Nucleotide sequence and evolutionary relationships of cucumber mosaic virus (CMV) strains: CMV RNA 1.

Abstract

The nucleotide sequence of RNA 1 of the Fny strain (Subgroup I) of cucumber mosaic virus (CMV) was determined and compared at both the nucleic acid and protein levels with the corresponding sequence of RNA 1 of the Q strain (Subgroup II) of CMV. Fny-CMV RNA 1 consisted of 3357 nucleotides and contained a single long open reading frame (ORF) of 2979 nucleotides, whereas Q-CMV RNA 1 consists of 3389 nucleotides and contains a single ORF of 2973 nucleotides. The levels of sequence homology between the two RNAs were 76% at the nucleotide level and 85% at the protein level. These homologies were distributed widely over the molecules, with 45% of the non-conservative differences in amino acid sequence located between amino acids 503 and 705, and another 15% of the differences located between amino acids 224 and 298. While the C-terminal 141 amino acids contain more basic than acidic amino acids, the region of greatest amino acid sequence heterogeneity, amino acids 503 to 600, contained a preponderance of acidic amino acids in the putative translation products of RNAs 1 of both Q-CMV and Fny-CMV. The last 180 nucleotides of the 3'-terminal non-coding region of Fny-CMV RNAs 1 and 2 were 96% homologous, whereas the sequence homology between Fny-CMV RNA 1 and Q-CMV RNA 1 was 64% in this region. Furthermore, the tRNA-like secondary structures formed by the 3'-terminal non-coding regions of Fny-CMV RNAs 1 and 2 were virtually identical. By contrast, there was only 84% sequence homology between the 5'-terminal non-coding regions of these two RNAs and 81% sequence homology between the 5'-terminal non-coding regions of Q-CMV RNA 1 and Fny-CMV RNA 1. The non-equivalent divergence in the non-coding regions of these RNAs, as well as possible functions for the translation product of RNA 1, are discussed.