Directed Evolution of a Bacterial Leucyl tRNA in Mammalian Cells for Enhanced Noncanonical Amino Acid Mutagenesis
Rachel L. Huang, Delilah Jewel, Rachel E. Kelemen, Quan Pham, Tarah J. Yared, Shu Wang, Soumya Jyoti Singha Roy, Zeyi Huang, Samantha D. Levinson, Bharathi Sundaresh, Suyen Espinoza Miranda, Tim van Opijnen, Abhishek Chatterjee
Abstract
The Escherichia coli leucyl-tRNA synthetase (EcLeuRS)/tRNA EcLeu pair has been engineered to genetically encode a structurally diverse group of enabling noncanonical amino acids (ncAAs) in eukaryotes, including those with bioconjugation handles, environment-sensitive fluorophores, photocaged amino acids, and native post-translational modifications. However, the scope of this toolbox in mammalian cells is limited by the poor activity of tRNA EcLeu . Here, we overcome this limitation by evolving tRNA EcLeu directly in mammalian cells by using a virus-assisted selection scheme. This directed evolution platform was optimized for higher throughput such that the entire acceptor stem of tRNA EcLeu could be simultaneously engineered, which resulted in the identification of several variants with remarkably improved efficiency for incorporating a wide range of ncAAs. The advantage of the evolved leucyl tRNAs was demonstrated by expressing ncAA mutants in mammalian cells that were challenging to express before using the wild-type tRNA EcLeu, by creating viral vectors that facilitated ncAA mutagenesis at a significantly lower dose and by creating more efficient mammalian cell lines stably expressing the ncAA-incorporation machinery.