Structural features unique to a new 405-nucleotide satellite RNA of cucumber mosaic virus inducing tomato necrosis

The complete nucleotide sequence of a new satellite RNA (KN-satRNA) of cucumber mosaic virus (CMV) strain KN, isolated from tomato plants showing severe necrosis, has been determined by the analysis of a full-length cDNA clone from which biologically active transcript was produced. KN-satRNA was 405 nucleotides and is the largest among the known CMV-satRNAs. Comparison of the sequence with D-CARNA5 (335 nucleotides) revealed three extensive homologous regions, which were the 5' region (position 1-80), the 3' half (position 213-405), and a middle section (position 116-177) of the molecule. The total length of the three regions covers almost the entire molecule of D-CARNA5. Thus, it is apparent that insertions would occur at two sites of D-CARNA5, positions 81-86 and 146, to evolve the larger size satRNA. These insertions did not alter the proposed secondary structure model of Q-satRNA. The in vitro transcript of the cDNA clone of KN-satRNA induced necrosis on tomato which was identical to that of native KN-satRNA. The 3'half of the RNA contained the "necrogenic consensus" sequence reported for other satRNAs, to which the pathogenicity of KN-satRNA may be attributed.