Host-dependent effects of the 3′ untranslated region of turnip crinkle virus RNA on accumulation in Hibiscus and Arabidopsis

The 3' untranslated region (UTR) of turnip crinkle virus (TCV) RNA is 253 nt long (nt 3798-4050) with a 27 nt hairpin structure near its 3' terminus. In this study, the roles of the 3' UTR in virus accumulation were investigated in protoplasts of Hibiscus cannabinus L. and Arabidopsis thaliana (L.) Heynh. Our results showed that, in Hibiscus protoplasts, the minimal 3' UTR essential for TCV accumulation extends from nt 3922 to 4050, but that maintenance of virus accumulation at wild-type (wt) levels requires the full-length 3' UTR. However, in Arabidopsis protoplasts, only 33 nt (nt 4018-4050) at the 3' extremity of the UTR is required for wt levels of accumulation, whereas other parts of the 3' UTR are dispensable. The 27 nt hairpin within the 33 nt region is essential for virus accumulation in both Hibiscus and Arabidopsis protoplasts. However, transposition of nucleotides in base pairs within the upper or lower stems has no effect on virus accumulation in either Hibiscus or Arabidopsis protoplasts, and alterations of the loop sequence also fail to affect replication. Disruption of the upper or lower stems and deletion of the loop sequence reduce viral accumulation in Arabidopsis protoplasts, but abolish virus accumulation in Hibiscus protoplasts completely. These results indicate that strict conservation of the hairpin structure is more important for replication in Hibiscus than in Arabidopsis protoplasts. In conclusion, both the 3' UTR primary sequence and the 3'-terminal hairpin structure influence TCV accumulation in a host-dependent manner.