What is (lab) directed evolution?

What is (lab) directed evolution?

Oct 04, 2022 Posted by: Cameron Davidson-Pilon

Directed evolution is the technique of controlling an organism's evolutionary trajectory such that its descendants have more of a desired properties. Most often, the engineers will have a strict control of the organism's environment. By controlling the environment and responding to the organism's simultaneous adaption, an organism can be directed to have novel or desirable properties. In particular, the directed evolution of microorganisms is more easily achieved due to their short generation time, high cell density, and isolated environments.

An example graph of increasing the temperature of a culture in response to the culture evolving to tolerate the higher temperature.

Figure 1. An example graph of increasing the temperature of a culture in response to the culture evolving to tolerate the higher temperature.

For microorganisms, directed evolution can be done in-situ by using bioreactor systems like chemostats, turbidostats, and morbidostats.

What applications are there for directed evolution?

  1. Evolving a traditional brewer's yeast to thrive in new brewing environments. New environments for brewer's yeast could be higher/lower temperature, higher (alcohol, IBU, caffeine), concentration, lower pH, salt %.

  2. Yeast can only ferment a short list of carbohydrates. By slowly depleting yeast's traditional carbon sources, it forces the yeast to adapt to new carbon sources, like lactose. See [Attfield, 2006]

  3. Similarly, filamentous fungi can be evolved to consume new carbon sources, like raffinose, a sugar which is a cause of digestive discomfort after eating soybean tempeh.

  4. Lactobacillus, used in sour beer production, can be evolved to be more alcohol, pH or IBU tolerant.

  5. Some algae are facultative heterotrophs. A morbidostat can be used to evolve a stronger and faster growing heterotrophic metabolism.

  6. Triton Algae Innovations has used directed evolution to evolve heme in algae. They accelerated the process by flashing the microbes with UV light which caused a high mutation rate.

  7. Algae can be evolved to produce more carotenoids by changing the light conditions, see [Fu, 2013]

  8. Improving yeast culture density, as demonstrated in [Wong, 2018]

  9. Improving growth rates after "rational design". When modifying the genes of a microorganism though modern genetic engineering, the growth rate is typically lowered due to new proteins or metabolites being constructed. By subjecting the organism to an environment with abundant nutrients, over time, the population will evolve to increase its growth rate.

  10. Improving metabolite production after rational design. After adding the genes of carotenoid production to yeast but wanting a higher yield, [Reyes, 2013] exploited the antioxidant of carotenoids. They exposed the yeast to high levels of hydrogen peroxide. The yeast evolved to counteract the hydrogen peroxide by producing more carotenoids.

  11. The original inventors of the morbidostat [Toprak, 2013] were interested in antibiotic resistance in bacteria. They subjected E. coli to a slowly increasing level of antibiotics, and after two weeks, the bacteria had grown resistance to the highest antibiotic concentration in their experiment design.

  12. In [Ekkers, 2020], the authors hint at evolving an anticipatory response to changes in environments. 

References

  1. Toprak, E., Veres, A., Yildiz, S. et al. Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition. Nat Protoc 8, 555–567 (2013). https://doi.org/10.1038/nprot.2013.021

  2. A low-cost, open source, self-contained bacterial EVolutionary biorEactor (EVE) Vishhvaan Gopalakrishnan, Nikhil P. Krishnan, Erin McClure, Julia Pelesko, Dena Crozier, Drew F.K. Williamson, Nathan Webster, Daniel Ecker, Daniel Nichol, Jacob G Scott bioRxiv 729434; doi: https://doi.org/10.1101/729434

  3. A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter Hoffmann SA, Wohltat C, Müller KM, Arndt KM (2017) A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter. PLOS ONE 12(7): e0181923. https://doi.org/10.1371/journal.pone.0181923

  4. Wong, B., Mancuso, C., Kiriakov, S. et al. Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. Nat Biotechnol 36, 614–623 (2018). https://doi.org/10.1038/nbt.4151

  5. Ekkers, DM, Branco dos Santos, F, Mallon, CA, Bruggeman, F, van Doorn, GS. The omnistat: A flexible continuous‐culture system for prolonged experimental evolution. Methods Ecol Evol. 2020; 11: 932– 942. https://doi.org/10.1111/2041-210X.13403

  6. Luis H. Reyes, Jose M. Gomez, Katy C. Kao, Improving carotenoids production in yeast via adaptive laboratory evolution, Metabolic Engineering, Volume 21, 2014, Pages 26-33, ISSN 1096-7176, https://doi.org/10.1016/j.ymben.2013.11.002

  7. Fu W, Guethmundsson O, Paglia G, Herjolfsson G, Andresson OS, Palsson BO, et al. 2013. Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. Appl. Microbiol. Biotechnol. 97: 2395-2403.

  8. Attfield PV Bell PJL (2006) Use of population genetics to derive nonrecombinant Saccharomyces cerevisiae strains that grow using xylose as a sole carbon source. FEMS Yeast Res6: 862–868.