Rewriting the Genetic Code

Literature Cited

1. Acevedo-Rocha CG, Budisa N. 1.  2016. Xenomicrobiology: a roadmap for genetic code engineering. Microb. Biotechnol. 9:666–76 [Google Scholar]
2. Aldag C, Bröcker MJ, Hohn MJ, Prat L, Hammond G. 2.  et al. 2013. Rewiring translation for elongation factor Tu-dependent selenocysteine incorporation. Angew. Chem. Int. Ed. Engl. 52:1441–45 [Google Scholar]
3. Amiram M, Haimovich AD, Fan C, Wang Y-S, Aerni H-R. 3.  et al. 2015. Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat. Biotechnol. 33:1272–79 [Google Scholar]
4. Asano K, Mizobuchi K. 4.  1998. Copy number control of IncIα plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site. EMBO J 17:5201–13 [Google Scholar]
5. Atkins JF, Baranov PV. 5.  2010. The distinction between recoding and codon reassignment. Genetics 185:1535–36 [Google Scholar]
6. Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW. 6.  et al. 2016. Alternative Watson–Crick synthetic genetic systems. Cold Spring Harb. Perspect. Biol. 8:a023770 [Google Scholar]
7. Berry MJ, Banu L, Chen YY, Mandel SJ, Kieffer JD. 7.  et al. 1991. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature 353:273–76 [Google Scholar]
8. Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ. 8.  et al. 2016. Accurate de novo design of hyperstable constrained peptides. Nature 538:329–35 [Google Scholar]
9. Biddle W, Schmitt MA, Fisk JD. 9.  2016. Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. Nucleic Acids Res 44:10042–50 [Google Scholar]
10. Brar GA. 10.  2016. Beyond the triplet code: Context cues transform translation. Cell 167:1681–92 [Google Scholar]
11. Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A. 11.  et al. 2013. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. PNAS 110:5540–45 [Google Scholar]
12. Caron F, Meyer E. 12.  1985. Does Paramecium primaurelia use a different genetic code in its macronucleus?. Nature 314:185–88 [Google Scholar]
13. Cellitti SE, Ou W, Chiu HP, Grünewald J, Jones DH. 13.  et al. 2011. d-Ornithine coopts pyrrolysine biosynthesis to make and insert pyrroline-carboxy-lysine. Nat. Chem. Biol. 7:528–30 [Google Scholar]
14. Chen T, Hongdilokkul N, Liu Z, Thirunavukarasu D, Romesberg FE. 14.  2016. The expanding world of DNA and RNA. Curr. Opin. Chem. Biol. 34:80–87 [Google Scholar]
15. Chin JW. 15.  2014. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem. 83:379–408 [Google Scholar]
16. Chin JW, Cropp TA, Anderson JC, Mukherji M, Zhang Z, Schultz PG. 16.  2003. An expanded eukaryotic genetic code. Science 301:964–67 [Google Scholar]
17. Cocquyt E, Gile GH, Leliaert F, Verbruggen H, Keeling PJ, De Clerck O. 17.  2010. Complex phylogenetic distribution of a non-canonical genetic code in green algae. BMC Evol. Biol. 10:327 [Google Scholar]
18. Costantino N, Court DL. 18.  2003. Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants. PNAS 100:15748–53 [Google Scholar]
19. de Koning AP, Noble GP, Heiss AA, Wong J, Keeling PJ. 19.  2008. Environmental PCR survey to determine the distribution of a non-canonical genetic code in uncultivable oxymonads. Environ. Microbiol. 10:65–74 [Google Scholar]
20. Dedkova LM, Fahmi NE, Golovine SY, Hecht SM. 20.  2003. Enhanced d-amino acid incorporation into protein by modified ribosomes. J. Am. Chem. Soc. 125:6616–17 [Google Scholar]
21. Dedkova LM, Fahmi NE, Golovine SY, Hecht SM. 21.  2006. Construction of modified ribosomes for incorporation of d-amino acids into proteins. Biochemistry 45:15541–51 [Google Scholar]
22. Dedkova LM, Fahmi NE, Paul R, del Rosario M, Zhang L. 22.  et al. 2012. β-Puromycin selection of modified ribosomes for in vitro incorporation of β-amino acids. Biochemistry 51:401–15 [Google Scholar]
23. Doi Y, Ohtsuki T, Shimizu Y, Ueda T, Sisido M. 23.  2007. Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system. J. Am. Chem. Soc. 129:14458–62 [Google Scholar]
24. Dong H, Nilsson L, Kurland CG. 24.  1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260:649–63 [Google Scholar]
25. Döring V, Mootz HD, Nangle LA, Hendrickson TL, de Crécy-Lagard V. 25.  et al. 2001. Enlarging the amino acid set of Escherichia coli by infiltration of the valine coding pathway. Science 292:501–4 [Google Scholar]
26. Dumas A, Lercher L, Spicer CD, Davis BG. 26.  2015. Designing logical codon reassignment—expanding the chemistry in biology. Chem. Sci. 6:50–69 [Google Scholar]
27. Dymond JS, Richardson SM, Coombes CE, Babatz T, Müller H. 27.  et al. 2011. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477:471–76 [Google Scholar]
28. Ellefson JW, Meyer AJ, Hughes RA, Cannon JR, Brodbelt JS, Ellington AD. 28.  2014. Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat. Biotechnol. 32:97–101 [Google Scholar]
29. Esvelt KM, Carlson JC, Liu DR. 29.  2011. A system for the continuous directed evolution of biomolecules. Nature 472:499–503 [Google Scholar]
30. Fahnestock S, Rich A. 30.  1971. Ribosome-catalyzed polyester formation. Science 173:340–43 [Google Scholar]
31. Fan C, Ho JM, Chirathivat N, Söll D, Wang YS. 31.  2014. Exploring the substrate range of wild-type aminoacyl-tRNA synthetases. ChemBioChem 15:1805–9 [Google Scholar]
32. Fan C, Ip K, Söll D. 32.  2016. Expanding the genetic code of Escherichia coli with phosphotyrosine. FEBS Lett 590:3040–47 [Google Scholar]
33. Fischer N, Neumann P, Bock LV, Maracci C, Wang Z. 33.  et al. 2016. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 540:80–85 [Google Scholar]
34. Forster AC, Church GM. 34.  2006. Towards synthesis of a minimal cell. Mol. Syst. Biol. 2:45 [Google Scholar]
35. Fournier GP, Andam CP, Gogarten JP. 35.  2015. Ancient horizontal gene transfer and the last common ancestors. BMC Evol. Biol. 15:70 [Google Scholar]
36. Fried SD, Schmied WH, Uttamapinant C, Chin JW. 36.  2015. Ribosome subunit stapling for orthogonal translation in E. coli. Angew. Chem. Int. Ed. Engl. 54:12791–94 [Google Scholar]
37. Gan R, Perez JG, Carlson ED, Ntai I, Isaacs FJ. 37.  et al. 2016. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins. Biotechnol. Bioeng. 114:1074–86 [Google Scholar]
38. Gaston MA, Zhang L, Green-Church KB, Krzycki JA. 38.  2011. The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine. Nature 471:647–50 [Google Scholar]
39. Giegé R, Sissler M, Florentz C. 39.  1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 26:5017–35 [Google Scholar]
40. Grosjean H, Westhof E. 40.  2016. An integrated, structure- and energy-based view of the genetic code. Nucleic Acids Res 44:8020–40 [Google Scholar]
41. Guo J, Wang J, Anderson JC, Schultz PG. 41.  2008. Addition of an α-hydroxy acid to the genetic code of bacteria. Angew. Chem. Int. Ed. Engl. 47:722–25 [Google Scholar]
42. Guo LT, Wang YS, Nakamura A, Eiler D, Kavran JM. 42.  et al. 2014. Polyspecific pyrrolysyl-tRNA synthetases from directed evolution. PNAS 111:16724–29 [Google Scholar]
43. Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE. 43.  2014. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nat. Chem. Biol. 10:178–80 [Google Scholar]
44. Haruna K, Alkazemi MH, Liu Y, Söll D, Englert M. 44.  2014. Engineering the elongation factor Tu for efficient selenoprotein synthesis. Nucleic Acids Res 42:9976–83 [Google Scholar]
45. Heaphy SM, Mariotti M, Gladyshev VN, Atkins JF, Baranov PV. 45.  2016. Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in Condylostoma magnum. Mol. Biol. Evol. 33:2885–89 [Google Scholar]
46. Himeno H, Nameki N, Kurita D, Muto A, Abo T. 46.  2015. Ribosome rescue systems in bacteria. Biochimie 114:102–12 [Google Scholar]
47. Hoesl MG, Oehm S, Durkin P, Darmon E, Peil L. 47.  et al. 2015. Chemical evolution of a bacterial proteome. Angew. Chem. Int. Ed. Engl. 54:10030–34 [Google Scholar]
48. Hui AS, Eaton DH, de Boer HA. 48.  1988. Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli. EMBO J. 7:4383–88 [Google Scholar]
49. Ikeda-Boku A, Ohno S, Hibino Y, Yokogawa T, Hayashi N, Nishikawa K. 49.  2013. A simple system for expression of proteins containing 3-azidotyrosine at a pre-determined site in Escherichia coli. J. Biochem. 153:317–26 [Google Scholar]
50. Iraha F, Oki K, Kobayashi T, Ohno S, Yokogawa T. 50.  et al. 2010. Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNA^Tyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion. Nucleic Acids Res 38:3682–91 [Google Scholar]
51. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B. 51.  et al. 2011. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333:348–53 [Google Scholar]
52. Italia JS, Addy PS, Wrobel CJJ, Crawford CC, Lajoie MJ. 52.  et al. 2017. An orthogonalized platform for genetic code expansion in both bacteria and eukaryotes. Nat. Chem. Biol. 13:446–50 [Google Scholar]
53. Ito K, Uno M, Nakamura Y. 53.  1998. Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. PNAS 95:8165–69 [Google Scholar]
54. Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A. 54.  et al. 2014. Stop codon reassignments in the wild. Science 344:909–13 [Google Scholar]
55. Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ. 55.  et al. 2012. Release factor one is nonessential in Escherichia coli. ACS Chem. Biol. 7:1337–44 [Google Scholar]
56. Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD. 56.  et al. 2011. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7:779–86 [Google Scholar]
57. Johnson JA, Lu YY, Van Deventer JA, Tirrell DA. 57.  2010. Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications. Curr. Opin. Chem. Biol. 14:774–80 [Google Scholar]
58. Kane JF. 58.  1995. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol. 6:494–500 [Google Scholar]
59. Karpov SA, Mikhailov KV, Mirzaeva GS, Mirabdullaev IM, Mamkaeva KA. 59.  et al. 2013. Obligately phagotrophic aphelids turned out to branch with the earliest-diverging fungi. Protist 164:195–205 [Google Scholar]
60. Kawaguchi Y, Honda H, Taniguchi-Morimura J, Iwasaki S. 60.  1989. The codon CUG is read as serine in an asporogenic yeast Candida cylindracea. Nature 341:164–66 [Google Scholar]
61. Keeling PJ. 61.  2016. Genomics: evolution of the genetic code. Curr. Biol. 26:R851–53 [Google Scholar]
62. Keeling PJ, Doolittle WF. 62.  1997. Widespread and ancient distribution of a noncanonical genetic code in diplomonads. Mol. Biol. Evol. 14:895–901 [Google Scholar]
63. Kollmar M, Mühlhausen S. 63.  2017. Nuclear codon reassignments in the genomics era and mechanisms behind their evolution. BioEssays 39:1600221 [Google Scholar]
64. Krishnakumar R, Prat L, Aerni HR, Ling J, Merryman C. 64.  et al. 2013. Transfer RNA misidentification scrambles sense codon recoding. ChemBioChem 14:1967–72 [Google Scholar]
65. Kuthning A, Durkin P, Oehm S, Hoesl MG, Budisa N, Sussmuth RD. 65.  2016. Towards biocontained cell factories: An evolutionarily adapted Escherichia coli strain produces a new-to-nature bioactive lantibiotic containing thienopyrrole-alanine. Sci. Rep. 6:33447 [Google Scholar]
66. Kuznetsov G, Goodman DB, Filsinger GT, Landon M, Rohland N. 66.  et al. 2017. Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biol. 18:100
67. Kwon I, Kirshenbaum K, Tirrell DA. 67.  2003. Breaking the degeneracy of the genetic code. J. Am. Chem. Soc. 125:7512–13 [Google Scholar]
68. Lajoie MJ, Kosuri S, Mosberg JA, Gregg CJ, Zhang D, Church GM. 68.  2013. Probing the limits of genetic recoding in essential genes. Science 342:361–63 [Google Scholar]
69. Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD. 69.  et al. 2013. Genomically recoded organisms expand biological functions. Science 342:357–60 [Google Scholar]
70. Lajoie MJ, Söll D, Church GM. 70.  2016. Overcoming challenges in engineering the genetic code. J. Mol. Biol. 428:1004–21 [Google Scholar]
71. Lau YH, Stirling F, Kuo J, Karrenbelt MAP, Chan YA. 71.  et al. 2017. Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA. Nucleic Acids Res 45:6971–-80 [Google Scholar]
72. Lee S, Oh S, Yang A, Kim J, Söll D. 72.  et al. 2013. A facile strategy for selective incorporation of phosphoserine into histones. Angew. Chem. Int. Ed. Engl. 52:5771–75 [Google Scholar]
73. Lemeignan B, Sonigo P, Marlière P. 73.  1993. Phenotypic suppression by incorporation of an alien amino acid. J. Mol. Biol. 231:161–66 [Google Scholar]
74. Lennen RM, Wallin AI, Pedersen M, Bonde M, Luo H. 74.  et al. 2016. Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects. Nucleic Acids Res 44:e36 [Google Scholar]
75. Ling J, Daoud R, Lajoie MJ, Church GM, Söll D, Lang BF. 75.  2014. Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Res 42:499–508 [Google Scholar]
76. Ling J, O'Donoghue P, Söll D. 76.  2015. Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology. Nat. Rev. Microbiol. 13:707–21 [Google Scholar]
77. Liu CC, Schultz PG. 77.  2010. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79:413–44 [Google Scholar]
78. Liu DR, Magliery TJ, Pastrnak M, Schultz PG. 78.  1997. Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo. PNAS 94:10092–97 [Google Scholar]
79. Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S. 79.  et al. 2017. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat. Struct. Mol. Biol. 24:61–68 [Google Scholar]
80. Lu C. 80.  2016. Imaginary proteins made real. Cell 164:7 [Google Scholar]
81. Ma NJ, Isaacs FJ. 81.  2016. Genomic recoding broadly obstructs the propagation of horizontally transferred genetic elements. Cell Syst 3:199–207 [Google Scholar]
82. Mandell DJ, Lajoie MJ, Mee MT, Takeuchi R, Kuznetsov G. 82.  et al. 2015. Biocontainment of genetically modified organisms by synthetic protein design. Nature 518:55–60 [Google Scholar]
83. Maranhao AC, Ellington AD. 83.  2016. Evolving orthogonal suppressor tRNAs to incorporate modified amino acids. ACS Synth. Biol. 6:108–19 [Google Scholar]
84. Mat WK, Xue H, Wong JT. 84.  2010. Genetic code mutations: the breaking of a three billion year invariance. PLOS ONE 5:e12206 [Google Scholar]
85. Mehl RA, Anderson JC, Santoro SW, Wang L, Martin AB. 85.  et al. 2003. Generation of a bacterium with a 21 amino acid genetic code. J. Am. Chem. Soc. 125:935–39 [Google Scholar]
86. Melo Czekster C, Robertson WE, Walker AS, Söll D, Schepartz A. 86.  2016. In vivo biosynthesis of a β-amino acid-containing protein. J. Am. Chem. Soc. 138:5194–97 [Google Scholar]
87. Merkel L, Schauer M, Antranikian G, Budisa N. 87.  2010. Parallel incorporation of different fluorinated amino acids: on the way to “Teflon” proteins. ChemBioChem 11:1505–7 [Google Scholar]
88. Meyer F, Schmidt HJ, Plümper E, Hasilik A, Mersmann G. 88.  et al. 1991. UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus. PNAS 88:3758–61 [Google Scholar]
89. Miller C, Bröcker MJ, Prat L, Ip K, Chirathivat N. 89.  et al. 2015. A synthetic tRNA for EF-Tu mediated selenocysteine incorporation in vivo and in vitro. FEBS Lett 589:2194–99 [Google Scholar]
90. Mills JH, Khare SD, Bolduc JM, Forouhar F, Mulligan VK. 90.  et al. 2013. Computational design of an unnatural amino acid dependent metalloprotein with atomic level accuracy. J. Am. Chem. Soc. 135:13393–99 [Google Scholar]
91. Mora L, Heurgué-Hamard V, de Zamaroczy M, Kervestin S, Buckingham RH. 91.  2007. Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J. Biol. Chem. 282:35638–45 [Google Scholar]
92. Mühlhausen S, Findeisen P, Plessmann U, Urlaub H, Kollmar M. 92.  2016. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes. Genome Res 26:945–55 [Google Scholar]
93. Mukai T, Crnković A, Umehara T, Ivanova NN, Kyrpides NC, Söll D. 93.  2017. RNA-dependent cysteine biosynthesis in bacteria and archaea. mBio 8:e00561–17 [Google Scholar]
94. Mukai T, Englert M, Tripp HJ, Miller C, Ivanova NN. 94.  et al. 2016. Facile recoding of selenocysteine in nature. Angew. Chem. Int. Ed. Engl. 55:5337–41 [Google Scholar]
95. Mukai T, Hayashi A, Iraha F, Sato A, Ohtake K. 95.  et al. 2010. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res 38:8188–95 [Google Scholar]
96. Mukai T, Hoshi H, Ohtake K, Takahashi M, Yamaguchi A. 96.  et al. 2015. Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon. Sci. Rep. 5:9699 [Google Scholar]
97. Mukai T, Kobayashi T, Hino N, Yanagisawa T, Sakamoto K, Yokoyama S. 97.  2008. Adding l-lysine derivatives to the genetic code of mammalian cells with engineered pyrrolysyl-tRNA synthetases. Biochem. Biophys. Res. Commun. 371:818–22 [Google Scholar]
98. Mukai T, Vargas-Rodriguez O, Englert M, Tripp HJ, Ivanova NN. 98.  et al. 2016. Transfer RNAs with novel cloverleaf structures. Nucleic Acids Res 45:2776–85 [Google Scholar]
99. Mukai T, Yamaguchi A, Ohtake K, Takahashi M, Hayashi A. 99.  et al. 2015. Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli. Nucleic Acids Res. 43:8111–22 [Google Scholar]
100. Mukai T, Yanagisawa T, Ohtake K, Wakamori M, Adachi J. 100.  et al. 2011. Genetic-code evolution for protein synthesis with non-natural amino acids. Biochem. Biophys. Res. Commun. 411:757–61 [Google Scholar]
101. Nakano S, Suzuki T, Kawarada L, Iwata H, Asano K, Suzuki T. 101.  2016. NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA^Met. Nat. Chem. Biol. 12:546–51 [Google Scholar]
102. Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L. 102.  et al. 2016. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli. PNAS 113:E5588–97 [Google Scholar]
103. Neumann H, Peak-Chew SY, Chin JW. 103.  2008. Genetically encoding N^ε-acetyllysine in recombinant proteins. Nat. Chem. Biol. 4:232–34 [Google Scholar]
104. Neumann H, Wang K, Davis L, Garcia-Alai M, Chin JW. 104.  2010. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464:441–44 [Google Scholar]
105. Norville JE, Gardner CL, Aponte E, Camplisson CK, Gonzales A. 105.  et al. 2016. Assembly of radically recoded E. coli genome segments. bioRxiv 070417. https://doi.org/10.1101/070417 [Crossref]
106. O'Donoghue P, Ling J, Wang YS, Söll D. 106.  2013. Upgrading protein synthesis for synthetic biology. Nat. Chem. Biol. 9:594–98 [Google Scholar]
107. O'Donoghue P, Prat L, Heinemann IU, Ling J, Odoi K. 107.  et al. 2012. Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNA^Pyl for genetic code expansion. FEBS Lett 586:3931–37 [Google Scholar]
108. Ohtake K, Sato A, Mukai T, Hino N, Yokoyama S, Sakamoto K. 108.  2012. Efficient decoding of the UAG triplet as a full-fledged sense codon enhances the growth of a prfA-deficient strain of Escherichia coli. J. Bacteriol 194:2606–13 [Google Scholar]
109. Ohtake K, Yamaguchi A, Mukai T, Kashimura H, Hirano N. 109.  et al. 2015. Protein stabilization utilizing a redefined codon. Sci. Rep. 5:9762 [Google Scholar]
110. Oki K, Sakamoto K, Kobayashi T, Sasaki HM, Yokoyama S. 110.  2008. Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog. PNAS 105:13298–303 [Google Scholar]
111. Orelle C, Carlson ED, Szal T, Florin T, Jewett MC, Mankin AS. 111.  2015. Protein synthesis by ribosomes with tethered subunits. Nature 524:119–24 [Google Scholar]
112. Osawa S, Jukes TH, Watanabe K, Muto A. 112.  1992. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56:229–64 [Google Scholar]
113. Ostrov N, Landon M, Guell M, Kuznetsov G, Teramoto J. 113.  et al. 2016. Design, synthesis, and testing toward a 57-codon genome. Science 353:819–22 [Google Scholar]
114. Packer MS, Liu DR. 114.  2015. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16:379–94 [Google Scholar]
115. Pánek T, Žihala D, Sokol M, Derelle R, Klimeš V. 115.  et al. 2017. Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biol 15:8 [Google Scholar]
116. Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM. 116.  et al. 2011. Expanding the genetic code of Escherichia coli with phosphoserine. Science 333:1151–54 [Google Scholar]
117. Pearson AD, Mills JH, Song Y, Nasertorabi F, Han GW. 117.  et al. 2015. Trapping a transition state in a computationally designed protein bottle. Science 347:863–67 [Google Scholar]
118. Peyru GM, Maas WK. 118.  1967. Inhibition of Escherichia coli B by homoarginine. J. Bacteriol. 94:712–18 [Google Scholar]
119. Preer JR Jr., Preer LB, Rudman BM, Barnett AJ. 119.  1985. Deviation from the universal code shown by the gene for surface protein 51A in Paramecium. Nature 314:188–90 [Google Scholar]
120. Quax TE, Claassens NJ, Söll D, van der Oost J. 120.  2015. Codon bias as a means to fine-tune gene expression. Mol. Cell 59:149–61 [Google Scholar]
121. Rackham O, Chin JW. 121.  2005. A network of orthogonal ribosome·mRNA pairs. Nat. Chem. Biol. 1:159–66 [Google Scholar]
122. Rauch BJ, Porter JJ, Mehl RA, Perona JJ. 122.  2016. Improved incorporation of noncanonical amino acids by an engineered tRNA^Tyr suppressor. Biochemistry 55:618–28 [Google Scholar]
123. Richardson CJ, First EA. 123.  2016. Hyperactive editing domain variants switch the stereospecificity of tyrosyl-tRNA synthetase. Biochemistry 55:2526–37 [Google Scholar]
124. Richardson SM, Mitchell LA, Stracquadanio G, Yang K, Dymond JS. 124.  et al. 2017. Design of a synthetic yeast genome. Science 355:1040–44 [Google Scholar]
125. Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT. 125.  et al. 2016. Comparative genomics of biotechnologically important yeasts. PNAS 113:9882–87 [Google Scholar]
126. Rogers JM, Suga H. 126.  2015. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org. Biomol. Chem. 13:9353–63 [Google Scholar]
127. Rovner AJ, Haimovich AD, Katz SR, Li Z, Grome MW. 127.  et al. 2015. Recoded organisms engineered to depend on synthetic amino acids. Nature 518:89–93 [Google Scholar]
128. Rydén SM, Isaksson LA. 128.  1984. A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors. Mol. Gen. Genet. 193:38–45 [Google Scholar]
129. Sakamoto K. 129.  2016. Innovative technology for recombinant protein production using engineered E.coli genetic codes. Kagaku Seibutsu 54:343–50 [Google Scholar]
130. Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H. 130.  et al. 2002. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 30:4692–99 [Google Scholar]
131. Schultz DW, Yarus M. 131.  1994. Transfer RNA mutation and the malleability of the genetic code. J. Mol. Biol. 235:1377–80 [Google Scholar]
132. Singh V, Braddick D. 132.  2015. Recent advances and versatility of MAGE towards industrial applications. Syst. Synth. Biol. 9:Suppl. 11–9 [Google Scholar]
133. Suzuki T, Numata T. 133.  2014. Convergent evolution of AUA decoding in bacteria and archaea. RNA Biol 11:1586–96 [Google Scholar]
134. Swart EC, Serra V, Petroni G, Nowacki M. 134.  2016. Genetic codes with no dedicated stop codon: context-dependent translation termination. Cell 166:691–702 [Google Scholar]
135. Tack DS, Ellefson JW, Thyer R, Wang B, Gollihar J. 135.  et al. 2016. Addicting diverse bacteria to a noncanonical amino acid. Nat. Chem. Biol. 12:138–40 [Google Scholar]
136. Terasaka N, Hayashi G, Katoh T, Suga H. 136.  2014. An orthogonal ribosome-tRNA pair via engineering of the peptidyl transferase center. Nat. Chem. Biol. 10:555–57 [Google Scholar]
137. Terasaka N, Iwane Y, Geiermann AS, Goto Y, Suga H. 137.  2015. Recent developments of engineered translational machineries for the incorporation of non-canonical amino acids into polypeptides. Int. J. Mol. Sci. 16:6513–31 [Google Scholar]
138. Thyer R, Filipovska A, Rackham O. 138.  2013. Engineered rRNA enhances the efficiency of selenocysteine incorporation during translation. J. Am. Chem. Soc. 135:2–5 [Google Scholar]
139. Thyer R, Robotham SA, Brodbelt JS, Ellington AD. 139.  2015. Evolving tRNA^Sec for efficient canonical incorporation of selenocysteine. J. Am. Chem. Soc. 137:46–49 [Google Scholar]
140. Tian F, Tsao ML, Schultz PG. 140.  2004. A phage display system with unnatural amino acids. J. Am. Chem. Soc. 126:15962–63 [Google Scholar]
141. Tizei PA, Csibra E, Torres L, Pinheiro VB. 141.  2016. Selection platforms for directed evolution in synthetic biology. Biochem. Soc. Trans. 44:1165–75 [Google Scholar]
142. Tuorto F, Lyko F. 142.  2016. Genome recoding by tRNA modifications. Open. Biol. 6:160287 [Google Scholar]
143. Turanov AA, Lobanov AV, Fomenko DE, Morrison HG, Sogin ML. 143.  et al. 2009. Genetic code supports targeted insertion of two amino acids by one codon. Science 323:259–61 [Google Scholar]
144. Ugwumba IN, Ozawa K, Xu ZQ, Ely F, Foo JL. 144.  et al. 2011. Improving a natural enzyme activity through incorporation of unnatural amino acids. J. Am. Chem. Soc. 133:326–33 [Google Scholar]
145. Uno M, Ito K, Nakamura Y. 145.  1996. Functional specificity of amino acid at position 246 in the tRNA mimicry domain of bacterial release factor 2. Biochimie 78:935–43 [Google Scholar]
146. Uyeda A, Watanabe T, Kato Y, Watanabe H, Yomo T. 146.  et al. 2015. Liposome-based in vitro evolution of aminoacyl-tRNA synthetase for enhanced pyrrolysine derivative incorporation. ChemBioChem 16:1797–802 [Google Scholar]
147. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. 147.  2012. Genome-scale promoter engineering by coselection MAGE. Nat. Methods 9:591–93 [Google Scholar]
148. Wang HH, Xu G, Vonner AJ, Church G. 148.  2011. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res 39:7336–47 [Google Scholar]
149. Wang K, Fredens J, Brunner SF, Kim SH, Chia T, Chin JW. 149.  2016. Defining synonymous codon compression schemes by genome recoding. Nature 539:59–64 [Google Scholar]
150. Wang K, Neumann H, Peak-Chew SY, Chin JW. 150.  2007. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25:770–77 [Google Scholar]
151. Wang K, Schmied WH, Chin JW. 151.  2012. Reprogramming the genetic code: from triplet to quadruplet codes. Angew. Chem. Int. Ed. Engl. 51:2288–97 [Google Scholar]
152. Wang L, Brock A, Herberich B, Schultz PG. 152.  2001. Expanding the genetic code of Escherichia coli. Science 292:498–500 [Google Scholar]
153. Xiang Z, Ren H, Hu YS, Coin I, Wei J. 153.  et al. 2013. Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. Nat. Methods 10:885–88 [Google Scholar]
154. Xiao H, Nasertorabi F, Choi SH, Han GW, Reed SA. 154.  et al. 2015. Exploring the potential impact of an expanded genetic code on protein function. PNAS 112:6961–66 [Google Scholar]
155. Yamao F, Muto A, Kawauchi Y, Iwami M, Iwagami S. 155.  et al. 1985. UGA is read as tryptophan in Mycoplasma capricolum. PNAS 82:2306–9 [Google Scholar]
156. Yu AC, Yim AK, Mat WK, Tong AH, Lok S. 156.  et al. 2014. Mutations enabling displacement of tryptophan by 4-fluorotryptophan as a canonical amino acid of the genetic code. Genome Biol. Evol. 6:629–41 [Google Scholar]
157. Záhonová K, Kostygov AY, Ševčíková T, Yurchenko V, Eliáš M. 157.  2016. An unprecedented non-canonical nuclear genetic code with all three termination codons reassigned as sense codons. Curr. Biol. 26:2364–69 [Google Scholar]
158. Zhang Y, Baranov PV, Atkins JF, Gladyshev VN. 158.  2005. Pyrrolysine and selenocysteine use dissimilar decoding strategies. J. Biol. Chem. 280:20740–51 [Google Scholar]