Analysis of the genome structure of tobacco rattle virus strain PSG

Abstract

The sequence of the 3'-terminal 2077 nucleotides of genomic RNA 1 and the complete sequence of genomic RNA 2 of tobacco rattle virus (TRV, strain PSG) has been deduced. RNA 2 (1905 nucleotides) contains a single open reading frame for the viral coat protein (209 amino acids), flanked by 5'- and 3'-noncoding regions of 570 and 708 nucleotides, respectively. A subgenomic RNA (RNA 4) was found to lack the 5'-terminal 474 nucleotides of RNA 2 and is the putative messenger for coat protein. The deduced RNA 1 sequence contains the 3'-terminal part of a reading frame that probably corresponds to the TRV 170K protein and reading frames for a 29K protein and a 16K protein. Proteins encoded by the first two reading frames show significant amino acid sequence homology with corresponding proteins encoded by tobacco mosaic virus. Subgenomic RNAs 3 (1.6 kb) and 5 (0.7 kb) were identified as the putative messengers for the 29K and 16K proteins, respectively. At their 3'-termini all PSG-RNAs have an identical sequence of 497 nucleotides; at the 5'-termini homology is limited to 5 to 10 bases.

Conservation of the 3'-Terminal Sequences of the Genome RNA Species of Tomato Black Ring Virus

“…Taken together, the two kinds of experiment show that the bulk of the sequences in RNA-1 and RNA-2 are generally dissimilar, but that the 3' ends are an exception. Similar sequences at the 3' ends of each of the genome parts have been found for several other plant viruses with divided genomes, including alfalfa mosaic virus (Koper-Zwarthoff et aL, 1979), brome mosaic virus (Dasgupta & Kaesberg, 1977), CPMV (Davies et al, 1979), cucumber mosaic virus (Symons, 1979) and tobacco rattle virus (Bergh et al, 1985;Cornelissen et al, 1986). It seems likely that these similarities are of functional significance, probably as recognition signals for one or more proteins involved in the viruses' life cycles.…”

The location of the 5' end of the potato leafroll luteovirus subgenomic coat protein mRNA

“…For example, there is a match of 12 nucleotides in maize chlorotic mottle virus R N A (Lommel et al, 1991), up to 10 in tobacco rattle virus R N A (TRV; Cornelissen et al, 1986) and up to 11 in alfalfa mosaic virus R N A (Symons, 1985). As suggested by Cornelissen et al (1986) for T R V R N A , this sequence similarity at the 5' ends may reflect a replicase recognition signal in the corresponding minus-strand RNA.…”

A model for the generation of tobacco rattle virus (TRV) anomalous isolates: pea early browning virus RNA-2 acquires TRV sequences from both RNA-1 and RNA-2

“…The partial sequence obtained for the anomalous TRV isolate N5 RNA-2 is not inconsistent with it having a similar origin. We suggest that the existence of such a common region at the 5' termini of tobravirus RNA-2 molecules, combined with spurious subgenomic promoter-like elements at the 3' termini of RNA-I molecules (Angenent et al, 1986;Cornelissen et al, 1986), may provide the tobraviruses with the previously suggested means to accommodate RNA-2 molecules with different termini. These sequences could enable their replication by enzymes encoded by the different RNA-1 molecules of the three tobraviruses (Angenent et al, 1986).…”