Study : Genome-wide expression analysis of PTI and ETI responses in wild type and PRR-deficient Arabidopsis plants
Genome-wide expression analysis of PTI and ETI responses in wild type and PRR-deficient Arabidopsis plants
Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and PRR mutant plants in response to PTI- and ETI-eliciting strains of Pseudomonas syringae pv tomato (Pst) bacterium. Methods: Four-week-old Arabidopsis plant leaves were infiltrated with sterile water (Mock) or different Pst strains and harvested at 3h or 6h after infiltration for RNA extraction and deep sequencing by Illumina. Raw data were cleaned up and trimmed and reads were mapped to Arabidopsis genome. Gene expression levels were calculated using the TPM method (Transcripts per Kb of exon model per Million mapped reads). Results and Conclusions: This study showed that Pst DC3000 D36E and D36E(avrRpt2) strains both induced significant gene expression changes (with changes of more than 3000 and 7000 genes respectively) in Col-0 plant, and D36E(avrRpt2) strain induced stronger expression changes globally. Furthermore, many genes are differentially regulated in the PRR mutant plants in response to D36E inoculation compared with wild type plant; however, D36E(avrRpt2) inoculation induced very similar expression patterns in two genotypes, suggesting that ETI can largely restore PTI-associated gene expression in the PRR mutant plant. In addition, we also found that ETI can largely induce the expression levels of many key PTI signaling components. Overall design: Investigation of genome-wide expression profiles of Arabidopsis wildtype and PRR mutants in response to PTI- and ETI-inducing bacterial strains.