The Escherichia coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNA EcTyr pair offers an attractive platform for genetically encoding new noncanonical amino acids (ncAA) in eukaryotes. However, challenges associated with a eukaryotic selection system, which is needed to engineer the platform, have impeded its success in the past. Recently, using a facile E. coli -based selection system, we showed that EcTyrRS could be engineered in a strain where the endogenous tyrosyl pair was substituted with an archaeal counterpart. However, significant cross-reactivity between the UAG-suppressing tRNA CUA EcTyr and the bacterial glutaminyl-tRNA synthetase limited the scope of this strategy, preventing the selection of moderately active EcTyrRS mutants. Here we report an engineered tRNA CUA EcTyr that overcomes this cross-reactivity. Optimized selection systems based on this tRNA enabled the efficient enrichment of both strongly and weakly active ncAA-selective EcTyrRS mutants. We also developed a wide dynamic range (WiDR) antibiotic selection to further enhance the activities of the weaker first-generation EcTyrRS mutants. We demonstrated the utility of our platform by developing several new EcTyrRS mutants that efficiently incorporated useful ncAAs in mammalian cells, including photoaffinity probes, bioconjugation handles, and a nonhydrolyzable mimic of phosphotyrosine.

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Site-specific incorporation of multiple distinct noncanonical amino acids (ncAAs) into proteins in mammalian cells is a promising technology, where each ncAA must be assigned to a different orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pair that reads a distinct nonsense codon. Available pairs suppress TGA or TAA codons at a considerably lower efficiency than TAG, limiting the scope of this technology. Here we show that the E. coli tryptophanyl (EcTrp) pair is an excellent TGA-suppressor in mammalian cells, which can be combined with the three other established pairs to develop three new routes for dual-ncAA incorporation. Using these platforms, we site-specifically incorporated two different bioconjugation handles into an antibody with excellent efficiency, and subsequently labeled it with two distinct cytotoxic payloads. Additionally, we combined the EcTrp pair with other pairs to site-specifically incorporate three distinct ncAAs into a reporter protein in mammalian cells.

The site-specific incorporation of multiple distinct noncanonical amino acids (ncAAs) into proteins in mammalian cells is an emergent technology with much potential. For each different ncAA to be incorporated, this technology requires a distinct orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pair that recognizes a distinct nonsense codon. The aaRS/tRNA pairs currently available for ncAA mutagenesis in eukaryotes are all traditionally used to decode the TAG nonsense codon. Unfortunately, these pairs suppress the other two nonsense codons, TGA or TAA, at a significantly lower level, compromising the scope of multi-ncAA mutagenesis. Here we report that the bacteria-derived tryptophanyl (EcTrp) pair is an excellent TGA-suppressor in mammalian cells. Additionally, we show that this pair does not cross-react with any of the three previously established aaRS/tRNA pairs. Consequently, the TGA-suppressing EcTrp pair can be combined with TAG-suppressing pyrrolysyl (archaeal), tyrosyl (bacterial), or leucyl (bacterial) pairs to develop three new routes for dual-ncAA incorporation in mammalian cells. We show that all three platforms enable site-specific incorporation of two distinct ncAAs into proteins – including a full-length humanized antibody – with excellent fidelity and good efficiency. Finally, we combined the EcTrp pair with the bacterial Tyr pair and the archaeal pyrrolysyl pair to site-specifically incorporate different combinations of three distinct ncAAs into a reporter protein in mammalian cells.

The E. coli tyrosyl-tRNA synthetase (EcTyrRS)/tRNAEcTyr pair offers an attractive platform to genetically encode new noncanonical amino acids (ncAA) in eukaryotes. However, challenges associated with a eukaryotic selection system, which is needed for its engineering, has impeded its success in the past. Recently, we showed that EcTyrRS can be engineered using a facile E. coli based selection system, in a strain where the endogenous tyrosyl pair has been substituted with an archaeal counterpart. However, a significant cross-reactivity between the UAG-suppressing tRNACUAEcTyr and the bacterial glutaminyl-tRNA synthetase limited the scope of this strategy, preventing the selection of moderately active EcTyrRS mutants. Here we report an engineered tRNACUAEcTyr that overcomes this cross-reactivity. Optimized selection systems using this tRNA enabled efficient enrichment of both strongly and weakly active ncAA-selective EcTyrRS mutants. We also developed a wide-dynamic range (WiDR) antibiotic selection to further enhance the activities of the weaker first-generation EcTyrRS mutants. We demonstrated the utility of our platform by developing several new EcTyrRS mutants that efficiently incorporate useful ncAAs in mammalian cells, including photo-affinity probes, bioconjugation handles, and a non-hydrolyzable mimic of phosphotyrosine.