SELF-CLEAVING CIRCULAR RNA ASSOCIATED WITH RICE YELLOW MOTTLE VIRUS IS THE SMALLEST VIROID-LIKE RNA

We report the sequence, structural features, and self-cleaving activit y of the small circular RNA (sc-RNA) associated with rice yellow mottl e sobemovirus (RYMV). At 220 nucleotides, the RYMV sc-RNA represents t he smallest naturally occurring viroid-like RNA currently documented i n the literature. It is similar to other circular satellite RNAs (sat- RNAs) and viroids in being G-C-rich with a high level of self-compleme ntarity. The predicted native structure is essentially a rod with one branched terminus. A region of the RYMV sc-RNA, constituting 24% of th e sequence, exhibits 89% identity to the sat-RNA associated with the A ustralasian isolates of lucerne transient streak sobemovirus. This reg ion is also structurally similar in all three RNAs in that it forms th e left terminus of each rod. Dimeric runoff transcripts of cloned RYMV sc-RNA undergo efficient autocatalytic in vitro cleavage in the (+) b ut not the (-) polarity. Analysis of the (+) sequence indicates the pr esence of a hammerhead ribozyme resembling that of carnation small ret roviroid-like RNA and the genomic satellite transcript of newt. Ineffi cient cleavage of (+) monomeric transcripts, and a short stem III in t he hammerhead, are features consistent with a double-hammerhead mode o f self-cleavage. The presence of sat-RNA and retroviroid-like structur es within a single RNA suggests a possible role for the RYMV sc-RNA as an evolutionary intermediate between these subviral RNAs. (C) 1998 Ac ademic Press.