Efficient reassignment of a frequent serine codon in wild-type Escherichia coli.

Expansion of the genetic code through the engineering of the translation machinery has greatly increased the chemical repertoire of the proteome. This has mainly been accomplished by read-through of UAG or UGA stop codons by the non-canonical aminoacyl-tRNA of choice. While stop codon read-through involves competition with the translation release factors, sense codon reassignment entails competition with a large pool of endogenous tRNAs. We used an engineered pyrrolysyl-tRNA synthetase to incorporate 3-iodo-L-phenylalanine (3-I-Phe) at a number of different serine and leucine codons in wild-type Escherichia coli. Quantitative LC-MS/MS measurements of amino acid incorporation yields carried out in a selected reaction monitoring experiment revealed that the 3-I-Phe abundance at the Ser208AGU codon in super-folder GFP was 65±17%. This method also allowed quantification of other amino acids (serine, 33±17%; phenylalanine, 1±1%; threonine, 1±1%) that compete with 3-I-Phe at both the aminoacylation and decoding steps of translation for incorporation at the same codon position. Reassignments of different serine (AGU, AGC, UCG) and leucine (CUG) codons with the matching tRNAPyl anticodon variants were met with varying success, and our findings provide a guideline for the choice of sense codons to be reassigned. Our results indicate that the 3-iodo-L-phenylalanyl-tRNA synthetase (IFRS)/ tRNAPyl pair can efficiently outcompete the cellular machinery to reassign select sense codons in wild-type E. coli.