Multi-domain packing in the aminoacylatable 3′ end of a plant viral RNA

摘要

Turnip yellow mosaic virus (TYMV) contains a tRNA-like structure (TLS) in its 3′ untranslated region (3′ UTR). This highly structured element induces valylation of the viral RNA by host cell enzymes and is important for virus proliferation. Directly upstream of the TYMV TLS is an upstream pseudoknot domain (UPD) that has been considered to be structurally distinct from the TLS. However, using a combination of functional, biochemical, and biophysical assays, we show that the entire 3′ UTR of the viral genome is a single structured element in the absence of cellular protein. This packing architecture stabilizes RNA structure and creates a better substrate for aminoacylation, and thus the UPD and TLS are functionally and structurally coupled. It has been proposed that the TYMV TLS acts as a molecular switch between translation and replication. Our results suggest that this putative switch could be based on structural changes within the global architecture the UTR induced by interactions with the ribosome. The TYMV·TLS UPD may demonstrate how RNA structural plasticity can play a role in regulation of biological processes.