We have all heard of domesticating cows and dogs, but now it is possible to domesticate bacteria. Scientists have been able to “redirect bacterial evolution” and change certain traits of bacteria by making slight changes in the makeup of their enzymes. Enzymes are primarily proteins that are catalysts of biochemical reactions, so they do the heavy lifting in biology. Enzymes are the reason we see, breathe, and derive energy from food – in short – live! By using a process called “directed evolution”, scientists have created bacterial strains that can perform tasks that they would not have been able to do naturally. Directed evolution has tremendous potential for creating bacteria with useful new traits, such as eating up plastic in the environment. They can also be imbued with special abilities to produce compounds that are otherwise extremely difficult to extract from natural sources like plants.
Directed evolution can be thought of as a platform to give these little bugs power-ups (do you remember those video game cheat codes?). Perhaps these little changes can accumulate over time and create bacterial strains that are truly unrecognizable. After all, we humans evolved from tiny crawly things that we are now disgusted by! Evolution, in general, would bring up images of monkeys becoming humans or fish flopping on a beach and learning how to walk. We may think that evolution happened a long time ago, but evolution is occurring now, every moment, deep down in the molecular realms. Evolution is often defined as a shift in how genes are distributed. For instance, if in a town, only 2% of the citizens have blue eyes, and then in 20 years (with no one moving in or out), 20% of the citizens have blue eyes, then you should chalk it up to evolution. But genetic features like blue eyes can also appear when no one in the population has blue eyes. This brand-new feature is due to spontaneous mutations in genes that are responsible for eye color. Mutations can have harmless effects like changes in eye color. Mutations can also cause deadly diseases like cancers. Mutations are also known to impart superpowers to some, but that’s limited to the world of fiction for now. At its most fundamental level, mutations are random – they are the wild card of genetics, God’s dice in biology.
So, what is directed evolution? Directed evolution is essentially evolution controlled in a lab. Just like early humans domesticated wolves to be man’s best friend or bred chickens to have the prettiest feathers, we can force bacteria to change by altering their proteins. Directed evolution is distinct from gene editing techniques, or the introduction of plasmids, because it uses the natural phenomena of evolution to create an altered protein at a faster time scale. The protein of interest is randomly mutated with a chemical or radiation. This generates a library of mutants of that protein. Like a library full of books, a library of proteins can be “browsed” to find the one for the job. But how do we determine the best protein, you may ask? There are many clever strategies scientists use to identify the best protein from a library. A popular method used to grab the desired protein is to add a tag, such as histidine. This tag is unique to the protein it is bound to and helps the experimenter pick the desired protein from a collection of proteins – like first finding the fiction section in a large library building, then narrowing down the search to an author’s last name and then to the specific book. Once the desired protein is identified, it is easy to figure out the gene sequence that codes for that protein. This gene sequence can be introduced to any bacteria via a process called transformation. With a successful transformation, the bacteria should be able to make the new protein. And viola – we have created a bacterial version of X-men!
Studies on directed evolution began in 1967 when Sol Spiegelman did RNA selection studies to create “Spiegelman’s monsters”. This field grew to expand into evolving various macromolecules: enzymes, antibodies, and RNA. The 2018 Nobel Prize was shared amongst three scientists for their work in directed evolution. Dr. Frances Arnold pioneered enzyme engineering, Dr. George Smith developed a “phage display” method that mediates antibody directed evolution, and Sir Dr. Gregory Winter, who worked on cancer therapy applications for the phage display method. This phage display method used phages as the tags to filter out antibodies, which has led to pharmaceutical therapies for metastatic cancer. With this method we could have plastic removal and the cure for cancer.
Frances Arnold at CalTech was the brains behind this idea of using directed evolution for enzymes. She and her team have used directed evolution to make bacteria perform feats that they would not have been able to do otherwise. Arnold’s team created bacteria that can live in hot temperatures by evolving enzymes that function at temperatures as high as 80 ℃ (176 ℉). Most enzymes are destroyed at such high temperatures. While this seems like a simple temperature adaptation, heat-stable enzymes may help in biofuel production where higher temperatures are required. A huge reason for her success was her courage to explore ideas that seemed too crazy to work for most scientists. For example, there was a long-standing misconception that mutations to the surface of an enzyme do not affect its function, as enzyme function is generally thought to happen in interior pockets called active sites. Arnold discovered that sometimes a mutation located on the surface (and not in a pocketed active site) can not only change but improve enzyme function. Her willingness to explore often-overlooked topics such as this has opened up a brave world of completely new biology that promises to impact diverse areas of manufacturing, medicine, and diagnostics, among others that we can only start to imagine.
Bacteria created by directed evolution may be able to generate pharmaceuticals or biofuels in bulk. Artificially evolved bacterial strains could be the cheapest tool for cleaning up forever plastics of oil spills. Research on directed evolution started with a basic curiosity-driven question. Can we rewire evolution – something that has been fundamental in shaping all of life? That curiosity has led to boundless technological opportunities generating tremendous hope for the future. In that sense – the story of directed evolution is a story about science itself.
Author
Olympia Otulakowski is an early career biochemistry graduate student who loves teaching science to others, whether to students that she TAs for or to family members. She loves to incorporate fun anecdotes to make students more excited about science and is happy that she got the opportunity to do so in freelance writing. When she isn’t in the lab tinkering with her project, she is at home either reading a book, cross-stitching, or playing video games.
Illustrator
Taylor Opolka is a second-year biochemistry graduate student at the University of Notre Dame. She finds great fulfillment in teaching science to others, and has a passion for making science more accessible, engaging, and fun. She hopes to pursue a future career in which she can continue to exercise this passion! When she is not working in the lab, she enjoys reading books, buying books (a separate hobby entirely), creating art, and playing basketball for the women’s club basketball team at Notre Dame.
