Ancestral protein reconstruction: techniques and applications

Abstract

Ancestral sequence reconstruction (ASR) is the calculation of ancient protein sequences on the basis of extant ones. It is most powerful in combination with the experimental characterization of the corresponding proteins. Such analyses allow for the study of problems that are otherwise intractable. For example, ASR has been used to characterize ancestral enzymes dating back to the Paleoarchean era and to deduce properties of the corresponding habitats. In addition, the historical approach underlying ASR enables the identification of amino acid residues key to protein function, which is often not possible by only comparing extant proteins. Along these lines, residues responsible for the spectroscopic properties of protein pigments were identified as well as residues determining the binding specificity of steroid receptors. Further applications are studies related to the longevity of mutations, the contribution of gene duplications to enzyme functionalization, and the evolution of protein complexes. For these applications of ASR, we discuss recent examples; moreover, we introduce the basic principles of the underlying algorithms and present state-of-the-art protocols.

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins

“…Emerging techniques combining ancestral sequence reconstruction (ASR) with laboratory functional assays and structure determination have allowed researchers to meticulously characterize the evolutionary and structural bases for changes in molecular function (Malcolm et al 1990; Shih et al 1993; Ugalde et al 2004; Bridgham et al 2006, 2009; Zmasek and Godzik 2011; Voordeckers et al 2012; van Hazel et al 2013; Ogawa and Shirai 2014; Whitfield et al 2015; Clifton and Jackson 2016). While these approaches provide unprecedented opportunities to rigorously investigate the molecular-functional evolution of protein families (Shih et al 1993; Hanson-Smith et al 2010; Harms and Thornton 2010; Merkl and Sterner 2016), their reliance on detailed experimental methods limits the scale at which ancestral protein resurrection can be applied.…”

Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex

“…Based on the MSA and this model, the most likely phylogenetic tree is calculated and used to infer for the parental nodes the sequences of these predecessors, including the one that corresponds to the last common ancestor of all included present-day proteins. After synthesizing the genes encoding these sequences and their expression in host organisms such as Escherichia coli, the ancient proteins can be purified and characterized 13,14 .…”

Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures

“…On the other hand, exploring the evolutionary history and resurrecting intermediate ancestral forms of enzymes can help to explain the mechanistic basis of enzymes function, to disclose new functionalities, and even to evolve artificially these ancestral proteins in laboratory conditions [16, 17]. Evolutionary studies have been used to reconstruct a growing number of ancestral proteins, including hormone receptors [18, 19], visual pigments [20, 21], carbohydrate binding proteins [22], and elongation factors [23, 24].…”