Nucleotide Sequence of a Set of cDNA Clones Derived from the Brome Mosaic Virus ATCC66 Strain and Comparison with the Russian Strain Genome.

Abstract

The complete nucleotide sequence of a set of cDNA clones designated KU1 strain, from which infectious in vitro transcripts can be transcribed, of the ATCC66 strain of brome mosaic virus (BMV) was determined and compared with the Russian strain of BMV in both nucleotide and the deduced amino acid sequence. Each corresponding genomic RNA in the KU1 strain and the Russian strain was homologous by more than 97% in nucleotide sequence. Base substitution of the transition type was more frequent than that of the transversion type in all three genomic RNAs. Amino acid changes in three regions where significant amino acid sequence homology is shown among the Sindbis-like plant RNA viruses were mostly substitutions for amino acids categorized to similar groups. The nucleotide sequence of the 5′ noncoding region in RNA1 and RNA3 was identical in the corresponding RNAs of the two strains while seven base changes were observed in RNA2. Any base change in the 3′ noncoding region did not disrupt a predicted secondary structure. Two adjacent adenine residues were absent in the noncoding leader sequence of the coat protein gene of both KU1 strain and ATCC66 strain. The intercistronic oligo(A) tract in RNA3 of the ATCC66 strain was heterogeneous in length in which more than two guanine residues were observed by direct RNA sequencing, while one guanine residue was present in the RNA3 of the cDNA clone of the KU1 strain.