Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus

SatC is a noncoding subviral RNA associated with Turnip crinkle virus (TCV). A 100-nt stretch in the 3′ UTR of TCV contains three hairpins and two pseudoknots that fold into a tRNA-shaped structure (TSS) that binds 80S ribosomes. The 3′ half of satC is derived from TCV and contains 6-nt differences in the TSS-analogous region. SatC binds poorly to 80S ribosomes, and molecular modeling that predicted the 3D structure of the TSS did not predict a similar structure for satC. When the satC TSS region was step-wise converted to the original TCV TSS bases, ribosome binding increased to TCV TSS levels without significantly affecting satC replication. However, mutant satC was less fit when accumulating in plants and gave rise to numerous second site changes that weakened one of two satC conformations. These results suggest that minor changes from the original TCV sequence in satC reflect requirements other than elimination of ribosome binding.