Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene

Presented here is an analysis of the molecular evolutionary dynamics of the P gene among 76 representative sequences of the Paramyxoviridae and Rhabdo viridae RNA virus families. In a number of Paramyxoviridae taxa, as well as in vesicular stomatitis viruses of the Rhabdoviridae, the P gene encodes m ultiple 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 pers pective. Amino acid sequence alignments of the proteins encoded at the P an d N loci were used in independent phylogenetic reconstructions of the Param yxoviridae and Rhabdoviridae families. P-gene-coding capacities were mapped onto the Paramyxoviridae phylogeny, and the most parsimonious path of mult iple-coding-capacity evolution was determined. Levels of amino acid variati on for Paramyxoviridae and Rhabdoviridae P-gene-encoded products were also analyzed. Proteins encoded in overlapping reading frames from the same nucl eotides have different levels of amino acid variation. The nucleotide archi tecture that underlies the amino acid variation was determined in order to evaluate the role of selection in the evolution of the P gene overlapping r eading frames. In every case, the evolution of one of the proteins encoded in the overlapping reading frames has been constrained by negative selectio n while the other has evolved more rapidly. The integrity of the overlappin g 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 vi ruses to selective pressure to maximize genomic information content while m aintaining small genome size. The ability to evolve such a complex genomic strategy is intimately related to the dynamics of the viral quasispecies, w hich allow enhanced exploration of the adaptive landscape.