Nucleotide sequence of apple mosaic ilarvirus RNA 4

The complete nucleotide sequence of apple mosaic ilavirus RNA 4 was obtained from cloned cDNAs and direct sequencing of the 5'-terminal RNA region. The sequence is 891 nucleotides long and can encode a protein of 226 amino acids (M(r) 25,171) that, by analogy to alfalfa mosaic virus (AlMV) and tobacco streak virus (TSV), should correspond to the coat protein (CP). Database comparisons showed that no significant similarity to other proteins was apparent. Analysis of the CP sequence revealed a putative 'zinc finger' domain and a region rich in basic residues at the amino-terminal portion of the protein, similar to that of TSV. The secondary structure proposed for the 3'-terminal region of RNA 4 shows the presence of three hairpin structures flanked by the tetranucleotide AUGC that are highly similar to those previously described in the RNA 4 species from AlMV and TSV. These results support the idea that both features (metal-binding domain and highly conserved hairpin structures) are characteristics of ilarviruses and are probably involved in the peculiar 'genome activation' phenomenon described in these viruses.