DMS-MaPseq and DREEM Analyses Implicate the Critical Role of RNA Structural Dynamics in Turnip Yellow Mosaic Virus Pathogenicity.

Increasing evidence indicates that RNA secondary structure (RSS) affects the life cycle of the RNA viruses in mammals. However, the specific roles of RSS in plant virus propagation are under-studied. Here we decoded the in vivo genome-wide RSS of Turnip Yellow Mosaic Virus (TYMV). We found that TYMV possesses a complicated RSS landscape across the genome in vivo. Furthermore, the viral RSS is dynamic in most parts of the genome. We discovered that the earlier reported pseudoknot on the 3' tRNA-like structure (3' TLS) from in vitro assays indeed exists in vivo. Importantly, 3' TLS also forms a novel alternative conformation that lacks the pseudoknot character, suggestive of the dynamics between two conformations. The 3' TLS structural dynamics is critical for viral replication, whereas the pseudoknot structure is pivotal for translation. Thus, our findings characterized the in vivo genome-wide RNA structural feature of TYMV and provided valuable insights for viral replication and translation in cells.