On the variability of the 3′ terminal sequence of the turnip mosaic virus genome

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Abstract
The sequence of the 3′-terminal 1223 nucleotides (nts) of a Japanese isolate of turnip mosaic virus (TuMV-Jap) RNA has been determined. The sequence reveals a single open reading frame (ORF) which terminates at a position 212 nts upstream of the 3′ poly(A)-tract. Determination of the N-terminal amino acids of TuMV-Jap coat protein (CP) mapped the CP cistron within this ORF and revealed a Glu-Ala dipeptide sequence as the putative cleavage site by which the CP is released from the viral polyprotein. The predicted amino acid sequence of the TuMV-Jap CP shows 97.2% identity with that of a Canadian isolate of TuMV (TuMV-Can) and 99% with a second, Chinese, isolate (TuMV-Chi). However, the 3′-terminal non-translated region (NTR) of TuMV-Jap RNA is significantly shorter (212 nts) than the 3′-NTR of TuMV-Can RNA (668 nts), but of equal length as the 3′-NTR of the TuMV-Chi isolate which also measures 212 nts. The 3′-NTRs of both the TuMV-Jap and TuMV-Chi RNAs show homology with the first 201 nucleotides of the TuMV-Can RNA 3′-NTR. A search in the EMBL nucleotide sequence database revealed that the 467 nt-long unique extension of the 3′-NTR of TuMV-Can RNA has 89.8% homology to a part of the chloroplast ribosomal protein 12 gene (rsp 12-gene). Irrespective of the origin of this extra sequence in the reported TuMV-Can sequence, which may have been introduced by a genuine RNA recombination event, it is concluded that the standard TuMV genome has a CP gene of 864 nts and an conserved 3′-NTR of approximately 212 nucleotides in length.