Remarkable variability of apple mosaic virus capsid protein gene after nucleotide position 141.
Eight new sequences of European isolates from almond, apple, hop, prune and pear of the Apple mosaic ilarvirus (ApMV) capsid protein gene are presented. A consensus sequence was established as having 654 nucleotides (nt) and two American and two European isolates were identified to have insertions 6 to 15 nucleotides after nt position 141. The insertion resulted in the American isolate A inframeshift repaired with two point insertions 17 and 68 nt downstream. The RNA around the insertion point can potentially form a stable secondary structure with three hairpins. The insertions could stabilise this structure or could be neutral. The predicted folding of the translated protein is not influenced by the insertions or frameshift, and we speculate that the region after nt position 141 is without reasonable selection pressure and represents a hot spot for the accumulation of insertion mutations in ApMV.
Department of Plant Virology, Academy of Sciences of the Czech Republic, Ceské Budejovice, Czech Republic. petrzik@umbr.cas.cz
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D000595:Amino Acid Sequence; D001483:Base Sequence; D002213:Capsid / Q000737:chemistry / Q000235:genetics*; D005060:Europe; D005814:Genes, Viral; D014644:Genetic Variation; D027582:Humulus / Q000821:virology; D019179:Ilarvirus / Q000737:chemistry / Q000235:genetics*; D027845:Malus / Q000821:virology; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D027861:Prunus / Q000821:virology; D012367:RNA, Viral / Q000737:chemistry; D016415:Sequence Alignment
D012367:RNA, Viral