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.