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J Gen Virol. 2016 Sep;97(9):2333-45. doi: 10.1099/jgv.0.000526. Epub 2016 Jun 17.

Conservation of the E8 CDS of the E8^E2 protein among mammalian papillomaviruses.

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1​Department of Bioinformatics, University of Tartu, Riia 23, Tartu 51010, Estonia.
2​Estonian Biocentre, Riia 23, Tartu 51010, Estonia.


Papillomaviridae are small dsDNA viruses with a limited coding capacity. To fulfill all of the functional requirements for propagation and spreading, papillomaviruses use double coding and alternative protein isoforms. E8 ^ E2 is an alternative E2 protein isoform that is generated by fusing the short E8 CDS that completely overlaps E1 to the 'hinge' and the DNA-binding region of the E2 protein via alternative transcription/splicing. The papillomaviruses in which E8 ^ E2 mRNA sequences have been described exhibit a sparse phylogenomic distribution. Thus, it is not clear whether E8 ^ E2 is an ancestral protein that has not been described for other papillomavirus types or whether it randomly appears because of the conservation of the E1 protein and occurs only coincidentally. We searched for potential E8 coding sequences in a non-redundant set of papillomaviruses and applied SynPlot2 and an in-house-developed algorithm (cRegions) to determine the most plausible of the above-mentioned scenarios. Beginning with nine experimentally described E8 ^ E2 mRNAs, we predicted the potential E8 CDSs for more than 300 mammalian papillomavirus genomes. According to our analysis, E8 ^ E2 is not a result of E1 coding and represents a protein in its own right, and it most likely has an ancestral origin that precedes the divergence of major mammalian papillomavirus genera.

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