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Ancestral gene resurrection
Ancestral gene resurrection is a technique that belongs to the study of molecular evolution. The method consists in the synthesis of an ancestral gene and expression of the corresponding ancestral protein.〔 The idea of protein resurrection was suggested in 1963 by Pauling and Zuckerkandl.〔Pauling, L. & Zuckerkandl, E. Chemical paleogenetics: molecular restoration studies of extinct forms of life. Acta Chem. Scand. supl. 17, S9–S16 (1963) (Acta Chemica Scandinavica Online Archive )〕 Some early efforts were made in the nineties, led by the laboratory of Steven A. Benner, a biochemist at the Swiss Federal Institute of Technology and later the University of Florida.〔Jermann TM, Opitz JG, Stackhouse J, Benner SA. Reconstructing the evolutionaryhistory of the artiodactyl ribonuclease superfamily. Nature. 1995 Mar2;374(6517):57-9. PubMed PMID 7532788.〕 Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of much more ancient genes.〔Thornton JW, Need E, Crews D. Resurrecting the ancestral steroid receptor:ancient origin of estrogen signaling. Science. 2003 Sep 19;301(5640):1714-7.PubMed PMID 14500980.〕 Over the next decade, ancestral protein resurrection was developed as a strategy to reveal the mechanisms and dynamics of protein evolution, led mainly by Joseph Thornton, an evolutionary biologist at the University of Oregon.〔Pearson, Helen (March 21, 2012) "(Prehistoric proteins: raising the dead )" Nature (London)〕
==The method==
The ancient protein is inferred by means of phylogenetic methods and a DNA molecule coding for that protein is synthesized. This DNA is expressed in cultured cells or ''in vitro'' whereafter the obtained ancestral protein may be tested for its properties. Sequences of extant proteins with the same function obtained from more or less distant related organisms are aligned and the best-fitting evolutionary model is determined. The ancestral protein is reconstructed by maximum likelihood. This virtual sequence of aminoacids allows for the synthesis of oligonucleotides that are subsequently assembled into the gene for the ancestral protein. This gene is amplified by means of PCR and transcribed ''in vitro'' or ''in vivo.'' The resulting ancestral protein is eventually purified and ready to be tested for its properties.〔Thornton J.W. (2004) "Resurrecting ancient genes: experimental analysis of extinct molecules". Nature Reviews Genetics 5, 366-375 doi:(10.1038/nrg1324 )〕〔Figure 1 from reference 3. "(The ancestral gene resurrection strategy )"〕
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