Reconstruction of ancestral enzymes

Abstract

The amino acid sequences of primordial enzymes from extinct organisms can be determined by an in silico approach termed ancestral sequence reconstruction (ASR). In the first step of an ASR, a multiple sequence alignment (MSA) comprising extant homologous enzymes is being composed. On the basis of this MSA and a stochastic model of sequence evolution, a phylogenetic tree is calculated by means of a maximum likelihood approach. Finally, the sequences of the ancestral proteins at all internal nodes including the root of the tree are deduced. We present several examples of ASR and the subsequent experimental characterization of enzymes as old as four billion years. The results show that most ancestral enzymes were highly thermostable and catalytically active. Moreover, they adopted three-dimensional structures similar to those of extant enzymes. These findings suggest that sophisticated enzymes were invented at a very early stage of biological evolution.