced transcriptome changes in the systemic leaves of the wild-type Col-0, lecrk-VI.2-2, and bak1-5 plants. Results showed that local Psm inoculation induced dramatic transcriptional changes in Col-0, with 564 and 151 genes up- and down-regulated at least twofold with a low q value (≤ 0.05), respectively. However, only 55 and 26 genes in lecrk-VI.2-2 and 221 and 121 genes in bak1-5 were up- and down-regulated, respectively. The majority of the genes that were induced or suppressed twofold or more with a low q value (≤ 0.05) in Col-0 were induced or suppressed to a smaller extent in bak1-5 and the smallest extent in lecrk-VI.2-2. These results indicate that both lecrk-VI.2-2 and bak1-5 suppressed Psm-induced systemic signaling with the lecrk-VI.2-2 mutation having a stronger effect than bak1-5. Three replicates with systemic leaves from 12 plants per sample were collected at 48 hr after Psm inoculation of the local leaves. Systemic leaf tissues were collected as the control at 48 hr after the local leaves were treated with 10 mM MgCl2. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the biological replicates were used for microarray analysis.