Nucleotide sequence analysis of six satellite RNAs of cucumber mosaic virus: primary sequence and secondary structure...

The nucleotide sequences of six satellite RNAs of cucumber mosaic virus (CMV) differing in their pathological properties have been determined. Although these RNAs varied in length from 333 to 342 nucleotides, the extent of nucleotide sequence homology to each other and to four other satellite RNAs ranged from 84 to 97%, allowing satellite RNA subgrouping on the basis of nucleotide sequence. This subgrouping was further extended by an analysis of the nature of the differences in nucleotide sequence, with most of the variation occurring within nucleotides 129 to 190 and 318 to the 3'-end. Enzymatic and chemical secondary structure probing of four satellite RNAs yielded a common structure in which 48-52% of the nucleotides were base paired. Although there were discrepancies between the experimental data and the model in two out of seven hairpins, the model contained structural elements and consensus sequences in common with the 3'-end sequences of two satellite RNA helper viruses: CMV and tomato aspermy virus. Specific sequence changes, secondary structure characteristics, or proteins potentially encoded by any of 10 satellite RNAs did not correlate with the known pathogenic responses attributable to individual satellite RNAs.