Evolution is nature’s way of engineering biological systems. Inside cells, many variations of DNA, RNA, and proteins arise, and natural selection favors the organisms that function most effectively. Humans began harnessing this process long ago. Early farmers influenced evolution by choosing which crops and livestock reproduced, allowing the most productive plants and animals to pass on their traits.
Today, scientists apply similar principles in the lab through a technique known as directed evolution. Researchers use it to improve proteins such as enzymes and antibodies that play important roles in medicine, industrial manufacturing, and even everyday products like laundry detergents.
Limits of Traditional Directed Evolution
Despite its success, standard directed evolution methods have a key limitation. They usually impose a constant selection pressure that favors proteins that remain highly active all the time. However, real biological systems rarely function this way. Many proteins serve as signals, molecular switches, or “logic gates” (proteins that combine multiple inputs to make a yes-or-no decision), meaning they must change states as conditions shift.
For example, a protein might briefly activate, then turn off, and later switch on again. When evolution experiments only reward a single state, other necessary states can degrade. As a result, proteins may lose the ability to switch properly, which can be harmful for cells (e.g. kill a cell). Because of this challenge, creating proteins with complex multi-state behavior has proven difficult with existing directed evolution approaches.
A Light-Based Strategy for Protein Evolution
Researchers led by Sahand Jamal Rahi at EPFL’s Laboratory of the Physics of Biological Systems have introduced a new approach called “optovolution.” This method uses light to steer the evolution of proteins that can perform dynamic functions and even carry out simple computational tasks that follow yes-or-no rules.
The study, published in Cell, helps bring directed evolution closer to how cells naturally operate. In living systems, timing and switching between states are just as important as the strength of a signal.
Engineering Yeast Cells to Select the Best Proteins
To build their system, the researchers used the budding yeast Saccharomyces cerevisiae, an organism widely used both in brewing and scientific research. They redesigned the yeast cell cycle so that cell division depended on the behavior of the protein being evolved. The protein needed to switch cleanly between active and inactive states for the cell to survive.
The scientists connected the protein’s output signal to a regulator that controls the cell cycle. This regulator is essential during one stage but becomes toxic during another. If the protein remained on or off for too long, the yeast cell would stall or die. Only cells containing proteins that switched at the correct time continued to divide.
Using Light to Control Evolution in Real Time
Light provided a way to control this process with precision. The researchers used optogenetics, a technique that activates or deactivates genes using light. By delivering timed pulses of light, they forced the protein to alternate between states.
Each yeast cell cycle lasts about 90 minutes, creating a rapid pass or fail test of whether the protein switched at the correct moment. Proteins that performed best allowed the cell to survive and reproduce, while poorly switching variants were eliminated. This allowed optovolution to automatically select proteins with better dynamic behavior without manual screening or repeated adjustments.
New Protein Variants and Expanded Color Sensitivity
Using optovolution, the team evolved several different types of proteins. They first improved a commonly used light controlled transcription factor. The researchers generated 19 new variants that showed greater sensitivity to light, reduced activity in darkness, or the ability to respond to green light rather than only blue light. Engineering proteins that respond to warmer colors than blue has long been considered extremely difficult because of how these proteins absorb light.
The scientists also evolved a red light optogenetic system so that yeast cells no longer required an added chemical cofactor. Evolution produced a mutation that disabled a normal yeast transport protein. This unexpected change allowed the system to use light sensitive molecules already present inside the cell, making the system easier to use in experiments.
Proteins That Act Like Tiny Computers
The study also demonstrated that optovolution can extend beyond light sensing proteins. The researchers evolved a transcription factor that functions like a single protein computer. It activated genes only when two different inputs appeared at the same time – one light signal and one chemical signal.
Dynamic protein behavior is essential for many biological processes, including sensing environmental changes, making decisions inside cells, and controlling cell division. By enabling these behaviors to evolve continuously within living cells, optovolution offers new possibilities for synthetic biology, biotechnology, and fundamental research.
The technique may help scientists design smarter cellular circuits, create optogenetic tools that respond independently to different colors of light, and better understand how complex protein behaviors arise through evolution.
Other contributors
- EPFL Laboratory of Protein and Cell Engineering
- University of Bayreuth
- Lausanne University Hospital (CHUV)
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