Picking Up The Pace Of Evolution
Harvard University’s David R. Liu and coworkers reported this year a system for carrying out the directed evolution of biomolecules in a fraction of the time of previous methods (C&EN, April 18, page 7; Nature, DOI: 10.1038/nature09929). Called phage-assisted continuous evolution (PACE), the technique could help scientists in their quest to evolve proteins or RNA with newly acquired functions. Such molecules could be used as drugs and may help scientists better understand natural evolution. In PACE, bacteriophages (viruses that infect bacteria) expressing the biomolecule to be evolved infect Escherichia coli cells as the bacteria flow through a flask. Genes needed for phage replication are divvied up between the phage and the bacteria. In particular, the gene for pIII, a protein the bacteriophage needs to infect the bacteria, is removed from the phage’s genome and encoded on a plasmid in the E. coli cells. Production of pIII in E. coli is linked to the activity of the evolving biomolecule encoded in the phage genome, and the gene for that biomolecule changes with each replication cycle. Phages that encode biomolecules with more of the desired activity cause the bacteria they infect to express more pIII, resulting in the production of progeny phages that can infect other host cells and persist in the vessel. Less active biomolecules result in a less infectious phage that can’t propagate fast enough to survive the constant outflow from the flask. In the first examples of PACE, Liu’s team evolved RNA polymerase to recognize and bind different promoters. The phage population can go through approximately 30 rounds of evolution in a day and more than 200 rounds in a week. With conventional methods of directed evolution, a single round can take several days.