Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells

Site-specific incorporation of unnatural amino acids (Uaas) in living cells relies on engineered aminoacyl-transfer RNA synthetase-tRNA pairs borrowed from a distant domain of life. Such heterologous suppressor tRNAs often have poor intrinsic activity, presumably due to suboptimal interaction with a non-native translation system. This limitation can be addressed in Escherichia coli using directed evolution. However, no suitable selection system is currently available to do the same in mammalian cells. Here we report virus-assisted directed evolution of tRNAs (VADER) in mammalian cells, which uses a double-sieve selection scheme to facilitate single-step enrichment of active yet orthogonal tRNA mutants from naive libraries. Using VADER we developed improved mutants of Methanosarcinamazei pyrrolysyl-tRNA, as well as a bacterial tyrosyl-tRNA. We also show that the higher activity of the most efficient mutant pyrrolysyl-tRNA is specific for mammalian cells, alluding to an improved interaction with the unique mammalian translation apparatus.

Automated summary

Virus-assisted directed evolution of tRNAs (VADER) allows for the efficient enrichment of active and orthogonal tRNA mutants from naive libraries in mammalian cells. Using this method, improved mutants of Methanosarcina mazei pyrrolysyl-tRNA and a bacterial tyrosyl-tRNA were obtained. The most efficient mutant pyrrolysyl-tRNA showed specific activity for mammalian cells, suggesting improved interaction with the unique mammalian translation machinery.