Short virion RNA in barley stripe mosaic virus

Small cysteine-rich proteins of different groups of plant RNA viruses are related to different families of nucleic acid-binding proteins

The 3'-terminal genes in genomic RNAs of four groups of plant positive strand RNA viruses (hordei-, furo-, tobra-, and carlaviruses) encode small proteins enriched in Cys residues. The arrangement of Cys and in some cases also His residues in these proteins is compatible with finger formation. A computer-assisted sequence comparison of viral Cys-rich proteins reveals no significant similarity between them. It is shown that the hordeivirus Cys-rich protein (17K) is related to a group of chloroplast tRNA intron-encoded proteins, whereas the respective furovirus protein (14K) is similar to E6 proteins of papillomaviruses. Somewhat less significant similarity, marked, however, by conservation of a number of positively charged residues, was observed between the sequences of tobravirus Cys-rich proteins and the basic domains of high mobility group chromatin proteins. It can be speculated that plant RNA virus Cys-rich proteins bind RNA and/or DNA and might be involved in regulation of virus and/or host genome expression. In the course of evolution these virus proteins may have originated from different nucleic acid-binding proteins.

Infectious barley stripe mosaic virus RNA transcribed in vitro from full-length genomic cDNA clones

Full-length genomic cDNA clones of the Type and ND18 strains of barley stripe mosaic virus (BSMV) were transcribed in vitro using T7 RNA polymerase. The combination of RNAs alpha, beta, and gamma synthesized in the presence of 5' cap analogs was infectious after inoculation onto barley plants, conclusively demonstrating the tripartite nature of the BSMV genome. Transcripts synthesized in the absence of cap analogs were not infectious. A gamma-specific subgenomic RNA which is normally present in BSMV virions was not required to establish a systemic infection. In vitro transcripts of variant cDNA clones which were isolated from the ND18 strain, containing either a simple nucleotide substitution or a 372-nucleotide duplication similar to one found in the genome of the Type strain, were also found to be biologically active. Two dicotyledonous hosts which have a differential response to infection with the Type and ND18 strains of BSMV were identified and these phenotypes were shown to be faithfully reproduced by inoculation with in vitro transcripts derived from the appropriate full-length cDNA clones.

Probable reassortment of genomic elements among elongated RNA-containing plant viruses

The relationships of genome organization among elongated (rod-shaped and filamentous) plant viruses have been analyzed. Sequences in coding and noncoding regions of barley stripe mosaic virus (BSMV) RNAs 1, 2, and 3 were compared with those of the monopartite RNA genomes of potato virus X (PVX), white clover mosaic virus (WClMV), and tobacco mosaic virus, the bipartite genome of tobacco rattle virus (TRV), the quadripartite genome of beet necrotic yellow vein virus (BNYVV), and icosahedral tricornaviruses. These plant viruses belong to a supergroup having 5'-capped genomic RNAs. The results suggest that the genomic elements in each BSMV RNA are phylogenetically related to those of different plant RNA viruses. RNA 1 resembles the corresponding RNA 1 of tricornaviruses. The putative proteins encoded in BSMV RNA 2 are related to the products of BNYVV RNA 2, PVX RNA, and WClMV RNA. Amino acid sequence comparisons suggest that BSMV RNA 3 resembles TRV RNA 1. Also, it can be proposed that in the case of monopartite genomes, as a rule, every gene or block of genes retains phylogenetic relationships that are independent of adjacent genomic elements of the same RNA. Such differential evolution of individual elements of one and the same viral genome implies a prominent role for gene reassortment in the formation of viral genetic systems.

Nucleotide sequence of barley stripe mosaic virus RNA alpha: RNA alpha encodes a single polypeptide with homology to corresponding proteins from other viruses

The complete nucleotide sequence of RNA alpha from the Type strain of barley stripe mosaic virus has been determined. The RNA is 3768 nucleotides long and contains a single open reading frame which codes for a polypeptide of 1139 amino acids (mw 129,634). The open reading frame is flanked by a 5'-terminal sequence of 91 nucleotides and a 3'-nontranslated region composed of a short poly(A) tract followed by a 238-nucleotide tRNA-like structure. The amino acid sequence of the polypeptide (alpha a) encoded by the open reading frame has homology with the TMV 126K protein and with related polypeptides from other viruses. The carboxy-terminal portion of the alpha a polypeptide also has limited homology with the 58K (beta b) protein encoded by BSMV RNA beta and includes a consensus sequence found in mononucleotide-binding polypeptides.