PRIMARY AND SECONDARY STRUCTURE OF A 360-NUCLEOTIDE ISOLATE OF POTATO SPINDLE TUBER VIROID

Full-length complementary DNAs (cDNA) of a mild (KF 5) and a severe (S-PSTVd) isolate of potato spindle tuber viroid (PSTVd) were constructed. DNA sequencing of four KF 5 cDNA clones (M 3, M 4, M 5, and M 7) revealed that KF 5 is comprised of 360 nucleotides. By comparison, all three cDNA clones (S 2, S 9, and S 10) of S-PSTVd possess 359 nucleotides. Sequence microheterogeneity was observed among the KF 5 cDNA clones. Clone M 5 differs from mild PSTVd isolate KF 6 by a U-to-A transversion at position 303 followed by an A addition at the lower half of the ''virulence-modulating'' (VM) region. These changes modified the PSTVd consensus sequence of the VM region from 5' UCUAUCU 3' to 5' UCAAAUCU 3'. Additionally, clones M 4 and M 7 have a G-to-A transition at position 65 of the pathogenic domain, and M 3 has a G-to-A transition at position 133 of the variable domain. The sequence of the three cDNA clones of S-PSTVd was identical to that of PSTVd isolate 440-1. An improved computer program was used to predict the secondary structure of the above two sequence variants' as well as that of other PSTVd variants of which the structure has been reported previously. The data provides support for the hypothesis that increasing thermodynamic instability of the VM region is correlated with increasing virulence of the respective naturally occurring PSTVd isolate.