Directed Evolution of Protein Enzymes Using Nonhomologous Random Recombination

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 18; pp. 7011 - 7016
• Main Authors: Bittker, Joshua A., Le, Brian V., Liu, Jane M., Liu, David R., Joyce, Gerald F.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 04.05.2004; National Acad Sciences
• Subjects: Biological Sciences; Chorismate Mutase - genetics; Crossovers; Dimers; Directed Molecular Evolution; DNA; Enzymes; Escherichia coli - chemistry; Escherichia coli - genetics; Escherichia coli - metabolism; Evolution; Libraries; Ligation; Mutation; Nucleic acids; Plasmids; Polymerase chain reaction; Protein Structure, Tertiary; Proteins; Recombinant Fusion Proteins - chemistry; Recombinant Fusion Proteins - genetics; Recombinant Fusion Proteins - metabolism
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.0402202101

We recently reported the development of nonhomologous random recombination (NRR) as a method for nucleic acid diversification and applied NRR to the evolution of DNA aptamers. Here, we describe a modified method, protein NRR, that enables proteins to access diversity previously difficult or impossible to generate. We investigated the structural plasticity of protein folds and the ability of helical motifs to function in different contexts by applying protein NRR and in vivo selection to the evolution of chorismate mutase (CM) enzymes. Functional CM mutants evolved using protein NRR contained many insertions, deletions, and rearrangements. The distribution of these changes was not random but clustered in certain regions of the protein. Topologically rearranged but functional enzymes also emerged from these studies, indicating that multiple connectivities can accommodate a functional CM active site and demonstrating the ability to generate new domain connectivities through protein NRR. Protein NRR was also used to randomly recombine CM and fumarase, an unrelated but also α-helical protein. Whereas the resulting library contained fumarase fragments in many contexts before functional selection, library members surviving selection for CM activity invariably contained a CM core with fumarase sequences found only at the termini or in one loop. These results imply that internal helical fragments cannot be swapped between these proteins without the loss of nearly all CM activity. Our findings suggest that protein NRR will be useful in probing the functional requirements of enzymes and in the creation of new protein topologies.