Using resurrected ancestral proteins to map function along diverging evolutionary pathways

A recurring theme in the molecular evolution of proteins is that an ancestral protein diversifies into a diverse family of proteins that exhibits a range functional properties. A central and influential notion in evolutionary biology is that that evolution proceeds via gradual changes. Here we use an approach based on deriving and then resurrecting ancestral proteins to test if the gradual nature of evolution holds at the molecular level for protein function. We used photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system in this work because PYP has multiple functional properties that can be readily quantified, and because members of the PYP family exhibit considerable divergence in these properties. We find that functional values along reconstructed evolutionary pathways strongly deviate from the gradual pattern. We refer to these deviations as evolutionary molecular meandering and propose that this effect has important implications for understanding the process of molecular evolution.