Genetically encoding phosphotyrosine and its nonhydrolyzable analog in bacteria (original) (raw)

References

1. Manning, G., Whyte, D.B., Martinez, R., Hunter, T. & Sudarsanam, S. The protein kinase complement of the human genome. Science 298, 1912–1934 (2002).
   Article CAS PubMed Google Scholar
2. Pawson, T. Specificity in signal transduction: from phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 116, 191–203 (2004).
   Article CAS PubMed Google Scholar
3. Hunter, T. & Cooper, J.A. Protein-tyrosine kinases. Annu. Rev. Biochem. 54, 897–930 (1985).
   Article CAS PubMed Google Scholar
4. Alonso, A. et al. Protein tyrosine phosphatases in the human genome. Cell 117, 699–711 (2004).
   Article CAS PubMed Google Scholar
5. Eckhart, W., Hutchinson, M.A. & Hunter, T. An activity phosphorylating tyrosine in polyoma T antigen immunoprecipitates. Cell 18, 925–933 (1979).
   Article CAS PubMed Google Scholar
6. Tailor, P., Gilman, J., Williams, S., Couture, C. & Mustelin, T. Regulation of the low molecular weight phosphotyrosine phosphatase by phosphorylation at tyrosines 131 and 132. J. Biol. Chem. 272, 5371–5374 (1997).
   Article CAS PubMed Google Scholar
7. Feng, G.S., Hui, C.C. & Pawson, T. SH2-containing phosphotyrosine phosphatase as a target of protein-tyrosine kinases. Science 259, 1607–1611 (1993).
   Article CAS PubMed Google Scholar
8. Tarrant, M.K. et al. Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat. Chem. Biol. 8, 262–269 (2012).
   Article CAS PubMed PubMed Central Google Scholar
9. Chen, Z. & Cole, P.A. Synthetic approaches to protein phosphorylation. Curr. Opin. Chem. Biol. 28, 115–122 (2015).
   Article CAS PubMed PubMed Central Google Scholar
10. Serwa, R. et al. Chemoselective Staudinger-phosphite reaction of azides for the phosphorylation of proteins. Angew. Chem. Int. Ed. Engl. 48, 8234–8239 (2009).
    Article CAS PubMed Google Scholar
11. Olsen, J.V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648 (2006).
    Article CAS PubMed Google Scholar
12. Arslan, T., Mamaev, S.V., Mamaeva, N.V. & Hecht, S.M. Structurally modified firefly luciferase. Effects of amino acid substitution at position 286. J. Am. Chem. Soc. 119, 10877–10887 (1997).
    Article CAS Google Scholar
13. Liu, C.C. & Schultz, P.G. Recombinant expression of selectively sulfated proteins in Escherichia coli. Nat. Biotechnol. 24, 1436–1440 (2006).
    Article CAS PubMed Google Scholar
14. Liu, C.C. et al. Protein evolution with an expanded genetic code. Proc. Natl. Acad. Sci. USA 105, 17688–17693 (2008).
    Article CAS PubMed PubMed Central Google Scholar
15. Liu, C.C., Choe, H., Farzan, M., Smider, V.V. & Schultz, P.G. Mutagenesis and evolution of sulfated antibodies using an expanded genetic code. Biochemistry 48, 8891–8898 (2009).
    Article CAS PubMed Google Scholar
16. Liu, C.C., Cellitti, S.E., Geierstanger, B.H. & Schultz, P.G. Efficient expression of tyrosine-sulfated proteins in E. coli using an expanded genetic code. Nat. Protoc. 4, 1784–1789 (2009).
    Article CAS PubMed PubMed Central Google Scholar
17. Liu, C.C., Brustad, E., Liu, W. & Schultz, P.G. Crystal structure of a biosynthetic sulfo-hirudin complexed to thrombin. J. Am. Chem. Soc. 129, 10648–10649 (2007).
    Article CAS PubMed PubMed Central Google Scholar
18. Xie, J., Supekova, L. & Schultz, P.G. A genetically encoded metabolically stable analogue of phosphotyrosine in Escherichia coli. ACS Chem. Biol. 2, 474–478 (2007).
    Article CAS PubMed Google Scholar
19. Rust, H.L. et al. Using unnatural amino acid mutagenesis to probe the regulation of PRMT1. ACS Chem. Biol. 9, 649–655 (2014).
    Article CAS PubMed PubMed Central Google Scholar
20. Guerra-Castellano, A. et al. Mimicking tyrosine phosphorylation in human cytochrome c by the evolved tRNA synthetase technique. Chemistry 21, 15004–15012 (2015).
    Article CAS PubMed Google Scholar
21. Zheng, Y., Lv, X. & Wang, J. A genetically encoded sulfotyrosine for VHR function research. Protein Cell 4, 731–734 (2013).
    Article PubMed PubMed Central Google Scholar
22. Lu, W., Shen, K. & Cole, P.A. Chemical dissection of the effects of tyrosine phosphorylation of SHP-2. Biochemistry 42, 5461–5468 (2003).
    Article CAS PubMed Google Scholar
23. Zhang, Z., Shen, K., Lu, W. & Cole, P.A. The role of C-terminal tyrosine phosphorylation in the regulation of SHP-1 explored via expressed protein ligation. J. Biol. Chem. 278, 4668–4674 (2003).
    Article CAS PubMed Google Scholar
24. Lu, W., Gong, D., Bar-Sagi, D. & Cole, P.A. Site-specific incorporation of a phosphotyrosine mimetic reveals a role for tyrosine phosphorylation of SHP-2 in cell signaling. Mol. Cell 8, 759–769 (2001).
    Article CAS PubMed Google Scholar
25. Leive, L. A nonspecific increase in permeability in Escherichia coli produced by EDTA. Proc. Natl. Acad. Sci. USA 53, 745–750 (1965).
    Article CAS PubMed PubMed Central Google Scholar
26. Fickel, T.E. & Gilvarg, C. Transport of impermeant substances in E. coli by way of oligopeptide permease. Nat. New Biol. 241, 161–163 (1973).
    Article CAS PubMed Google Scholar
27. Ames, B.N., Ames, G.F., Young, J.D., Tsuchiya, D. & Lecocq, J. Illicit transport: the oligopeptide permease. Proc. Natl. Acad. Sci. USA 70, 456–458 (1973).
    Article CAS PubMed PubMed Central Google Scholar
28. Parrish, A.R. et al. Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. ACS Chem. Biol. 7, 1292–1302 (2012).
    Article CAS PubMed PubMed Central Google Scholar
29. Payne, J.W. & Gilvarg, C. The role of the terminal carboxyl group on peptide transport in Escherichia coli. J. Biol. Chem. 243, 335–340 (1968).
    Article CAS PubMed Google Scholar
30. Verkamp, E., Backman, V.M., Björnsson, J.M., Söll, D. & Eggertsson, G. The periplasmic dipeptide permease system transports 5-aminolevulinic acid in Escherichia coli. J. Bacteriol. 175, 1452–1456 (1993).
    Article CAS PubMed PubMed Central Google Scholar
31. Brustad, E. et al. A genetically encoded boronate-containing amino acid. Angew. Chem. Int. Ed. Engl. 47, 8220–8223 (2008).
    Article CAS PubMed PubMed Central Google Scholar
32. 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
33. Zitterbart, R. & Seitz, O. Parallel chemical protein synthesis on a surface enables the rapid analysis of the phosphoregulation of SH3 domains. Angew. Chem. Int. Ed. Engl. 55, 7252–7256 (2016).
    Article CAS PubMed Google Scholar
34. 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
35. Viguera, A.R., Arrondo, J.L.R., Musacchio, A., Saraste, M. & Serrano, L. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry 33, 10925–10933 (1994).
    Article CAS PubMed Google Scholar
36. Young, D.D. et al. An evolved aminoacyl-tRNA synthetase with atypical polysubstrate specificity. Biochemistry 50, 1894–1900 (2011).
    Article CAS PubMed Google Scholar
37. H. S. Lu, C., Liu, K., Tan, L.P. & Yao, S.Q. Current chemical biology tools for studying protein phosphorylation and dephosphorylation. Chemistry 18, 28–39 (2012).
    Article PubMed CAS Google Scholar
38. 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).
    Article CAS PubMed PubMed Central Google Scholar
39. Park, H.-S. et al. Expanding the genetic code of Escherichia coli with phosphoserine. Science 333, 1151–1154 (2011).
    Article CAS PubMed PubMed Central Google Scholar
40. Fan, C., Ip, K. & Söll, D. Expanding the genetic code of Escherichia coli with phosphotyrosine. FEBS Lett. 590, 3040–3047 (2016).
    Article CAS PubMed PubMed Central Google Scholar
41. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
    Article CAS PubMed Google Scholar
42. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
    Article CAS PubMed PubMed Central Google Scholar
43. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
    Article PubMed CAS Google Scholar
44. Vagin, A.A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D Biol. Crystallogr. 60, 2184–2195 (2004).
    Article PubMed CAS Google Scholar
45. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
    Article CAS PubMed Google Scholar
46. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
    Article CAS PubMed PubMed Central Google Scholar

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