Nucleotide Sequence Analysis of an Andean Potato Mottle Virus Middle Component RNA cDNA Clone: Comparisons of the Encoded Proteins with Those of Other Comoviruses

Abstract

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.

Structural Fingerprinting: Subgrouping of Comoviruses by Structural Studies of Red Clover Mottle Virus to 2.4-Å Resolution and Comparisons with Other Comoviruses

“…However, the extensions of this approach to other comoviruses were not particularly revealing, and no obvious discriminating criteria could be derived for subgrouping Andean potato mottle virus (APMV) (46) and several strains of squash mosaic viruses (SqMV) (15,19). The results were especially ambiguous in the case of APMV, which shares a high degree of similarity with BPMV but a comparatively low degree of similarity with CPSMV (15).…”

“…It is therefore reasonable to suggest that, as in the case of BPMV, a pentameric annular structure is not formed, supporting the previous subgrouping of CPSMV with BPMV. When the structural alignments are extended to include the sequences of the S proteins of APMV (46) and SqMV (15,19), subgrouping with BPMV is predicted in each case (Fig. 8).…”

Diversity among isolates of squash mosaic virus.

“…Sequence data have been published for RNA-2 on single isolates of APMV (Shindo et al, 1993), BPMV (MacFarlane et al, 1991), CPMV (van Wezenbeek et al, 1983), CPSMV (Chen & Bruening, 1992) and RCMV (Shanks et al, 1986). Using the published nucleotide sequence data, Shindo et al (1993) aligned the deduced amino acid sequences for the MP, LCP and SCP for APMV, BPMV, CPMV, CPSMV and RCMV to show that the distantly related APMV had a genome structure consistent with that of other comoviruses.…”

“…Using the published nucleotide sequence data, Shindo et al (1993) aligned the deduced amino acid sequences for the MP, LCP and SCP for APMV, BPMV, CPMV, CPSMV and RCMV to show that the distantly related APMV had a genome structure consistent with that of other comoviruses. Sequence data were compared here for the published full RNA-2 sequences of five comoviruses, APMV, BPMV, CPMV, CPSMV and RCMV, and RNA-2 of the two SqMV isolates shown in Fig.…”

“…There is a conserved amino acid motif, LDD, at positions 9-11 at the amino terminus of the LCP (Shindo et al, 1993), and the site of cleavage between the two CPs was determined by protein sequencing of the amino terminus of the SCP (Hu et al, 1993). As can be seen in Fig.…”