Nucleotide sequence of the 3'-terminal region of clover yellow mosaic virus RNA -- Abouhaidar and Lai 70 (7): 1871 -- Journal of General Virology

This study describes the nucleotide sequence of the 3'-terminal region of clover yellow mosaic virus (CYMV) RNA, a potexvirus with a positive-sense single-stranded RNA genome. Researchers sequenced 1050 nucleotides from cDNA clones and identified a major open reading frame (ORF) encoding a 28.1 kilodalton protein and a smaller ORF encoding a 23.5 kilodalton protein similar to the viral capsid protein. The coat protein sequence shows significant similarity to coat proteins of four other potexviruses. Evidence suggests the coat protein is translated from a subgenomic mRNA that begins at a cap-site sequence identical to that found in potato virus X, with the smaller ORF likely serving as the translation start codon for this subgenomic RNA. The 3' non-coding region contains a putative polyadenylation signal (AAUAAA) located 110 nucleotides upstream of the poly(A) tail. Comparative amino acid sequence analysis reveals conserved regions in potexvirus coat proteins, particularly in central and C-terminal domains, with 26 identical amino acids shared among five potexviruses in a 67-amino-acid stretch. Basic amino acid residues at specific positions are conserved across species and may facilitate RNA binding.

Key findings

• The 3' terminal region of CYMV RNA contains two ORFs: a major 28.1K protein and a smaller 23.5K coat protein ORF used for capsid synthesis from subgenomic RNA
• CYMV coat protein shares 30-48% sequence identity with coat proteins of four other potexviruses, with strongest homology in central and C-terminal regions
• A putative polyadenylation signal (AAUAAA) is located 110 nucleotides upstream of the poly(A) tail, unusually far compared to eukaryotic mRNAs but similar to other plant viruses
• Conserved basic amino acid residues at specific positions across five potexviruses likely play a role in RNA binding