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All data supporting the findings of this study are available within the article and its Supplementary Information. Select representative plasmids and strains were deposited to Addgene. NGS data were uploaded to the National Center for Biotechnology Information Sequence Read Archive (PRJNA1111233). Source data are provided with this paper.
References
-
Chin, J. W. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem. 83, 379–408 (2014).
-
Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C. & Schultz, P. G. A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244, 182–188 (1989).
-
Wang, L., Brock, A., Herberich, B. & Schultz, P. G. Expanding the genetic code of Escherichia coli. Science 292, 498–500 (2001).
-
Chin, J. W., Martin, A. B., King, D. S., Wang, L. & Schultz, P. G. Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl Acad. Sci. USA 99, 11020–11024 (2002).
-
Young, T. S., Ahmad, I., Yin, J. A. & Schultz, P. G. An enhanced system for unnatural amino acid mutagenesis in E. coli. J. Mol. Biol. 395, 361–374 (2010).
-
Johnson, D. B. et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7, 779–786 (2011).
-
Chatterjee, A., Sun, S. B., Furman, J. L., Xiao, H. & Schultz, P. G. A versatile platform for single- and multiple-unnatural amino acid mutagenesis in Escherichia coli. Biochemistry 52, 1828–1837 (2013).
-
Chin, J. W. Expanding and reprogramming the genetic code. Nature 550, 53–60 (2017).
-
Dumas, A., Lercher, L., Spicer, C. D. & Davis, B. G. Designing logical codon reassignment—expanding the chemistry in biology. Chem. Sci. 6, 50–69 (2015).
-
Ostrov, N. et al. Synthetic genomes with altered genetic codes. Curr. Opin. Syst. Biol. 24, 32–40 (2020).
-
Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).
-
Zurcher, J. F. et al. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 619, 555–562 (2023).
-
Zhang, Y. et al. A semi-synthetic organism that stores and retrieves increased genetic information. Nature 551, 644–647 (2017).
-
Goto, Y. & Suga, H. The RaPID platform for the discovery of pseudo-natural macrocyclic peptides. Acc. Chem. Res. 54, 3604–3617 (2021).
-
Anderson, J. C. et al. An expanded genetic code with a functional quadruplet codon. Proc. Natl Acad. Sci. USA 101, 7566–7571 (2004).
-
Rackham, O. & Chin, J. W. A network of orthogonal ribosome⋅mRNA pairs. Nat. Chem. Biol. 1, 159–166 (2005).
-
Ohtsuki, T., Yamamoto, H., Doi, Y. & Sisido, M. Use of EF-Tu mutants for determining and improving aminoacylation efficiency and for purifying aminoacyl tRNAs with non-natural amino acids. J. Biochem. 148, 239–246 (2010).
-
Neumann, H., Wang, K., Davis, L., Garcia-Alai, M. & Chin, J. W. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464, 441–444 (2010).
-
Agarwal, D., Kamath, D., Gregory, S. T., O’Connor, M. & Gourse, R. L. Modulation of decoding fidelity by ribosomal proteins S4 and S5. J. Bacteriol. 197, 1017–1025 (2015).
-
Schmied, W. H. et al. Controlling orthogonal ribosome subunit interactions enables evolution of new function. Nature 564, 444–448 (2018).
-
Aleksashin, N. A. et al. A fully orthogonal system for protein synthesis in bacterial cells. Nat. Commun. 11, 1858 (2020).
-
Debenedictis, E. A., Carver, G. D., Chung, C. Z., Söll, D. & Badran, A. H. Multiplex suppression of four quadruplet codons via tRNA directed evolution. Nat. Commun. 12, 5706 (2021).
-
Kim, D. S. et al. Three-dimensional structure-guided evolution of a ribosome with tethered subunits. Nat. Chem. Biol. 18, 990–998 (2022).
-
Gamper, H., Masuda, I. & Hou, Y. M. Genome expansion by tRNA +1 frameshifting at quadruplet codons. J. Mol. Biol. 434, 167440 (2022).
-
Hohsaka, T., Ashizuka, Y., Taira, H., Murakami, H. & Sisido, M. Incorporation of nonnatural amino acids into proteins by using various four-base codons in an Escherichia coli in vitro translation system. Biochemistry 40, 11060–11064 (2001).
-
Chatterjee, A., Xiao, H. & Schultz, P. G. Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc. Natl Acad. Sci. USA 109, 14841–14846 (2012).
-
Tuller, T. et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141, 344–354 (2010).
-
Hooper, S. D. & Berg, O. G. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res. 28, 3517–3523 (2000).
-
Gamble, C. E., Brule, C. E., Dean, K. M., Fields, S. & Grayhack, E. J. Adjacent codons act in concert to modulate translation efficiency in yeast. Cell 166, 679–690 (2016).
-
Schinn, S. M. et al. Rapid in vitro screening for the location-dependent effects of unnatural amino acids on protein expression and activity. Biotechnol. Bioeng. 114, 2412–2417 (2017).
-
Xu, H. et al. Re-exploration of the codon context effect on amber codon-guided incorporation of noncanonical amino acids in Escherichia coli by the blue–white screening assay. ChemBioChem 17, 1250–1256 (2016).
-
Pott, M., Schmidt, M. J. & Summerer, D. Evolved sequence contexts for highly efficient amber suppression with noncanonical amino acids. ACS Chem. Biol. 9, 2815–2822 (2014).
-
Bartoschek, M. D. et al. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res. 49, e62 (2021).
-
Dunkelmann, D. L., Oehm, S. B., Beattie, A. T. & Chin, J. W. A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design. Nat. Chem. 13, 1110–1117 (2021).
-
Fluitt, A., Pienaar, E. & Viljoen, H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput. Biol. Chem. 31, 335–346 (2007).
-
Bryson, D. I. et al. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat. Chem. Biol. 13, 1253–1260 (2017).
-
Melnikov, S. V. & Söll, D.Aminoacyl-tRNA synthetases and tRNAs for an expanded genetic code: what makes them orthogonal? Int. J. Mol. Sci. 20, 1929 (2019).