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Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene
I K Jordan1, B A Sutter, M A McClure
1Department of Biological Sciences, University of Nevada at Las Vegas, USA.
Abstract:
Presented here is an analysis of the molecular evolutionary dynamics of the P gene among 76 representative sequences of the Paramyxoviridae and Rhabdoviridae RNA virus families. In a number of Paramyxoviridae taxa, as well as in vesicular stomatitis viruses of the Rhabdoviridae, the P gene encodes multiple proteins from a single genomic RNA sequence. These products include the phosphoprotein (P), as well as the C and V proteins. The complexity of the P gene makes it an intriguing locus to study from an evolutionary perspective. Amino acid sequence alignments of the proteins encoded at the P and N loci were used in independent phylogenetic reconstructions of the Paramyxoviridae and Rhabdoviridae families. P-gene-coding capacities were mapped onto the Paramyxoviridae phylogeny, and the most parsimonious path of multiple-coding-capacity evolution was determined. Levels of amino acid variation for Paramyxoviridae and Rhabdoviridae P-gene-encoded products were also analyzed. Proteins encoded in overlapping reading frames from the same nucleotides have different levels of amino acid variation. The nucleotide architecture that underlies the amino acid variation was determined in order to evaluate the role of selection in the evolution of the P gene overlapping reading frames. In every case, the evolution of one of the proteins encoded in the overlapping reading frames has been constrained by negative selection while the other has evolved more rapidly. The integrity of the overlapping reading frame that represents a derived state is generally maintained at the expense of the ancestral reading frame encoded by the same nucleotides. The evolution of such multicoding sequences is likely a response by RNA viruses to selective pressure to maximize genomic information content while maintaining small genome size. The ability to evolve such a complex genomic strategy is intimately related to the dynamics of the viral quasispecies, which allow enhanced exploration of the adaptive landscape.
Insights
Viral P genes in Paramyxoviridae and Rhabdoviridae families can encode multiple proteins, driving rapid evolution. This complex strategy maximizes genomic information in small RNA viruses.
Area of Science:
- Molecular evolution
- Virology
- Genomics
Background:
- The P gene in Paramyxoviridae and Rhabdoviridae RNA viruses is complex, encoding multiple proteins like phosphoprotein (P), C, and V from a single RNA sequence.
- This multicoding capacity presents an intriguing evolutionary puzzle.
Purpose of the Study:
- To analyze the molecular evolutionary dynamics of the P gene in Paramyxoviridae and Rhabdoviridae.
- To reconstruct phylogenies and map P-gene-coding capacities to understand evolutionary pathways.
- To investigate amino acid variation and the role of selection in overlapping reading frames.
Main Methods:
- Phylogenetic reconstructions using amino acid sequence alignments of P and N gene products.
- Mapping of P-gene-coding capacities onto the Paramyxoviridae phylogeny.
- Analysis of amino acid variation and nucleotide architecture in P-gene-encoded products.
Main Results:
- Independent phylogenetic reconstructions for Paramyxoviridae and Rhabdoviridae were achieved.
- The most parsimonious evolutionary path for multiple-coding capacity was determined.
- Proteins encoded in overlapping reading frames exhibit differential amino acid variation, with one constrained by negative selection and the other evolving rapidly.
Conclusions:
- Viral P genes evolve complex multicoding strategies to maximize genomic information within small RNA genomes.
- The integrity of derived overlapping reading frames is often maintained at the expense of ancestral frames.
- Viral quasispecies dynamics facilitate the exploration of adaptive landscapes for such complex genomic strategies.