The Evolution of Directed Evolution

THE ZYMVOL BLOG

The Evolution of Directed Evolution

Life on Earth has evolved over millions of years thanks to genetic variation

Imagine a tree species adapted to drought that starts to face frequent and abundant rains. 

The whole species would disappear!

Unless… There were a few individuals able to face the new situation because of slight, random genetic differences, allowing them to adapt to the changing environmental conditions.

Individuals with more favorable traits to a given environment will survive and reproduce more than others, transferring their genes to the next generation. 

This process, known as natural selection, is the major driver of evolution. But selection can also be fostered, and even controlled, in search for specific new traits by humans.

We started to learn how to intervene in the natural process of evolution long before calling it artificial selection or selective breeding.

Developing agriculture and livestock, we became a decisive selective force that kept, across generations, those traits of cattle and vegetables favorable to human sedentarism subsistence, like yield, resistance.

We were basically mimicking nature or ‘biomimicking’ at a pace that was enough to foster human civilization progress at that time. 

Nowadays, we are able to control this process in much more precise, sophisticated and faster ways.

A Nobel-Award Winning Workflow

Evolution occurs at an ample time scale, which is not compatible with fast changing industries and human lifetimes span.

This is where Directed Evolution comes in.

Directed Evolution  speeds up the natural selection process – in an iterative workflow that takes place in controlled laboratory conditions either in vivo (within microorganisms, that reproduce very fast) or in vitro (in artificial cell-like simple structures):

  1. Generation of genetic variation for the desired target enzyme through  different mutagenesis techniques.
  2. Differences in fitness are screened and deliberately selected for the desired conditions.
  3. Inheritance of the selected traits is substituted by the artificial amplification of the genes encoding those proteins with improved catalytic properties.

This cycle can be repeated several times, each starting with the last better performing obtained variant, to direct evolution towards the chosen goal – for example, improved performance or new catalytic properties –, optimizing the new functions up to a desired level.

Did you know…?

Frances H Arnold, professor of Chemical Engineering, Bioengineering and Biochemistry at Caltech (US), was awarded in 2018 the Nobel Prize in Chemistry for the conception and development of this directed evolution workflow.

Arnold shared the prize with other two scientists, George P Smith and Sir Gregory P Winter, for developing a different technique for binding-proteins selection, advantageous in the field of Immunology.

So why was Directed Evolution such a breakthrough?

Single enzyme types can be selected for specific biocatalytic properties and, then, evolved towards new functions, some of them not even existing in nature. 

Directed evolution is used as a research tool to study enzyme evolution, but specially, as a revolutionary method to obtain biocatalysts for industrial processes.

These natural catalysts accomplish a wide array of chemical reactions that take part in the production of a broad variety of products, such as drugs, perfumes, detergents or food.

For example, one of the widest known enzymes used in industry is lactase, which degrades lactose from milk, producing lactose-free milk as a result, a suitable option for those who cannot digest that sugar, normally present in dairy products.

Directed evolution has become an ally of industrial innovation, adapting and optimizing the reactions of enzymes towards precise and desired industrial goals regarding speed, substrate, type of reaction and more.

Beyond Bio-mimicking

Nowadays, technological advances in different areas, such as biotechnology, bioinformatics and IT, are allowing us to perform, in an increasingly improved way, directed evolution in silico, that is, in the computer

Computational enzyme engineering uses bioinformatics and molecular modeling tools to redesign existing enzymes performing the directed evolution process in silico.

Performing these first rounds in the computer (by virtually screening millions of variants) saves time and resources compared to traditional lab work. 

It also opened the door for rational design: protein design through algorithms and simulations that allow to obtain, in a short period, desired enzyme properties that are not easily reachable by the conventional workflow nor found in nature.

Big advances are taking place in order to combine both in silico methods with experimental data.

We are in the fascinating process of better knowing how enzymes work and constantly improving the accuracy to detect which amino acids can be mutated to be beneficial. But the progress done so far has already boosted the industrial use of enzymes since its onset 30 years ago.

It’s impressive how we’ve leveraged the power of evolution, as France Arnold emphasized at the end of her Nobel Lecture in 2018:

“I am continually amazed at the ease with which evolution innovates (…) Instead of asking what enzymes do in the natural world, we can now ask, “What might they do?” Enzymes will perform chemistry in more ways than we could have imagined, especially when we use evolution to unleash their latent potential.”

Frances Arnold, professor of Chemical Engineering, Bioengineering and Biochemistry at Caltech


References

[1] Heckmann, C. M. and Paradisi, F. (2020). Looking Back: A Short History of the Discovery of Enzymes and How They Became Powerful Chemical Tools. ChemCatChem, 2020, 12: 6082 – 6102.
[2] Chen, K. and Arnold, F.H. (1993). Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc Natl Acad Sci USA. 90:5618-5622.
[3] Tawfik, D.S. and Griffiths, A.D. (1998). Man-made cell-like compartments for molecular evolution. Nat Biotechnol. 16:652-656
[4] The Nobel Prize in Chemistry 2018. NobelPrize.org. Nobel Prize Outreach AB 2022. Mon. 3 Oct 2022
[5] Jäckel, C., Kast, P. and Hilvert, D. (2008.) Protein design by directed evolution. Annu Rev Biophys. 37:153-173.
[6] Arnold, F.H. (2019). Innovation by Evolution: Bringing New Chemistry to Life (Nobel Lecture). Angew. Chem. Int. Ed. 58: 14420 – 14426
[7] McLure, R.J., Radford, S.E. and Brockwell, D.J. (2022). High-throughput directed evolution: a golden era for protein science. Trends in Chemistry. 4: 278-291.