Molecular archeological evidence in support of the repeated loss of a papillomavirus gene.

Koenraad Van Doorslaer,Alison A Mcbride

doi:10.1038/srep33028

Koenraad Van Doorslaer, Alison A Mcbride

Open Access

https://doi.org/10.1038/srep33028

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Abstract

It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. However, gene loss is often associated with an increased mutation rate, thus quickly erasing evidence from the genome. The analysis of evolutionarily related sequences can provide empirical evidence for gene loss events. This paper analyzes the sequences of over 300 genetically distinct papillomaviruses and provides evidence for a role of gene loss during the evolution of certain papillomavirus genomes. Phylogenetic analysis suggests that the viral E6 gene was lost at least twice. Despite belonging to distant papillomaviral genera, these viruses lacking a canonical E6 protein may potentially encode a highly hydrophobic protein from an overlapping open reading frame, which we designate E10. Evolutionary pressure working on this alternative frame, may explain why, despite having lost the E6 open reading frame between 20 and 60 million years ago, evidence of an E6-like protein is conserved.

Highlights

It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms
Many viruses are able to limit the size of their genome by coding for proteins transcribed from overlapping open reading frames (ORFs), by utilizing alternative splicing, and by minimizing intergenic regions
It has been suggested that the reduction in the number of viral genes may be important during poxvirus speciation and environmental niche selection[3]

Summary

Introduction

It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. Despite the fact that these proteins are thought to be essential for the viral life cycle, comparative genomic analysis suggested that some viruses do not code for these “accessory” genes[13]. Certain papillomaviruses (i.e. the members of the Xi and Kappa-papillomavirus genera) encode a highly hydrophobic protein in the genomic location typically reserved for E612.

Results

Conclusion