Natural insertions within the N-terminal region of the coat protein of Maize dwarf mosaic potyvirus (MDMV) have an effect on the RNA stability

A 13 amino acid residue insertion was found in the N-terminal region of the coat protein of several Maize dwarf mosaic virus isolates (MDMV). These insertions seem to be the result of a direct duplication event, but differ in some positions. In order to evaluate the influence of the insertion on the RNA secondary structure and stability, the RNA secondary structures and minimum free energies (MFE) of all existing MDMV coat protein sequences were estimated using three different softwares, the Vienna RNA Package, NUPACK, and UNAFold, and compared to the secondary structure and MFE of various random sequence collections preserving the nucleotide distribution of MDMV. The bioinformatic analysis showed that the insertion stabilizes the RNA structure of the coat protein gene.