A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases

Using directed evolution, engineered aminoacyl-tRNA synthetases (aaRS) have been developed that enable co-translational incorporation of numerous noncanonical amino acids (ncAAs) into proteins in living cells. Until now, the selection of such novel aaRS mutants has relied on coupling their activity to the expression of a reporter protein with a selectable phenotype. However, such translation-dependent selection schemes are incompatible with exotic monomers that diverge structurally from canonical -amino acids and are suboptimal substrates for the ribosome. To enable the ribosomal incorporation of such exotic monomers, a two-step solution is needed: A) Engineering an aaRS to acylate its cognate tRNA with the exotic monomer, without relying on ribosomal translation as a readout, and B) Subsequent engineering of the ribosome to accept the resulting acylated tRNA for translation. Here, we report a platform for aaRS engineering that directly selects for tRNA-acylation without ribosomal translation (START). In START, each distinct aaRS mutant is correlated to a cognate tRNA containing a unique sequence barcode. Acylation by an active aaRS mutant protects the associated barcode-containing tRNAs from an oxidative treatment designed to damage the 3'-terminus of the uncharged tRNAs. Sequencing of these surviving barcode-containing tRNAs is then used to reveal the identity of aaRS mutants that acylated the correlated tRNA sequences. The efficacy of START was demonstrated by identifying novel mutants of the M. alvus pyrrolysyl-tRNA synthetase from a naive library that charge noncanonical amino acids.