CHARACTERIZATION AND ANALYSIS OF THE GENOME OF SONCHUS YELLOW NET VIRUS, A PLANT RHABDOVIRUS (LEADER RNA, GENE-JUNCTION, ORDER, NUCLEOTIDE SEQUENCE)
Abstract
Tobacco infected with sonchus yellow net virus (SYNV) contains short, 139- to 144-nucleotide-long transcripts complementary to the 3' terminus of the negative-stranded genomic RNA. These transcripts are similar to the leader RNAs associated with several animal rhabdovirus infections in that they are coded by the same region of the genome, but the SYNV transcripts are nearly three times longer than the animal rhabdovirus leader RNAs. The SYNV leader RNAs differ markedly in sequence from the leader RNAs associated with strains of vesicular stomatitis virus (VSV) and rabies virus, although the first 30 nucleotides of all three transcripts are rich in adenine residues. SYNV-specific recombinant DNA clones derived from the poly A+ RNA of SYNV-infected tobacco and SYNV genomic (g)RNA were used to construct a partial physical map of the SYNV genome and to detect six SYNV-specific transcripts (designated scRNAs 1 through 6). The order of genes, using scRNA designations, was found to be 3'...scRNA3-scRNA5-scRNA4-scRNA6-scRNA2...5'. The nucleotide sequence from the 3' terminus through position 2833 was determined directly from SYNV RNA and from recombinant DNA clones derived from SYNV-infected tobacco poly A+ RNA and SYNV gRNA. Primer extension experiments on poly A+ RNA from SYNV-infected tobacco plants revealed a start site for the N protein gene that is located 147 nucleotides from the 3'-end of genomic RNA. The sequence (UUGU) at this site is identical to the first four nucleotides of the N protein genes of animal rhabdoviruses. In SYNV, the first AUG codon in the putative N protein gene is located 57 nucleotides downstream, at positions 203-205, and is followed by an open reading frame of 1,428 nucleotides. A 14-base sequence at the lead RNA-scRNA3 gene junction, 3'-UUCUUUUUGGUUGU-5', is repeated in positions 1,690-1,703, and the next downstream AUG initiation codon is followed by a 1,017-nucleotide open reading frame believed to encode SYNV M1 protein. The positions of the 14-base repeated sequence and homology with the VSV gene-junction consensus sequence suggest that the 14-base sequences represent the SYNV gene-junction consensus sequence. Comparisons of SYNV RNA and deduced amino acid sequences with those known for the animal rhabdoviruses revealed no significant homologies.
Degree
Ph.D.
Subject Area
Plant pathology
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