Transcriptome analysis coupled with virus induced gene silencing delineates the unfolded protein response of tomato

The molecular details of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) and their functional significance in combating environmental stress in crop species remain inadequately elucidated. Tomato (Solanum lycopersicum) is an important crop, sensitive to temperature, and serves as a model crop plant for studying these pathways. To establish a tomato UPR transcriptome profile, we performed RNA sequencing (RNA-seq) analysis of tomato seedlings under tunicamycin (Tm)-induced ER stress. The 339 differentially expressed genes encompassed traditional ER stress markers, ER-associated degradation elements, transcription factors, and novel candidate genes. Our functional analysis of key UPR genes, viz., SlIRE1A, SlIRE1B, SlbZIP60, and SlbZIP28, using Virus-Induced Gene Silencing (VIGS) revealed differential requirements for SlIRE1A and SlIRE1B in the Tm-induced upregulation of downstream genes. Additionally, we found that the expression of most of the downstream genes we analyzed was equally dependent on both the IRE1 and bZIP28 pathways. The expression analysis of several of these genes under environmental stress conditions indicated that their expression patterns did not align with those observed during ER stress. Furthermore, our analysis of VIGS plants subjected to heat stress revealed that the regulation of reactive oxygen species (ROS) levels in tomato depends on the IRE1-bZIP60 pathway. Overall, this study provides a comprehensive analysis of UPR pathways in tomato and offers essential molecular insights for developing resilient tomato cultivars that can withstand adverse environmental conditions.