Directed Evolution of Pyrrolysyl-tRNA Synthetase Generates a Hyperactive and Highly Selective Variant.

Pyrrolysyl-tRNA synthetase (PylRS) is frequently used for site-specific incorporation of noncanonical amino acids (ncAAs) into proteins. Recently, the active site of PylRS (PylRS) has been rationally engineered to expand its substrate compatibility, enabling the incorporation of difficult ncAAs. However, mutations beyond the active site that enhance the enzymatic properties of PylRS have not been reported. We utilized phage-assisted non-continuous evolution (PANCE) to evolve PylRS to efficiently incorporate -Boc-l-lysine (BocK). Directed evolution yielded several mutations outside of the active site that greatly improve the activity of the enzyme. We combined the most effective mutations to generate a new PylRS variant (PylRS) that is highly active and selective towards several lysine and phenylalanine derivatives. The mutations in PylRS can be used to enhance previously engineered PylRS constructs such as PylRS, and PylRS is compatible in applications requiring dual ncAA incorporation and substantially improves the yield of these target proteins.