Comparative sequence and structure of viroid-like RNAs of two plant viruses

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Abstract
A newly discovered group of spherical plant viruses contains a bi partite enome consisting of a single-strand linear I molecule (F 1, Mr 1.5 × 105), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mγ˜ 125,000). The nucleotide sequences of the RNA 2 of two of these, velvet tobacco mottle virus and solanum nodiflorum mottle virus, have been determined. RNA 2 of solanum nodiflorum mottle virus consists of 377 residues whereas that of velvet tobacco mottle virus consists of two approximately equimolar species, one of 366 residues and the other, with a single nucleotide deletion, of 365 residues. There is 92 – 95% sequence homology between the RNA 2 species of the two viruses. The predicted second ary structures possess extensive intramolecular base pairing to give rod-like structures similar to those of viroids. The structural similarities between the RNAs 2 of velvet tobacco mottle virus and solanum nodiflorum mottle virus and viroids may reflect functional similarities.