The new origin of species: Directed Evolution

Eight legs, flowers, colorful feathers, flagella, horns or even viral spikes; how can it be possible? Evolution has been shaping every form of life ever since the DNA appeared on Earth, providing the biodiversity that reigns – and always has reigned – on our planet.

One of the basic principles of evolution is information being transferred from a species to its progeny via genes.  The  DNA can undergo  different mutations affecting the final phenotype (the way it looks) of the offspring. As Charles Darwin and Alfred Russel Wallace reflected in the renowned “Origin of Species”, every organism is subject to Natural Selection. Hence, any variation that confers an advantage will favor its survival and will be positively selected. In short, the survival of the fittest.

So, Nature has been deciding what is “better” and “worse”, but what if we become the judges and masters of this complex process?

For thousands of years, humans have been selecting animals and plants with desired properties, unconsciously mastering the process of evolution and natural selection. Just take a look at some of the most popular fruits now and then or think about the fierce wolves versus man’s best friends, dogs.

Figure 1. Bananas and watermelons are just two examples of how humanity has  shaped the world and the species that surround us. However, this took thousands of years, couldn’t it be accelerated a little bit?

Nonetheless, mankind has managed to go one step further. After decades of work, Frances H. Arnold et al. [1], reported for the first time the implementation of directed evolution in a laboratory, leading to a paradigm shift in molecular biology and eventually awarding her the Nobel Prize of Chemistry in 2018. Just imagine the world of possibilities that opens up if natural evolution’s timescale of thousands and thousands of years is compiled  in  only a few months of laboratory work.

Particularly, Frances H. Arnold applied this novel procedure to improve enzyme function and versatility. But why would we want to evolve enzymes?

To those  not acquainted with molecular biology, enzymes are proteins that act as biological catalysts (biocatalysts). They can be found in living organisms speeding up chemical reactions several magnitudes in rate, in order to reach fast enough rates to maintain life. As biocatalysts, enzymes present many  advantages for  industrial applications: 

1. They work in mild conditions, consequently requiring less energy, and have a low environmental impact, making them extremely efficient and reusable, among others. 
2. They have a  crucial role in the transition towards green chemistry and  it is essential to find and design suitable enzymes to substitute the currently – more polluting – chemical processes. 

Figure 2. Frances H. Arnold among the winners of the 2018 Chemistry Nobel Prize, George P. Smith and Sir Gregory P. Winter [4].

And here, is where Directed Evolution comes into play, since through this method it is possible to obtain enhanced enzymes à la carte in terms of catalytic activity, stability at high temperatures or organic solvents, higher specificity, substrate promiscuity, etc., that satisfy industrial conditions and necessities.

Directed Evolution relies on an iterative process in which the scientist recreates in the laboratory the key events (mutation, DNA recombination and selection) of natural evolution. Starting from a certain enzyme, the cycle begins with the random diversification of its gene. Then, genetic variety is expressed in a suitable microorganism (usually Escherichia coli or Saccharomyces cerevisiae) and is evaluated by a reliable screening method, where the feature that is desired to be improved is tested. Afterwards, the best candidates are selected and can be introduced again in the cycle as the new parental types, for further improvements in new rounds of evolution.

Up to now, there have been reported evolved enzymes with novel features – absent in our natural world – such as the catalysis of synthetic bonds [2] or new reactions with improved enantio-selectivity [3] highly demanded in the pharmaceutical industry. All of this led to the production of hundreds and hundreds of biofuels, materials, bulk and fine chemicals, detergents, consumer products, laboratory reagents and pharmaceuticals, as well as intermediates for the pharmaceutical industry.

Figure 3. Number of scientific articles regarding  Directed Evolution from 1991 to 2020. Information obtained through Scopus database introducing “Directed Evolution” as search item. This is just the beginning.

At the end of the day, Directed Evolution is one more proof of what humanity is able to do through science. We have still a long way to go, but one thing remains clear. Never stop understanding and learning from Nature, which is undoubtedly wiser than we are, because it will lead us to reach inconceivable fates.

References

1. Chen K, Arnold FH. Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media. Bio/Technology. 1991 Nov 1;9(11):1073–7.2.
2. Kan SBJ, Lewis RD, Chen K, Arnold FH. Directed evolution of cytochrome c for carbon-silicon bond formation: Bringing silicon to life. Science. 2016 Nov 25;354(6315):1048–51.
3.  McIntosh JA, Coelho PS, Farwell CC, Wang ZJ, Lewis JC, Brown TR, et al. Enantioselective intramolecular C-H amination catalyzed by engineered cytochrome P450 enzymes in vitro and in vivo. Angew Chem Int Ed Engl. 2013/07/24 ed. 2013 Aug 26;52(35):9309–12. 
4. El Premio Nobel de Química recae en Frances H. Arnold, George P. Smith y Gregory P. Winter [Internet]. Elmedicointeractivo.com. 2018 [cited 2021 Jun 11]. Available from: https://elmedicointeractivo.com/el-premio-nobel-de-quimica-recae-en-frances-h-arnold-george-p-smith-y-gregory-p-winter/