Complete nucleotide sequence of two new satellite RNAs associated with cucumber mosaic virus

Complete nucleotide sequences of two new satellite RNAs (satRNA) of cucumber mosaic virus (CMV), E-satRNA and OY2-satRNA, have been determined and compared with known satellite RNA sequences. E-satRNA contained 339 nucleotide residues and OY2-satRNA had 386 nucleotide residues. Comparison of the sequences among satRNAs including these new satRNAs revealed extensive homologous regions in the 5'-terminus and the 3'-half. The former region contains about 95 nucleotide residues (80-100% homology) and the latter has about 175 nucleotide residues (81-99% homology), but there was less homology in the middle of the RNA. A possible secondary structure for E-satRNA, OY2-satRNA, and Y-satRNA [S. Hidaka et al. (1984) FEBS Lett. 174, 38-42] was constructed and compared with that of a satellite RNA from CMV-Q (Q-satRNA) [K. H. J. Gordon and R. H. Symons (1983), Nucl. Acids Res. 11, 947-960]. Two similar hairpin-loop structures in the 5'-terminal region were common features of the RNAs; one of them was found in E-satRNA, the other in OY2-satRNA, and both in Y-satRNA and Q-satRNA. Analyses of in vitro messenger properties of the satRNAs suggested that the first open reading frame of E-sat and Y-satRNAs was a possible coding region for protein synthesis.