Tombusvirids Avoid and Exploit a Plant Exoribonuclease

Tombusviridae is a family of plus-strand RNA plant viruses that contain single-stranded RNA genomes with no 5' cap or 3' poly(A) tail. The 5' cap is an essential post-transcriptional modification that increases the stability of mRNA molecules, by protecting them from 5'-to-3' exoribonuclease decay. The lack of this modification in this virus family raised the question of how these viruses protect their vulnerable genomic 5' ends from nuclease attack during infections. Carnation Italian ringspot virus (CIRV) from the genus Tombusvirus, family Tombusviridae, has a plus-strand RNA genome with a structured 5' untranslated region that I hypothesized could serve as a protective substitute for the 5' cap. Results from my in vitro and in vivo studies with CIRV showed that the higher-order RNA structure at the 5' end of its genome was able to effectively prevent access of a 5'-to-3' exoribonuclease (Xrn), thereby protecting it from being degraded by Xrn during infections. In a second related study, I investigated a small viral RNA (svRNA) that accumulated in infections with another member of the family Tombusviridae, Tobacco necrosis virus-D (TNV-D; genus Betanecrovirus). In this case, I hypothesized that the svRNA represented a stable degradation product that could be functionally relevant to successful TNV-D infections. Through in vitro and in vivo analyses of TNV-D, I determined that the svRNA was indeed generated from incomplete digestion of the TNV-D genome by Xrn, and that its accumulation was beneficial in infections. Collectively, these findings extend and broaden our knowledge of the roles of novel viral RNA structures in facilitating successful viral infections by either evading (CIRV) or exploiting (TNV-D) the activity of the cellular exoribonuclease, Xrn