VIGOR extended to annotate genomes for additional 12 different viruses

Wang, Shiliang; Sundaram, Jaideep P.; Stockwell, Timothy B.

In many RNA viruses, such as measles virus, mumps virus and parainfluenza virus, the P gene is a polycistronic gene from which multiple proteins can be produced. For measles virus, hPIV-3, bovine parainfluenza virus 3 (bPIV-3) and Sendai virus, the faithful transcript of the P gene will guide synthesis of the P protein; the edited mRNA, in which one or more non-templated G residues are inserted, will be translated into the V or D protein. To identify the RNA editing site, reference V or D protein sequence is aligned to the protein sequence deduced from genomic sequence to locate the frame-shifting region. In measles virus, Sendai virus, bPIV-3, hPIV-3, the sequence string AAAAAGGG immediately upstream the editing site is conserved and is screened to identify the RNA editing site (4, 5) . A single G residue is added into the complementary DNA sequence of measles virus at the editing site and the reading frame shifts from +1 to +2; in hPIV-3, bPIV-3 and Sendai virus, two G residues are inserted at the editing site. V protein sequence will be deduced from this edited mRNA sequence. In mumps virus, hPIV-2 and hPIV-4, the faithful transcript encodes V protein, and the edited mRNA, in which two nontemplated G residues are added, encodes the P protein.