SlRBP1 induces target RNA structure remodeling in tomato

The secondary structure of RNA (RSS) plays a pivotal role in gene regulation. RNA-binding proteins (RBPs) dynamically alter RSS, thereby orchestrating various post-transcriptional regulatory processes, such as splicing, alternative polyadenylation, and translation. In this study, we delve into the function of SlRBP1, a glycine-rich RNA-binding protein, in eliciting structural remodeling of target RNAs in tomato plants. Using dimethyl sulfate mutational profiling coupled with high-throughput sequencing (DMS-MaPseq), we generated a specific profile of the in vivo secondary structure of target RNAs. The DMS treatment conditions were meticulously optimized for tomato leaves, ensuring that the resulting target-specific DMS-MaPseq data exhibited high quality and reproducibility. Knocking down SlRBP1 altered the RNA structure of its bona fide target PsaD , particularly in regions adjacent to the binding sites. Additionally, SlRBP1 interacted with the DEAH-box helicase 34 (SlDHX34). Collectively, these findings reveal that SlRBP1 remodels target RNA structures at localized binding sites. This study provides new insights into the structural remodeling effects of RBPs, illuminating the intricate regulatory networks in plant biology.