Abstract
Genetic code expansion enables the site-specific incorporation of noncanonical amino acids (ncAAs) into proteins both in vitro and in vivo. In addition to a widely applied nonsense suppression strategy, the use of quadruplet codons could further expand the genetic code. A general approach to genetically incorporate ncAAs in response to quadruplet codons is achieved by utilizing an engineered aminoacyl-tRNA synthetase (aaRS) together with a tRNA variant containing an expanded anticodon loop. Here we provide a protocol to decode quadruplet UAGA codon with a ncAA in mammalian cells. We also describe microscopy imaging and flow cytometry analysis of ncAA mutagenesis in response to quadruplet codons.
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References
Young DD, Schultz PG (2018) Playing with the molecules of life. ACS Chem Biol 13(4):854–870. https://doi.org/10.1021/acschembio.7b00974
Mukai T, Lajoie MJ, Englert M, Soll D (2017) Rewriting the genetic code. Annu Rev Microbiol 71:557–577. https://doi.org/10.1146/annurev-micro-090816-093247
Chin JW (2017) Expanding and reprogramming the genetic code. Nature 550(7674):53–60. https://doi.org/10.1038/nature24031
Wang K, Schmied WH, Chin JW (2012) Reprogramming the genetic code: from triplet to quadruplet codes. Angew Chem Int Ed 51(10):2288–2297. https://doi.org/10.1002/anie.201105016
Guo J, Niu W (2022) Genetic code expansion through quadruplet codon decoding. J Mol Biol 434(8):167346. https://doi.org/10.1016/j.jmb.2021.167346
Anderson JC, Wu N, Santoro SW, Lakshman V, King DS, Schultz PG (2004) An expanded genetic code with a functional quadruplet codon. Proc Natl Acad Sci U S A 101(20):7566–7571. https://doi.org/10.1073/pnas.0401517101
Neumann H, Wang K, Davis L, Garcia-Alai M, Chin JW (2010) Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464(7287):441–444. https://doi.org/10.1038/nature08817
Rackham O, Chin JW (2005) A network of orthogonal ribosome·mRNA pairs. Nat Chem Biol 1(3):159–166. https://doi.org/10.1038/nchembio719
Wang K, Sachdeva A, Cox DJ, Wilf NM, Lang K, Wallace S, Mehl RA, Chin JW (2014) Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 6(5):393–403. https://doi.org/10.1038/nchem.1919
Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG (2014) A bacterial strain with a unique quadruplet codon specifying non-native amino acids. Chembiochem 15(12):1782–1786. https://doi.org/10.1002/cbic.201402104
Wang N, Shang X, Cerny R, Niu W, Guo J (2016) Systematic evolution and study of UAGN decoding tRNAs in a genomically recoded bacteria. Sci Rep 6:21898. https://doi.org/10.1038/srep21898
Hankore ED, Zhang L, Chen Y, Liu K, Niu W, Guo J (2019) Genetic incorporation of noncanonical amino acids using two mutually orthogonal quadruplet codons. ACS Synth Biol 8(5):1168–1174. https://doi.org/10.1021/acssynbio.9b00051
Dunkelmann DL, Willis JCW, Beattie AT, Chin JW (2020) Engineered triply orthogonal pyrrolysyl-tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. Nat Chem 12(6):535–544. https://doi.org/10.1038/s41557-020-0472-x
Dunkelmann DL, Oehm SB, Beattie AT, Chin JW (2021) A 68-codon genetic code to incorporate four distinct non-canonical amino acids enabled by automated orthogonal mRNA design. Nat Chem 13(11):1110–1117. https://doi.org/10.1038/s41557-021-00764-5
Niu W, Schultz PG, Guo J (2013) An expanded genetic code in mammalian cells with a functional quadruplet codon. ACS Chem Biol 8(7):1640–1645. https://doi.org/10.1021/cb4001662
Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J (2018) Controlling the replication of a Genomically recoded HIV-1 with a functional quadruplet codon in mammalian cells. ACS Synth Biol 7(6):1612–1617. https://doi.org/10.1021/acssynbio.8b00096
Mills EM, Barlow VL, Jones AT, Tsai Y-H (2021) Development of mammalian cell logic gates controlled by unnatural amino acids. Cell Rep Methods 1:100073
Xi Z, Davis L, Baxter K, Tynan A, Goutou A, Greiss S (2021) Using a quadruplet codon to expand the genetic code of an animal. bioRxiv. https://doi.org/10.1101/2021.07.17.452788
Chen Y, Wan Y, Wang N, Yuan Z, Niu W, Li Q, Guo J (2018) Controlling the replication of a genomically recoded HIV-1 with a functional quadruplet codon in mammalian cells. ACS Synth Biol 7:1612–1617
Serfling R, Lorenz C, Etzel M, Schicht G, Boettke T, Moerl M, Coin I (2018) Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells. Nucleic Acids Res 46(1):1–10. https://doi.org/10.1093/nar/gkx1156
Acknowledgments
This work was supported by the National Science Foundation (grant 1553041 to J.G.), National Institute of Health (grant 1R01GM138623 to J.G. and W.N.), and NIH National Institutes of General Medical Sciences (grant P20 GM113126 to J.G. and W.N.).
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Chen, Y., Gao, T., He, X., Niu, W., Guo, J. (2023). Genetic Code Expansion in Mammalian Cells Through Quadruplet Codon Decoding. In: Tsai, YH., Elsässer, S.J. (eds) Genetically Incorporated Non-Canonical Amino Acids. Methods in Molecular Biology, vol 2676. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3251-2_13
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DOI: https://doi.org/10.1007/978-1-0716-3251-2_13
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