Position and function of amino acids under positive selection
Our data suggest that amino acids under positive selection are more often exposed to the solvent than expected by chance. However, this result should be viewed with caution because it is based on a relatively low number of amino acids, and this result reflects the data of only some of the sampled proteins; for others, we could not reject the null hypothesis. Some studies have led to similar conclusions, on an ad hoc basis, but without addressing this issue at a large scale. For instance, amino acids under positive selection were identified in Toll-like receptor (Fornůsková et al., 2013), which are likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In the particular case of our medium-scale study, more data on the position of amino acids and of associated 3D structures will need to be gathered to reach firm conclusions on this point. Our new results about the position of amino acids suggest that positive selection affected preferentially amino acids involved in interactions with partners rather than other functions of the proteins, as most such amino acids are located at the surface rather than in the vicinity of an eventual enzymatic pocket.
Ultimately, we have confirmed here that MFGE8 was under positive selection in the dog and in the human/chimpanzee clade. This protein binds to the zona pellucida of unfertilised (but not fertilised) oocytes, because recombinant protein or specific antibody raised against MFGE8 competitively inhibit sperm-egg interaction. For this protein, positioning the positively selected amino acids on a 3D model was particularly informative. In particular, ten sites under positive selection (92R, 94T, 149L, 152H, 214T, 259L, 279V, 281G, 285N, 312S) are located within or in the vicinity of the three β-hairpin loops also called ‘spikes’, which allow interaction with phospholipids and between membranes (Rodrigues et al., 2013). Interestingly, among the whole family of F5/8 type C domains, there is a particularly high variability in the domain interfaces. One can then hypothesise that the position of the amino acids under positive selection on a same platform, displayed by the alignment of the spikes, provides support to the hypothesis that both F5/8 type C domains participate in a species-dependent function of MFGE8. More generally and as observed in our previous work on the evolution of genes encoding Odorant Binding Proteins and proteins involved in gamete fertilisation, amino acids under positive selection are located almost always at the surface of the proteins rather than in the vicinity of the enzymatic pocket or other functional domain (Meslin et al., 2011, 2012). This suggests that this evolution is driven by species-dependent interaction with partners, as described for example for the positively selected sites on the surface glycoprotein (G) of infectious hematopoietic necrosis virus (LaPatra et al., 2008).