VIGOR extended to annotate genomes for additional 12 different viruses

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

Parainfluenza viruses and Sendai virus are also members of the paramyxovirus family. They are negative-strand RNA viruses with genome sizes of 15-17 kb. hPIV-2 and hPIV-4 belong to the rubulavirus genus, whereas hPIV-1 and hPIV-3, bPIV-3 and Sendai virus constitute the respirovirus genus (21) . Like other members of the paramyxovirus family, the P gene is also polycistronic and encodes two to six different proteins. Sendai virus is the best studied virus in the paramyxovirus family. The P gene gives rise to a maximum of six different proteins by means of RNA editing, overlapping frames and ribosomal shunting (5, 22, 23, 12) . The V protein is produced from the edited mRNA. The faithful transcript encodes the P protein. Four additional proteins (C', C, Y1 and Y2) are also encoded in the polycistronic P gene by a process known as ribosomal shunting (12, 23) . Here, different start codons including a non-ATG codon (ACG or GCG for C' protein in the UTR region of the P gene) are used by ribosome to initiate translations. In the hPIV-1 genome, the P gene doesn't encode the edited mRNA that will be translated into V or D protein as is the case in other related viruses (24) . However, the small proteins (C', C, Y1 and Y2) encoded by the alternative start codons are detected in hPIV-1 genomes. The P gene of hPIV-3 encodes at least four proteins (P, D, C and V) (25) . P and C proteins are encoded by the non-edited mRNA with different frames. The D protein will be translated from this edited mRNA with the insertion of two non-templated Gs at the RNA editing site (25) . The edited mRNA of bPIV-3 encodes the D protein with two non-templated G residues inserted at the RNA editing site. A C protein is also encoded in the P gene with a different reading frame (26) . hPIV-2 and hPIV-4 are members of the rubulavirus genus. Like other members in the same genus, the P protein is encoded by the edited mRNA with the addition of two G residues at the editing site, while the faithfully transcribed mRNA encodes the V protein (8, 27) . The genome size of hPIV-4 is 17.7 kb, 2 kb longer than other parainfluenza virus genomes.