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Infographic: Resurrecting Ancient Proteins

Learn the basic steps researchers take when reconstructing proteins from the past and how these biomolecules can inform engineering projects.

Jul 1, 2018
Amber Dance

Ancestral sequence reconstruction relies on phylogeny and statistics to infer the most likely amino acid

SEQUENCE ALIGNMENT

Scientists collect sequences from databanks of the modern versions of the protein of interest from different organisms.

© wikimedia commons/Miguel Andrade

TREE BUILDING

Computer algorithms construct a phylogenetic tree for the proteins (Curr Opin Struct Biol, 38:37–43, 2016).

ANCESTRAL RECONSTRUCTION

The programs can then infer the sequences that likely existed at nodes of the tree, before the modern species evolved.

LABORATORY TESTS

Finally, the scientists order synthetic DNA and generate those proteins in the lab to use for experiments.

Ensuring accuracy

One way to ensure that an ASR protein behaves like the true ancestor is to resurrect and test not only the best amino acid sequence generated by the algorithms, but a few proteins with the second-best guesses, or third-best guesses, and so on. If those alternative ancestors act like the best-guess version, then researchers figure the conclusions are probably robust. Recently, evolutionary synthetic biologist Eric Gaucher of Georgia State University tested ASR accuracy in a different way. He generated an entirely artificial phylogenetic tree, starting with red fluorescent protein and randomly mutating it to evolve 19 diversely colored fluorescent proteins. Then he used ASR to predict the ancestor of those 19 descendants, and compared the results to the true ancestors. The results were reassuring. Overall, the five different ASR algorithms he tried identified the ancestral sequence with about 97 percent accuracy (Nat Commun, 5:12847, 2016).

EVOLVING PROTEINS: The experimental evolution began with a red fluorescent protein gene (left). The 19 resulting proteins were sequenced, and the data were used to infer the sequences of the node proteins. (Colors represent protein fluorescence. The number of nonsynonymous and synonymous substitutions are shown along each branch.)
Nat Commun, 5:12847, 2016

The Perfect Starting Point

Bioengineers love resurrected proteins because they often combine two desirable features: thermostability and promiscuity. For example, researchers at the University of Granada in Spain reconstructed several versions of an antibiotic-resistance protein called beta-lactamase, going back as far as 3 million years. As the protein evolved, its melting point dropped from more than 80 °C  to less than 60 °C. It also became more specific for penicillin, losing its ability to neutralize other drugs (J Am Chem Soc, 135:2899–902, 2013).


J Am Chem Soc, 135:2899–902, 2013

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