Analysis of the determinants of the satellite RNA of cucumber mosaic cucumovirus for high accumulation in squash.

Ix-satRNA is a 334-nt cucumber mosaic cucomovirus satellite RNA (CMV-satRNA) with the unusual property of accumulating to high levels in host plants of the family Cucurbitaceae. To identify the determinants for this unusual phenotype, recombinant satRNAs were obtained, by in vitro manipulation of full-length cDNA clones between clone-derived Ix5-satRNA and two other CMV-satRNAs that do not accumulate efficiently in squash: D4-satRNA, which differs in 7 positions from Ix5-satRNA, and B21-satRNA, which differs in 45 positions. The analysis of the accumulation in squash of these hybrid satRNAs showed that determinants for high accumulation in squash occur in three molecular domains: nucleotides 1-46 (a C at position 20), 47-185 (a C at position 102), and 185-334 (not identified). None of these determinants seemed to be necessary or sufficient to confer a phenotype of high accumulation in squash. They resulted, or did not result, in such a phenotype according to the sequences that occur in other parts of the satRNA molecule. Not all of the identified determinants were equally affected by sequence context. These results may suggest that the phenotype in squash is determined by the conformation of the satRNA.