Studies on encapsidated viroid-like RNA. III. Comparative studies on RNAs isolated from velvet tobacco mottle virus and Solanum nodiflorum mottle virus.

Solanum nodiforum mottle virus (SNMV) encapsidates two unique RNA species as shown by 3H-complementary DNA hybridization analysis. They are RNA 1, a long linear single-stranded molecule with a molecular weight of 1.5 x 10(6) and RNA 2 and RNA 3 which are circular and linear forms of the same molecule, respectively. Electron microscopic examination and thermal denaturation studies indicate a viroid-like structure for RNA 2 of SNMV. Electrophoretic analysis of the viroid-like RNA encapsidated by SNMV indicates it has a slightly larger molecular weight (0.13 x 108) than the viroid-like RNA recently isolated from velvet tobacco mottle virus (VTMoV). Complementary DNA (cDNA) analysis revealed that SNMV RNA 2 contains the entire nucleotide sequence of VTMoV RNA 2, plus an additional 40-50 nucleotides not present in the latter. Comparative sequence homology studies between the large RNAs encapsidated by SNMV and VTMoV (both of MW 1.5 x 10(6)) revealed only partial homology (20%). However, the level of S1 nuclease resistance could be increased by the presence of higher salt concentrations during hybridization and subsequent S1 nuclease assay. This indicates that many smaller regions of homology are present between VTMoV RNA 1 and SNMV RNA 1. This is the second example of an encapsidated viroid-like RNA.