Sequence analysis of the 3' termini of RNA1 and RNA2 of blueberry leaf mottle virus

Bacher, J. W.; Warkentin, D.; Ramsdell, D.; Hancock, J. F.

Abstract The 3' termini of RNA1 and RNA2 of blueberry leaf mottle virus (BBLMV) were cloned and the cDNA sequence of a portion of the putative polymerase gene, the complete coat protein (CP) gene, and the 3' non-coding regions was determined. The N terminus of the coat protein gene was precisely located by comparison with the amino acid sequence determined by the Edman degradation sequencing of the purified coat protein. The coat protein gene encoded a polypeptide of 521 amino acids with a predicted Mr of 57,542. Homology to BBLMV coat protein was highest with tomato ringspot virus (TomRSV) and cherry leaf roll virus (CLRV); two other nepoviruses also belonging to a sub-group defined by the presence of large RNA2 components. The 3' terminal 1390 nt of RNA1 and RNA2 were nearly identical and apparently non-coding. No statistically significant sequence homology was found between the 3' non-coding regions of BBLMV and other nepoviruses. A highly conserved 3' non-coding region of this length is unusual, but has been reported for two other related viruses, TomRSV and CLRV. The biological function of the long 3' non-coding region and how the high level of sequence homology is maintained between RNA1 and RNA2, is unknown. Possible mechanisms for conservation of the 3' terminus are discussed.