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).
Liu, F., Bratulic, S., Costello, A., Miettinen, T. P. & Badran, A. H. Directed evolution of rRNA improves translation kinetics and recombinant protein yield. Nat. Commun. 12, 5638 (2021).
Willis, J. C. W. & Chin, J. W. Mutually orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs. Nat. Chem. 10, 831–837 (2018).
Chatterjee, A., Lajoie, M. J., Xiao, H., Church, G. M. & Schultz, P. G. A bacterial strain with a unique quadruplet codon specifying non‐native amino acids. ChemBioChem 15, 1782–1786 (2014).
Dunkelmann, D. L., Willis, J. C. W., Beattie, A. T. & Chin, J. W. Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. Nat. Chem. 12, 535–544 (2020).
Ikeda-Boku, A. et al. A simple system for expression of proteins containing 3-azidotyrosine at a pre-determined site in Escherichia coli. J. Biochem. 153, 317–326 (2013).
Chatterjee, A., Xiao, H., Yang, P. Y., Soundararajan, G. & Schultz, P. G. A tryptophanyl‐tRNA synthetase/tRNA pair for unnatural amino acid mutagenesis in E. coli. Angew. Chem. Int. Ed. Engl. 52, 5106–5109 (2013).
Hughes, R. A. & Ellington, A. D. Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA. Nucleic Acids Res. 38, 6813–6830 (2010).
Cervettini, D. et al. Rapid discovery and evolution of orthogonal aminoacyl-tRNA synthetase–tRNA pairs. Nat. Biotechnol. 38, 989–999 (2020).
Kwon, I., Wang, P. & Tirrell, D. A. Design of a bacterial host for site-specific incorporation of p-bromophenylalanine into recombinant proteins. J. Am. Chem. Soc. 128, 11778–11783 (2006).
Park, H.-S. et al. Expanding the genetic code of Escherichia coli with phosphoserine. Science 333, 1151–1154 (2011).
Rogerson, D. T. et al. Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog. Nat. Chem. Biol. 11, 496–503 (2015).
Anderson, J. C. & Schultz, P. G. Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression. Biochemistry 42, 9598–9608 (2003).
Liu, D. R. & Schultz, P. G. Progress toward the evolution of an organism with an expanded genetic code. Proc. Natl Acad. Sci. USA 96, 4780–4785 (1999).
Zambaldo, C. et al. An orthogonal seryl-tRNA synthetase/tRNA pair for noncanonical amino acid mutagenesis in Escherichia coli. Bioorg. Med. Chem. 28, 115662 (2020).
Makino, Y. et al. An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism. Nat. Commun. 7, 13446 (2016).
Wang, K. et al. Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat. Chem. 6, 393–403 (2014).
Jaric, J. & Budisa, N. in Hydrocarbon and Lipid Microbiology Protocols (eds McGenity, T. et al.) 71–82 (Springer, 2015).
Wang, J. et al. A biosynthetic route to photoclick chemistry on proteins. J. Am. Chem. Soc. 132, 14812–14818 (2010).
Abdelkader, E. H. et al. Genetic encoding of cyanopyridylalanine for in-cell protein macrocyclization by the nitrile–aminothiol click reaction. Angew. Chem. Int. Ed. Engl. 61, e202114154 (2022).
Xiao, H. et al. Genetic incorporation of histidine derivatives using an engineered pyrrolysyl-tRNA synthetase. ACS Chem. Biol. 9, 1092–1096 (2014).
Yanagisawa, T. et al. Structural basis for genetic-code expansion with bulky lysine derivatives by an engineered pyrrolysyl-tRNA synthetase. Cell Chem. Biol. 26, 936–949 (2019).
Robertson, W. E. et al. Sense codon reassignment enables viral resistance and encoded polymer synthesis. Science 372, 1057–1062 (2021).
Tianero, M. D., Donia, M. S., Young, T. S., Schultz, P. G. & Schmidt, E. W. Ribosomal route to small-molecule diversity. J. Am. Chem. Soc. 134, 418–425 (2012).
Young, T. S. et al. Evolution of cyclic peptide protease inhibitors. Proc. Natl Acad. Sci. USA 108, 11052–11056 (2011).
Vamisetti, G. B. et al. Selective macrocyclic peptide modulators of Lys63-linked ubiquitin chains disrupt DNA damage repair. Nat. Commun. 13, 6174 (2022).
Katoh, T. & Suga, H. In vitro selection of foldamer-like macrocyclic peptides containing 2-aminobenzoic acid and 3-aminothiophene-2-carboxylic acid. J. Am. Chem. Soc. 144, 2069–2072 (2022).
Spinck, M. et al. Genetically programmed cell-based synthesis of non-natural peptide and depsipeptide macrocycles. Nat. Chem. 15, 61–69 (2023).
Townend, J. E. & Tavassoli, A. Traceless production of cyclic peptide libraries in E. coli. ACS Chem. Biol. 11, 1624–1630 (2016).
Miranda, E. et al. A cyclic peptide inhibitor of HIF-1 heterodimerization that inhibits hypoxia signaling in cancer cells. J. Am. Chem. Soc. 135, 10418–10425 (2013).
Cheriyan, M., Pedamallu, C. S., Tori, K. & Perler, F. Faster protein splicing with the Nostoc punctiforme DnaE intein using non-native extein residues. J. Biol. Chem. 288, 6202–6211 (2013).
Stevens, A. J. et al. A promiscuous split intein with expanded protein engineering applications. Proc. Natl Acad. Sci. USA 114, 8538–8543 (2017).
Kolber, N. S., Fattal, R., Bratulic, S., Carver, G. D. & Badran, A. H. Orthogonal translation enables heterologous ribosome engineering in E. coli. Nat. Commun. 12, 599 (2021).
Geu-Flores, F., Nour-Eldin, H. H., Nielsen, M. T. & Halkier, B. A. USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 35, e55 (2007).
