Identification of a novel structural interaction in Columnea latent viroid

Pairwise sequence comparisons suggest that Columnea latent viroid (CLVd) may have originated from a recombination event involving Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd). To examine the role of specific structural features in determining the host range of CLVd, we constructed a series of interspecific chimeras by replacing increasing portions of its terminal left and pathogenicity domains with the corresponding portions of PSTVd. Exchanges involving the left side of the pathogenicity domain led to lower rates of progeny accumulation in tomato, but one of the resulting chimeras was still able to replicate in cucumber. Exchanges involving the right side of the pathogenicity domain severely inhibited replication in tomato and appeared to abolish replication in cucumber. To identify potential interactions between nucleotides comprising the right side of the pathogenicity domain and other portions of CLVd, melting behaviors of circularized CLVd and PSTVd RNA transcripts were compared using a combination of temperature gradient gel electrophoresis and structural calculations. These analyses revealed an unexpected complementarity between the upper portion of the pathogenicity and terminal right domains of CLVd that facilitates breakdown of the rod-like native structure and formation of secondary hairpin II. Unlike secondary hairpin II, CLVd hairpin IV appears likely to act within the context of the genomic RNA.