title: On the variability of the 3' terminal sequence of the turnip mosaic virus genome.
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 (rsp12-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.
authors.affiliation: Graduate School of Science and Technology, Niigata University, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Sano
authors.forename: R
authors.initials: R
authors.lastname: van der Vlugt
authors.forename: P
authors.initials: P
authors.lastname: de Haan
authors.forename: A
authors.initials: A
authors.lastname: Takahashi
authors.forename: M
authors.initials: M
authors.lastname: Kawakami
authors.forename: R
authors.initials: R
authors.lastname: Goldbach
authors.forename: M
authors.initials: M
authors.lastname: Kojima
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002213:Capsid / Q000737:chemistry / Q000235:genetics*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009029:Mosaic Viruses / Q000737:chemistry / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics*