1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Biochemistry
  4. Volume 83, 2014
  5. Article

Annual Review of Biochemistry

Volume 83, 2014

Expanding and Reprogramming the Genetic Code of Cells and Animals

Abstract

Genetic code expansion and reprogramming enable the site-specific incorporation of diverse designer amino acids into proteins produced in cells and animals. Recent advances are enhancing the efficiency of unnatural amino acid incorporation by creating and evolving orthogonal ribosomes and manipulating the genome. Increasing the number of distinct amino acids that can be site-specifically encoded has been facilitated by the evolution of orthogonal quadruplet decoding ribosomes and the discovery of mutually orthogonal synthetase/tRNA pairs. Rapid progress in moving genetic code expansion from bacteria to eukaryotic cells and animals ( and ) and the incorporation of useful unnatural amino acids has been aided by the development and application of the pyrrolysyl–transfer RNA (tRNA) synthetase/tRNA pair for unnatural amino acid incorporation. Combining chemoselective reactions with encoded amino acids has facilitated the installation of posttranslational modifications, as well as rapid derivatization with diverse fluorophores for imaging.

Keyword(s): amino acid, aminoacyl-tRNA synthetase, bioorthogonal reaction, genetic code expansion, posttranslational modification, protein chemistry, protein labeling, ribosome, synthetic biology, tRNA
Loading

Article metrics loading...

/content/journals/10.1146/annurev-biochem-060713-035737
2014-06-02
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/biochem/83/1/annurev-biochem-060713-035737.html?itemId=/content/journals/10.1146/annurev-biochem-060713-035737&mimeType=html&fmt=ahah

Literature Cited

  1. Davis L, Chin JW. 1.  2012. Designer proteins: applications of genetic code expansion in cell biology. Nat. Rev. Mol. Cell Biol. 13:168–82 [Google Scholar]
  2. Liu CC, Schultz PG. 2.  2010. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79:413–44 [Google Scholar]
  3. Xie J, Schultz PG. 3.  2005. An expanding genetic code. Methods 36:227–38 [Google Scholar]
  4. Chin JW.4.  2003. An expanded eukaryotic genetic code. Science 301:964–67 [Google Scholar]
  5. Chin JW, Cropp TA, Chu S, Meggers E, Schultz PG. 5.  2003. Progress toward an expanded eukaryotic genetic code. Chem. Biol. 10:511–19 [Google Scholar]
  6. Wu N, Deiters A, Cropp TA, King D, Schultz PG. 6.  2004. A genetically encoded photocaged amino acid. J. Am. Chem. Soc. 126:14306–7 [Google Scholar]
  7. Neumann H, Peak-Chew SY, Chin JW. 7.  2008. Genetically encoding Nϵ-acetyllysine in recombinant proteins. Nat. Chem. Biol. 4:232–34 [Google Scholar]
  8. Edwards H, Schimmel P. 8.  1990. A bacterial amber suppressor in Saccharomyces cerevisiae is selectively recognized by a bacterial aminoacyl-tRNA synthetase. Mol. Cell. Biol. 10:1633–41 [Google Scholar]
  9. Edwards H, Trezeguet V, Schimmel P. 9.  1991. An Escherichia coli tyrosine transfer RNA is a leucine-specific transfer RNA in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88:1153–56 [Google Scholar]
  10. Trezeguet V, Edwards H, Schimmel P. 10.  1991. A single base pair dominates over the novel identity of an Escherichia coli tyrosine tRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 11:2744–51 [Google Scholar]
  11. Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H. 11.  et al. 2002. Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res. 30:4692–99 [Google Scholar]
  12. Liu W, Brock A, Chen S, Chen S, Schultz PG. 12.  2007. Genetic incorporation of unnatural amino acids into proteins in mammalian cells. Nat. Methods 4:239–44 [Google Scholar]
  13. Hancock SM, Uprety R, Deiters A, Chin JW. 13.  2010. Expanding the genetic code of yeast for incorporation of diverse unnatural amino acids via a pyrrolysyl-tRNA synthetase/tRNA pair. J. Am. Chem. Soc. 132:14819–24 [Google Scholar]
  14. Mukai T, Kobayashi T, Hino N, Yanagisawa T, Sakamoto K, Yokoyama S. 14.  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]
  15. Chen PR, Groff D, Guo J, Ou W, Cellitti S. 15.  et al. 2009. A facile system for encoding unnatural amino acids in mammalian cells. Angew. Chem. Int. Ed. 48:4052–55 [Google Scholar]
  16. Gautier A, Nguyen DP, Lusic H, An W, Deiters A, Chin JW. 16.  2010. Genetically encoded photocontrol of protein localization in mammalian cells. J. Am. Chem. Soc. 132:4086–68 [Google Scholar]
  17. Greiss S, Chin JW. 17.  2011. Expanding the genetic code of an animal. J. Am. Chem. Soc. 133:14196–99 [Google Scholar]
  18. Bianco A, Townsley FM, Greiss S, Lang K, Chin JW. 18.  2012. Expanding the genetic code of Drosophila melanogaster. Nat. Chem. Biol. 8:748–50 [Google Scholar]
  19. Hao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK. 19.  2002. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296:1462–66 [Google Scholar]
  20. Wang L, Brock A, Herberich B, Schultz PG. 20.  2001. Expanding the genetic code of Escherichia coli. Science 292:498–500 [Google Scholar]
  21. Chin JW, Martin AB, King DS, Wang L, Schultz PG. 21.  2002. Addition of a photocrosslinking amino acid to the genetic code of Escherichia coli. Proc. Natl. Acad. Sci. USA 99:11020–24 [Google Scholar]
  22. Lin S, Zhang Z, Xu H, Li L, Chen S. 22.  et al. 2011. Site-specific incorporation of photo-cross-linker and bioorthogonal amino acids into enteric bacterial pathogens. J. Am. Chem. Soc. 133:20581–87 [Google Scholar]
  23. Farrell IS, Toroney R, Hazen JL, Mehl RA, Chin JW. 23.  2005. Photo-cross-linking interacting proteins with a genetically encoded benzophenone. Nat. Methods 2:377–84 [Google Scholar]
  24. Young TS, Ahmad I, Yin JA, Schultz PG. 24.  2010. An enhanced system for unnatural amino acid mutagenesis in E. coli. J. Mol. Biol. 395:361–74 [Google Scholar]
  25. Chatterjee A, Sun SB, Furman JL, Xiao H, Schultz PG. 25.  2013. A versatile platform for single- and multiple-unnatural amino acid mutagenesis in Escherichia coli. Biochemistry 52:1828–37 [Google Scholar]
  26. LaRiviere FJ, Wolfson AD, Uhlenbeck OC. 26.  2001. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 294:165–68 [Google Scholar]
  27. Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM. 27.  et al. 2011. Expanding the genetic code of Escherichia coli with phosphoserine. Science 333:1151–54 [Google Scholar]
  28. Ryden SM, Isaksson LA. 28.  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]
  29. Rackham O, Chin JW. 29.  2005. A network of orthogonal ribosome × mRNA pairs. Nat. Chem. Biol. 1:159–66 [Google Scholar]
  30. An W, Chin JW. 30.  2009. Synthesis of orthogonal transcription-translation networks. Proc. Natl. Acad. Sci. USA 106:8477–82 [Google Scholar]
  31. An W, Chin JW. 31.  2011. Orthogonal gene expression in Escherichia coli. Methods Enzymol. 497:115–34 [Google Scholar]
  32. Rackham O, Chin JW. 32.  2005. Cellular logic with orthogonal ribosomes. J. Am. Chem. Soc. 127:17584–85 [Google Scholar]
  33. Rackham O, Chin JW. 33.  2006. Synthesizing cellular networks from evolved ribosome–mRNA pairs. Biochem. Soc. Trans. 34:328–29 [Google Scholar]
  34. Rackham O, Wang K, Chin JW. 34.  2006. Functional epitopes at the ribosome subunit interface. Nat. Chem. Biol. 2:254–58 [Google Scholar]
  35. Wang K, Neumann H, Peak-Chew SY, Chin JW. 35.  2007. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25:770–77 [Google Scholar]
  36. Neumann H, Wang K, Davis L, Garcia-Alai M, Chin JW. 36.  2010. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464:441–44 [Google Scholar]
  37. Mukai T, Hayashi A, Iraha F, Sato A, Ohtake K. 37.  et al. 2010. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res. 38:8188–95 [Google Scholar]
  38. Mukai T, Yanagisawa T, Ohtake K, Wakamori M, Adachi J. 38.  et al. 2011. Genetic-code evolution for protein synthesis with non-natural amino acids. Biochem. Biophys. Res. Commun. 411:757–61 [Google Scholar]
  39. Ohtake K, Sato A, Mukai T, Hino N, Yokoyama S, Sakamoto K. 39.  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]
  40. Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD. 40.  et al. 2011. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7:779–86 [Google Scholar]
  41. Wu IL, Patterson MA, Carpenter Desai HE, Mehl RA, Giorgi G, Conticello VP. 41.  2013. Multiple site-selective insertions of noncanonical amino acids into sequence-repetitive polypeptides. Eur. J. Chem. Biol. 14:968–78 [Google Scholar]
  42. Heinemann IU, Rovner AJ, Aerni HR, Rogulina S, Cheng L. 42.  et al. 2012. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett. 586:3716–22 [Google Scholar]
  43. Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B. 43.  et al. 2011. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333:348–53 [Google Scholar]
  44. Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM. 44.  et al. 2006. Emergent properties of reduced-genome Escherichia coli. Science 312:1044–46 [Google Scholar]
  45. Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ. 45.  et al. 2012. Release factor one is nonessential in Escherichia coli. Am. Chem. Soc. Chem. Biol. 7:1337–44 [Google Scholar]
  46. Anderson JC, Wu N, Santoro SW, Lakshman V, King DS, Schultz PG. 46.  2004. An expanded genetic code with a functional quadruplet codon. Proc. Natl. Acad. Sci. USA 101:7566–71 [Google Scholar]
  47. Wan W, Huang Y, Wang Z, Russell WK, Pai PJ. 47.  et al. 2010. A facile system for genetic incorporation of two different noncanonical amino acids into one protein in Escherichia coli. Angew. Chem. 49:3211–14 [Google Scholar]
  48. Wu B, Wang Z, Huang Y, Liu WR. 48.  2012. Catalyst-free and site-specific one-pot dual-labeling of a protein directed by two genetically incorporated noncanonical amino acids. Eur. J. Chem. Biol. 13:1405–8 [Google Scholar]
  49. Kim CH, Axup JY, Schultz PG. 49.  2013. Protein conjugation with genetically encoded unnatural amino acids. Curr. Opin. Chem. Biol. 17:412–19 [Google Scholar]
  50. Ribas de Pouplana L, Schimmel P. 50.  2001. Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends Biochem. Sci. 26:591–96 [Google Scholar]
  51. Neumann H, Slusarczyk AL, Chin JW. 51.  2010. De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. J. Am. Chem. Soc. 132:2142–44 [Google Scholar]
  52. Chatterjee A, Xiao H, Schultz PG. 52.  2012. Evolution of multiple, mutually orthogonal prolyl-tRNA synthetase/tRNA pairs for unnatural amino acid mutagenesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 109:14841–46 [Google Scholar]
  53. Nguyen DP, Lusic H, Neumann H, Kapadnis PB, Deiters A, Chin JW. 53.  2009. Genetic encoding and labeling of aliphatic azides and alkynes in recombinant proteins viaa pyrrolysyl-tRNA synthetase/tRNACUA pair and click chemistry. J. Am. Chem. Soc. 131:8720–21 [Google Scholar]
  54. Chin JW, Santoro SW, Martin AB, King DS, Wang L, Schultz PG. 54.  2002. Addition of p-azido-l-phenylalanine to the genetic code of Escherichia coli. J. Am. Chem. Soc. 124:9026–27 [Google Scholar]
  55. Chen HT, Warfield L, Hahn S. 55.  2007. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat. Struct. Mol. Biol. 14:696–703 [Google Scholar]
  56. Wang Q, Wang L. 56.  2008. New methods enabling efficient incorporation of unnatural amino acids in yeast. J. Am. Chem. Soc. 130:6066–67 [Google Scholar]
  57. Hino N, Okazaki Y, Kobayashi T, Hayashi A, Sakamoto K, Yokoyama S. 57.  2005. Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nat. Methods 2:201–6 [Google Scholar]
  58. Mukai T, Wakiyama M, Sakamoto K, Yokoyama S. 58.  2010. Genetic encoding of non-natural amino acids in Drosophila melanogaster Schneider 2 cells. Protein Sci. 19:440–48 [Google Scholar]
  59. Wang W, Takimoto JK, Louie GV, Baiga TJ, Noel JP. 59.  et al. 2007. Genetically encoding unnatural amino acids for cellular and neuronal studies. Nat. Neurosci. 10:1063–72 [Google Scholar]
  60. Nguyen DP, Elliott T, Holt M, Muir TW, Chin JW. 60.  2011. Genetically encoded 1,2-aminothiols facilitate rapid and site-specific protein labeling via a bio-orthogonal cyanobenzothiazole condensation. J. Am. Chem. Soc. 133:11418–21 [Google Scholar]
  61. Lang K, Davis L, Wallace S, Mahesh M, Cox DJ. 61.  et al. 2012. Genetic encoding of bicyclononynes and trans-cyclooctenes for site-specific protein labeling in vitro and in live mammalian cells via rapid fluorogenic Diels–Alder reactions. J. Am. Chem. Soc. 134:10317–20 [Google Scholar]
  62. Lang K, Davis L, Torres-Kolbus J, Chou C, Deiters A, Chin JW. 62.  2012. Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction. Nat. Chem. 4:298–304 [Google Scholar]
  63. Plass T, Milles S, Koehler C, Szymański J, Mueller R. 63.  et al. 2012. Amino acids for Diels-Alder reactions in living cells. Angew. Chem. Int. Ed. 51:4166–70 [Google Scholar]
/content/journals/10.1146/annurev-biochem-060713-035737
Loading
Expanding and Reprogramming the Genetic Code of Cells and Animals
Annual Review of Biochemistry 83, 379 (2014); https://doi.org/10.1146/annurev-biochem-060713-035737
/content/journals/10.1146/annurev-biochem-060713-035737
/content/journals/10.1146/annurev-biochem-060713-035737
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error