Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness

Despite the potential advantages of encoding protein sequences with an expanded alphabet that includes new amino acids with unique side chain properties, the genetic code consisting of the common 20 amino acids is nearly universally conserved in living organisms. Post-translational modifications augment the chemical repertoire of proteins in an ad hoc manner, but truly expanded genetic codes that enable direct ribosomal incorporation of a 21st amino acid into proteins are found rarely in nature and only partially reassign shared codons. Technologies exist to synthetically add a non-canonical amino acid (ncAA) to a genetic code by introducing an orthogonal aminoacyl-tRNA synthetase (aaRS) and a cognate tRNA recognizing the amber stop codon. To date, these systems have been too inefficient and genetically unstable to examine how the proteomes of organisms will evolve to adjust to and utilize a newly expanded genetic code. Here we show that T7 bacteriophages evolved on an Escherichia coli host that incorporates 3-iodotyrosine at amber codons became dependent on an alternative genetic code as they adapted to higher fitness. The evolutionary response included compensatory mutations that restored native protein termination and substitutions of amber codons in key viral genes. In particular, a 3-iodotyrosine substitution in the T7 type II holin protein was associated with more rapid lysis times and phage with this mutation were more fit than isogenic phage with canonical amino acids tolerated at this position. Thus, the expanded genetic code created new possibilities for adaptive mutations. It is now possible to thaw the "frozen accident" that resulted in a genetic code with the 20 common amino acids to examine how new chemical functionalities influence the evolutionary potential of proteins and entire organisms.

Reference:
Hammerling, M. J. et al. Bacteriophages use an expanded genetic code on evolutionary paths to
higher fitness. Nat. Chem. Biol. 10, 178–80 (2014).