Characterization of PEP1-influenced transcriptional reprogramming at the Arabidopsis root meristem
The apical root growth is immensely affected by pathogen-associated molecular patterns (PAMPs) or plant-derived damage-associated molecular pattern (DAMPs). Upon perceiving the danger signals, elevated defense machinery often compromises root apical growth, resulting in the meristem's aberrant proliferative and formative divisions. In our previous study, we reported that one of the DAMP signals, PEP1, reprograms developmental pathways in the root apical meristem resulting in the reduction of stele cell numbers, alteration of the xylem vessel organizations, and disruption of cell-to-cell symplastic connections. However, a comprehensive atlas of the gene regulatory networks associated with the root growth-defense tradeoffs is yet to be elucidated. To gain an insight into the dynamic molecular framework that modulates root development under elevated pathogenic signals, we performed a time course RNA-sequencing analysis in the root meristem after PEP1 treatment. Based on expression dynamics of the DEGs (fold change = 1.5; p < 0.05), 12 clusters were obtained following K-means algorithm. Intriguingly, among the PEP1-induced gene clusters, we observed that a group of zinc finger proteins, comprising one of the most prominent transcription factor families, are highly enriched. On the contrary, the PEP1-repressed gene clusters included various developmental regulators expressed in the vascular tissues. Indeed, an in vitro network analysis using selected PEP1-induced and repressed clusters indicated STZ as a potential key mediator of the defense-induced developmental reprogramming pathway in the root stele. We also revealed the involvement of two related homologs of STZ, ZAT6, and AZF3, in this trade-off pathway. Our study provides a comprehensive overview of transcription factors that respond to the early hours of PEP1 induction and hijack cellular machinery, thereby contributing to cellular reorganization and growth in the root apical meristem. Overall design: We took 4-5 days old Arabidopsis seedling and treated them with 1µM PEP1 for 3h, 6h, 12h, and 24h. Following PEP1 treatment we dissected the root meristem from each mock or PEP1 treated samples. The RNA was isolated using RNeasy Micro kit (Qiagen). The purification of the samples and sequencing was done by Macrogen (Korea).