page hit counter Efficient genetic code expansion without host genome modifications - CNNNEWS.NEWS

Efficient genetic code expansion without host genome modifications

Efficient genetic code expansion without host genome modifications

Science and Nature news Data availability

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

  1. Chin, J. W. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem. 83, 379–408 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  2. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  3. Wang, L., Brock, A., Herberich, B. & Schultz, P. G. Expanding the genetic code of Escherichia coli. Science 292, 498–500 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  4. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  5. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  6. Johnson, D. B. et al. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat. Chem. Biol. 7, 779–786 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  7. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  8. Chin, J. W. Expanding and reprogramming the genetic code. Nature 550, 53–60 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  9. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  10. Ostrov, N. et al. Synthetic genomes with altered genetic codes. Curr. Opin. Syst. Biol. 24, 32–40 (2020).

    Article 

    Google Scholar
     

  11. Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  12. Zurcher, J. F. et al. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 619, 555–562 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  13. Zhang, Y. et al. A semi-synthetic organism that stores and retrieves increased genetic information. Nature 551, 644–647 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  14. Goto, Y. & Suga, H. The RaPID platform for the discovery of pseudo-natural macrocyclic peptides. Acc. Chem. Res. 54, 3604–3617 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  15. Anderson, J. C. et al. An expanded genetic code with a functional quadruplet codon. Proc. Natl Acad. Sci. USA 101, 7566–7571 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  16. Rackham, O. & Chin, J. W. A network of orthogonal ribosome⋅mRNA pairs. Nat. Chem. Biol. 1, 159–166 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  17. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  18. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  19. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  20. Schmied, W. H. et al. Controlling orthogonal ribosome subunit interactions enables evolution of new function. Nature 564, 444–448 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  21. Aleksashin, N. A. et al. A fully orthogonal system for protein synthesis in bacterial cells. Nat. Commun. 11, 1858 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  22. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  23. Kim, D. S. et al. Three-dimensional structure-guided evolution of a ribosome with tethered subunits. Nat. Chem. Biol. 18, 990–998 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  24. Gamper, H., Masuda, I. & Hou, Y. M. Genome expansion by tRNA +1 frameshifting at quadruplet codons. J. Mol. Biol. 434, 167440 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  25. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  26. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  27. Tuller, T. et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141, 344–354 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  28. Hooper, S. D. & Berg, O. G. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res. 28, 3517–3523 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  29. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  30. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  31. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  32. 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  33. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  34. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  35. 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  36. Bryson, D. I. et al. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat. Chem. Biol. 13, 1253–1260 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  37. 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).

    Article 
    CAS 

 » …
Read More