Nucleotide sequence analysis of an Andean potato mottle virus middle component RNA cDNA clone: comparisons of the encoded proteins with those of other comoviruses.

Andean potato mottle virus (APMV) is a comovirus whose genomic structure consists of two plus-strand RNA molecules (M- and B-RNA). Here we report the nucleotide sequence analysis of an APMV M-RNA cDNA clone with 3,669 nucleotide (nt) residues, exclusive of the polyadenylate at the 3' end, covering approximately 99% of the APMV M-RNA. The first initiation codon in register translates from nt 194 to 3185 a polyprotein of 997 amino acid (aa) residues. A second initiation codon in register, beginning at nt position 416, translates a polyprotein of 923 aa. The cleavage sites used in the processing of polyprotein were identified in the long open reading frame by N-terminal microsequencing of the large coat protein (LCP) and the small coat protein (SCP). These dipeptide cleavage sites are Q/M for the LCP and Q/F for the SCP. In a comparison of the deduced APMV polyprotein aa sequence with those of four other comoviruses, the coding regions for the putative movement protein, LCP and SCP, were found similar in length in all five species. Multiple alignment of the M-RNA sequences for each of the three genes from the five comoviruses revealed different degrees of homology. APMV was always the least homologous of the five comoviruses, showing significant aa substitutions in positions where the other comoviruses have identical residue or conservative substitutions.