Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus.

The complete nucleotide sequences of RNAs 1 and 2 of soil-borne wheat mosaic virus (SBWMV), type member of the furovirus group, were determined. RNA 1 is 7099 nucleotides (nt) and encodes a 150-kDa protein from the 5' end region, the UGA termination codon of which can be partially read through to produce a 209-kDa protein, and a 37-kDa protein in the 3' end region. The C-terminal region of the 150-kDa protein contains an NTP-binding helicase motif and the readthrough region, an RNA polymerase motif, indicating that these two overlapping proteins may form an RNA replication complex similar to those of tobamo- and tobraviruses. The 37-kDa protein has sequence similarity with the cell-to-cell transport protein of dianthoviruses. RNA 2 is 3593 nt and, from the 5' end region, encodes the 19-kDa capsid protein, whose UGA termination codon can be partially suppressed to produce an 84-kDa readthrough protein and, at the 3' proximity, a 19-kDa protein which is rich in cysteine residues. The 28K (kilodaltons, as estimated by SDS-PAGE) protein, previously considered as another capsid readthrough product, is apparently initiated at an in-frame non-AUG codon upstream from the capsid protein gene. In both RNAs 1 and 2, the 5' terminus is capped, and the 3' untranslated region possibly forms internal consecutive pseudoknots as found in tobamovirus RNA as well as a terminal tRNA-like structure similar to tymovirus RNA. An amino acid sequence comparison of RNA replicase genes indicates that, phylogenetically, SBWMV belongs to a cluster formed by tobamo-, tobra-, and hordeiviruses. Differences in the 3' end structure and in the cell-to-cell movement protein, and the distant phylogeny of the RNA replicase genes of SBWMV and beet necrotic yellow vein virus, suggest that the furoviruses should be divided into at least two groups.