Researchers have found a way to accelerate evolution of molecules by harnessing viruses.

A constant current of media and bacteria creates intense selection pressure for bacteriophage in the PACE apparatus developed in the lab of David Liu. The PACE system, diagrammed here, can increase the speed of laboratory evolution some 100 times over previous techniques.

Evolution continuously shapes life on our planet, all the way down to an organism’s molecular machinery. Surviving genetic variants thrive and move to the next round, where mutations might further improve them. The less fit perish.

This kind of natural selection can be a gradual and drawn-out process. But HHMI investigator David Liu wants speed.

Liu and his team have developed a system that uses phage, the viruses that infect bacteria, to accelerate evolution in the laboratory. By tying a virus’s fate to the function of a specific protein or nucleic acid, the system can improve that molecule’s existing ability, or coax it to evolve a new one. Called phage-assisted continuous evolution, or PACE, the system ushers the evolution of molecules along approximately 100 times faster than previous techniques.

It offers an exciting prospect for developing new pharmaceuticals as well as studying evolution.

A typical single round of directed evolution takes days to complete, and many rounds may be necessary to achieve a researcher’s goals. It’s tedious work, and a gamble. Even after dozens of evolutionary rounds—more than researchers can typically handle—targeted improvements to a molecule may be modest. Scientists patient enough to spend years with the process also bemoan the need to babysit equipment, reagents, microbes, and genetic sequences along the way.

Liu, a chemical biologist at Harvard University, and his graduate students Kevin Esvelt and Jacob Carlson wanted an end to the monotony. Their PACE system replaces the human grunt work of laboratory evolution with a partnership between fast-reproducing M13 bacteriophage and Escherichia coli bacteria. The system is a veritable self-sustained factory of biomolecular evolution.

In their first report describing PACE, published April 28, 2011, in Nature, Liu and his team used the system to continuously evolve an enzyme to gain three new abilities. In each case, the new version of the enzyme showed activity levels as high as, or higher than, the naturally occurring enzyme. In one example, they put a protein through 200 rounds of evolution in only eight days.

“Using a conventional protein evolution method, it would have taken us years,” Liu says. “The speed and throughput of PACE is pretty hard to match.”

In the system, a never-ending current of fluids and E. coli bacteria creates a life-or-death pressure for M13 bacteriophage. To survive in this evolutionary “river,” the phage must in effect swim upstream by infecting E. coli and reproducing more quickly than they are washed away. Since a phage can churn out hundreds of copies of itself in 10 minutes, this feat should not be a problem.

Image: VSA Partners

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