Resurrecting Enzymes by Ancestral Sequence Reconstruction

MASCOTTI ML

Enzyme Engineering Methods and Protocols

Springer Nature

Año: 2022; p. 111 - 136

Ancestral Sequence Reconstruction (ASR) allows one to infer the sequences of extinct proteins using thephylogeny of extant proteins. It consists of disclosing the evolutionary history?i.e., the phylogeny?of aprotein family of interest and then inferring the sequences of its ancestors?i.e., the nodes in the phylogeny.Assisted by gene synthesis, the selected ancestors can be resurrected in the lab and experimentally characterized. The crucial step to succeed with ASR is starting from a reliable phylogeny. At the same time, it isof the utmost importance to have a clear idea on the evolutionary history of the family under study andthe events that influenced it. This allows us to implement ASR with well-defined hypotheses and to applythe appropriate experimental methods. In the last years, ASR has become popular to test hypotheses aboutthe origin of functionalities, changes in activities, understanding physicochemical properties of proteins,among others. In this context, the aim of this chapter is to present the ASR approach applied to thereconstruction of enzymes?i.e., proteins with catalytic roles. The spirit of this contribution is to provide abasic, hands-to-work guide for biochemists and biologists who are unfamiliar with molecular phylogenetics.