Positive Darwinian selection in Vipera palaestinae phospholipase A2 genes is unexpectedly limited to the third exon

The venom of Vipera palaestinae contains a two-component toxin, consisting of an acidic phospholipase A2 (PLA2) and a basic protein. Here we report the cloning and sequence analysis of the complete V. palaestinae PLA2 genes. Since in all Viperidae PLA2 multigene families the 5' and 3' flanking regions are highly conserved, we designed oligonucleotide primers that allow amplification of the whole PLA2 multigene family in a single step. The structural organization of both genes is the same as in the Vipera ammodytes PLA2 multigene family, there being five exons separated by four introns. Comparison of V. palaestinae PLA2 genes with other Viperidae PLA2 genes has shown that the structural organization of the genes and the nucleotide sequence of all introns and flanking regions are highly conserved, whereas the third exon clearly shows a higher number of amino acid replacements, an indication of positive Darwinian selection. The positive Darwinian selection is surprisingly limited to the third exon, in contrast to other Viperidae PLA2 genes, where it is present in all mature protein coding exons.