Evolution of virus-derived sequences for high-level replication of a subviral RNA

Abstract

Turnip crinkle virus (TCV) and its 356-nt satellite RNA satC share 151 nt of 3'-terminal sequence, which contain 8 positional differences and are predicted to fold into virtually identical structures, including a series of four phylogenetically inferred hairpins. SatC and TCV containing reciprocal exchanges of this region accumulate to only 15% or 1% of wild-type levels, respectively. Step-wise conversion of satC and TCV 3'-terminal sequences into the counterpart's sequence revealed the importance of having the cognate core promoter (Pr), which is composed of a single hairpin that differs in both sequence and stability, and an adjacent short 3'-terminal segment. The negative impact of the more stable TCV Pr on satC could not be attributed to lack of formation of a known tertiary interaction involving the 3'-terminal bases, nor an effect of coat protein, which binds specifically to TCV-like Pr and not the satC Pr. The satC Pr was a substantially better promoter than the TCV Pr when assayed in vitro using purified recombinant TCV RdRp, either in the context of satC or when assayed downstream of non-TCV-related sequence. Poor activity of the TCV Pr in vitro occurred despite solution structure probing indicating that its conformation in the context of satC is similar to the active form of the satC Pr, which is thought to form following a required conformational switch. These results suggest that evolution of satC following its initial formation generated a Pr that can function more efficiently in the absence of additional TCV sequence that may be required for full functionality of the TCV Pr.

The 3′ proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits

“…(B) Structure of the 39 region of the TCV 39 UTR. All secondary and tertiary structures have been previously confirmed using single and compensatory mutations (Zhang et al 2006c;McCormack et al 2008). (LSL) large symmetrical loop.…”

Mimicry of molecular pretenders: The terminal structures of satellites associated with plant RNA viruses

“…15 Similar ψ1 structures are found in Tombusviridae, which implies their important role in the replication of viruses in this family.…”

“…15 Thus, the functional interchangeability of the required elements between the subviral RNAs and helper viruses does not hold true for all systems, despite similarities in sequences or structures between the 2 components ( Table 1).…”

Conformational organization of the 3′ untranslated region in the tomato bushy stunt virus genome

“…For SatC, it was proposed that a preactive conformation exists that must be converted to include the RSEÀ39CSS interaction before replication can occur (Zhang et al 2006a). A corresponding RSEÀ39CSS interaction in the TCV genome has also been found to be important for virus viability; however, it is possible that the preactive conformation in SatC is unique to this subviral RNA and does not extend to its helper genome (Zhang et al 2006b). Based on our results with TBSV, the closed structure is likely to be the conformation present in invading and newly synthesized viral genomes.…”

“…For TBSV (genus Tombusvirus, family Tombusviridae), this interaction mediates replicase complex formation in vivo and modulates negative-strand synthesis in vitro (Panaviene et al 2005;Pogany et al 2003). The latter activity has also been demonstrated in vitro for TCV (genus Carmovirus, family Tombusviridae) and the interaction is required for optimal virus accumulation in vivo (Zhang et al 2004(Zhang et al , 2006b). …”