SEQUENCE-ANALYSIS AND GENE CONTENT OF POTATO MOP-TOP VIRUS-RNA-3 - FURTHER EVIDENCE OF HETEROGENEITY IN THE GENOME ORGANIZATION OF FUROVIRUSES

The complete sequence of the 2315 nucleotides in RNA 3 of potato mop-t op furovirus (PMTV) isolate T was obtained by analysis of cDNA clones and by direct RNA sequencing. The sequence contains an open reading fr ame for the coat protein (20K) terminated by an amber codon, followed by an in-phase coding region for an additional 47K. PMTV therefore res embles soil-borne wheat mosaic (SBWMV) and beet necrotic yellow vein ( BNYVV) viruses (two other fungus-transmitted viruses with rod-shaped p articles) in having a coat protein-readthrough product. Comparison of the 3' untranslated regions of PMTV RNA 2 and RNA 3 reveals a long con served block of 150 nucleotides, which contains two repeated sequences and has the potential to form consecutive pseudoknot structures. PMTV RNA 3 ends a few nucleotides downstream of this conserved block, but RNA 2 extends for a further 140 nucleotides, which can potentially for m a 3'-terminal tRNA-like structure similar to those in the RNA specie s of SBWMV, tymoviruses, and some tobamoviruses. PMTV coat protein has amino acid sequence identities of 30 and 28% with SBWMV and BNYVV coa l proteins, respectively, and apparent structural similarities with to bacco mosaic virus coat protein. The coat protein readthrough domains of PMTV, SBWMV, and BNYVV have shared residues throughout their length but no extended sequences are conserved. The presence in RNA 3 of cod ing sequences for only the coat protein and readthrough domain disting uishes PMTV from SBWMV and BNYVV, both of which have them in RNA 2 alo ng with one or more other genes. Comparison of the genomes of PMTV, BN YVV, and SBWMV shows that furoviruses exhibit considerable heterogenei ty in genome organization. (C) 1995 Academic Press, Inc.