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

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus

Maximum likelihood phylogenetic tree representing the evolutionary relationships among the Papillomaviridae.Maximum likelihood phylogenetic tree of the Papillomaviridae. This tree is based on a partitioned supermatrix derived from the E1, E2, L2 and L1 nucleotide sequences. Viruses indicated with a red clade do not contain a canonical E6 ORF, purple clades identify the avian/turtle viruses that contain a “single domain” E6 protein. Classification was based on1819. The asterisk (*) indicates that some members of this clade have not yet been officially recognized as members of the Gammapapillomavirus genus. Colored nodes indicate bootstrap support (red = 100%, green >90%, blue >75%). The red triangle indicates the MRCA of Xi- and Gamma papillomaviruses. The arrowhead highlights CPV2, which was chosen to root the phylogenetic tree in Fig. 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5015084&req=5

f1: Maximum likelihood phylogenetic tree representing the evolutionary relationships among the Papillomaviridae.Maximum likelihood phylogenetic tree of the Papillomaviridae. This tree is based on a partitioned supermatrix derived from the E1, E2, L2 and L1 nucleotide sequences. Viruses indicated with a red clade do not contain a canonical E6 ORF, purple clades identify the avian/turtle viruses that contain a “single domain” E6 protein. Classification was based on1819. The asterisk (*) indicates that some members of this clade have not yet been officially recognized as members of the Gammapapillomavirus genus. Colored nodes indicate bootstrap support (red = 100%, green >90%, blue >75%). The red triangle indicates the MRCA of Xi- and Gamma papillomaviruses. The arrowhead highlights CPV2, which was chosen to root the phylogenetic tree in Fig. 2.

Mentions: It has been proposed that E6’s main function may be to neutralize some of the unwanted consequences of E7 expression10. However, not all papillomaviruses contain a canonical E6 ORF (Fig. 1 and13). Figure 1 summarizes the evolutionary history of the different papillomavirus genera, with the presence/absence of a canonical E6 mapped; red branches indicate individual papillomaviruses that do not contain a canonical E6 ORF (E6-minus viruses). Purple branches highlight the avian and reptilian papillomaviruses which contain a highly modified, ancestral E6 protein23. This analysis illustrates that certain viral clades are apomorphic for the presence/absence of E6. In other words, certain members of the Xi- and Gammapapillomavirus genera do not contain a canonical E6 ORF (E6-minus). The position of these E6-minus viruses in separate clades indicates that the E6 gene has been lost at least twice throughout papillomavirus evolution. An alternative, less likely explanation is that the most recent common ancestor (MRCA; indicated with triangle in Fig. 1) did not encode for an E6 ORF, with extant E6 proteins being the result of several convergent evolutionary events.


Molecular archeological evidence in support of the repeated loss of a papillomavirus gene
Maximum likelihood phylogenetic tree representing the evolutionary relationships among the Papillomaviridae.Maximum likelihood phylogenetic tree of the Papillomaviridae. This tree is based on a partitioned supermatrix derived from the E1, E2, L2 and L1 nucleotide sequences. Viruses indicated with a red clade do not contain a canonical E6 ORF, purple clades identify the avian/turtle viruses that contain a “single domain” E6 protein. Classification was based on1819. The asterisk (*) indicates that some members of this clade have not yet been officially recognized as members of the Gammapapillomavirus genus. Colored nodes indicate bootstrap support (red = 100%, green >90%, blue >75%). The red triangle indicates the MRCA of Xi- and Gamma papillomaviruses. The arrowhead highlights CPV2, which was chosen to root the phylogenetic tree in Fig. 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5015084&req=5

f1: Maximum likelihood phylogenetic tree representing the evolutionary relationships among the Papillomaviridae.Maximum likelihood phylogenetic tree of the Papillomaviridae. This tree is based on a partitioned supermatrix derived from the E1, E2, L2 and L1 nucleotide sequences. Viruses indicated with a red clade do not contain a canonical E6 ORF, purple clades identify the avian/turtle viruses that contain a “single domain” E6 protein. Classification was based on1819. The asterisk (*) indicates that some members of this clade have not yet been officially recognized as members of the Gammapapillomavirus genus. Colored nodes indicate bootstrap support (red = 100%, green >90%, blue >75%). The red triangle indicates the MRCA of Xi- and Gamma papillomaviruses. The arrowhead highlights CPV2, which was chosen to root the phylogenetic tree in Fig. 2.
Mentions: It has been proposed that E6’s main function may be to neutralize some of the unwanted consequences of E7 expression10. However, not all papillomaviruses contain a canonical E6 ORF (Fig. 1 and13). Figure 1 summarizes the evolutionary history of the different papillomavirus genera, with the presence/absence of a canonical E6 mapped; red branches indicate individual papillomaviruses that do not contain a canonical E6 ORF (E6-minus viruses). Purple branches highlight the avian and reptilian papillomaviruses which contain a highly modified, ancestral E6 protein23. This analysis illustrates that certain viral clades are apomorphic for the presence/absence of E6. In other words, certain members of the Xi- and Gammapapillomavirus genera do not contain a canonical E6 ORF (E6-minus). The position of these E6-minus viruses in separate clades indicates that the E6 gene has been lost at least twice throughout papillomavirus evolution. An alternative, less likely explanation is that the most recent common ancestor (MRCA; indicated with triangle in Fig. 1) did not encode for an E6 ORF, with extant E6 proteins being the result of several convergent evolutionary events.

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus