Nucleotide sequence of cucumber mosaic virus RNA 1

The nucleotide sequence of the 3389 residues of RNA 1 ( M r 1.15 × 10 6 ) of the Q strain of cucumber mosaic virus (CMV) was determined, completing the primary structure of the CMV genome (8617 nucleotides). CMV RNA 1 was sequenced by the dideoxy‐chain‐termination method using M13 clones carrying RNA 1 sequences as well as synthetic oligonucleotide primers on RNA 1 as a template. At the 5′ end of the RNA there are 97 noncoding residues between the cap structure and the first AUG (98–100), which is the start of a single long openreading frame. This reading frame encodes a translation product of 991 amino acid residues ( M r 110791) and stops 319 nucleotide residues from the 3′ end of RNA 1. In addition to the conserved 3′ region present in all CMV RNAs (307 residues in RNA 1), RNAs 1 and 2 have highly homologous 5′ leader sequences, a 12‐nucleotide segment of which is also conserved in the corresponding RNAs of brome mosaic virus (BMV). CMV satellite RNA can form stable base pairs with a region of CMV RNAs 1 and 2 including this 12‐nucleotide sequence, implying a regulatory function. This conserved sequence is part of a hairpin structure in RNAs 1 and 2 of CMV and BMV and in CMV satellite RNA. The entire translation products of RNA 1 of CMV and BMV could be aligned with significant homology. Less prominent homologies were found with alfalfa mosaic virus RNA 1 translation product and with tobacco mosaic virus M r ‐126000 protein.