Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog (original) (raw)

• 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 Google Scholar
• Olsen, J.V. et al. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635–648 (2006).
  Article CAS Google Scholar
• Cohen, P. The structure and regulation of protein phosphatases. Annu. Rev. Biochem. 58, 453–508 (1989).
  Article CAS Google Scholar
• Ottesen, J.J., Huse, M., Sekedat, M.D. & Muir, T.W. Semisynthesis of phosphovariants of Smad2 reveals a substrate preference of the activated TβRI kinase. Biochemistry 43, 5698–5706 (2004).
  Article CAS Google Scholar
• Hejjaoui, M. et al. Elucidating the role of C-terminal post-translational modifications using protein semisynthesis strategies: α-synuclein phosphorylation at tyrosine 125. J. Am. Chem. Soc. 134, 5196–5210 (2012).
  Article CAS Google Scholar
• Sauerwald, A. et al. RNA-dependent cysteine biosynthesis in archaea. Science 307, 1969–1972 (2005).
  Article CAS Google Scholar
• Chin, J.W. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem. 83, 379–408 (2014).
  Article CAS Google Scholar
• Liu, C.C. & Schultz, P.G. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413–444 (2010).
  Article CAS Google Scholar
• Fukunaga, R. & Yokoyama, S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nat. Struct. Mol. Biol. 14, 272–279 (2007).
  Article CAS Google Scholar
• Park, H.S. et al. Expanding the genetic code of Escherichia coli with phosphoserine. Science 333, 1151–1154 (2011).
  Article CAS Google Scholar
• Lee, S. et al. A facile strategy for selective incorporation of phosphoserine into histones. Angew. Chem. Int. Edn Engl. 52, 5771–5775 (2013).
  Article CAS Google Scholar
• Eargle, J., Black, A.A., Sethi, A., Trabuco, L.G. & Luthey-Schulten, Z. Dynamics of recognition between tRNA and elongation factor Tu. J. Mol. Biol. 377, 1382–1405 (2008).
  Article CAS Google Scholar
• Heinemann, I.U. et al. Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion. FEBS Lett. 586, 3716–3722 (2012).
  Article CAS Google Scholar
• Aerni, H.R., Shifman, M.A., Rogulina, S., O'Donoghue, P. & Rinehart, J. Revealing the amino acid composition of proteins within an expanded genetic code. Nucleic Acids Res. 43, e8 (2015).
  Article Google Scholar
• Wang, K. et al. Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat. Chem. 6, 393–403 (2014).
  Article CAS Google Scholar
• 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 Google Scholar
• Koyano, F. et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510, 162–166 (2014).
  Article CAS Google Scholar
• Kane, L.A. et al. PINK1 phosphorylates ubiquitin to activate parkin E3 ubiquitin ligase activity. J. Cell Biol. 205, 143–153 (2014).
  Article CAS Google Scholar
• Kazlauskaite, A. et al. Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65. Biochem. J. 460, 127–139 (2014).
  Article CAS Google Scholar
• Pizer, L.I. The pathway and control of serine biosynthesis in Escherichia coli. J. Biol. Chem. 238, 3934–3944 (1963).
  CAS PubMed Google Scholar
• Zhang, C.M., Liu, C., Slater, S. & Hou, Y.M. Aminoacylation of tRNA with phosphoserine for synthesis of cysteinyl-tRNA(Cys). Nat. Struct. Mol. Biol. 15, 507–514 (2008).
  Article CAS Google Scholar
• Swanson, R. et al. Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science 242, 1548–1551 (1988).
  Article CAS Google Scholar
• Wang, K., Neumann, H., Peak-Chew, S.Y. & Chin, J.W. Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion. Nat. Biotechnol. 25, 770–777 (2007).
  Article Google Scholar
• Tang, L. et al. Construction of “small-intelligent” focused mutagenesis libraries using well-designed combinatorial degenerate primers. Biotechniques 52, 149–158 (2012).
  Article CAS Google Scholar
• Nguyen, D.P., Garcia Alai, M.M., Kapadnis, P.B., Neumann, H. & Chin, J.W. Genetically encoding _N_ɛ-methyl-L-lysine in recombinant histones. J. Am. Chem. Soc. 131, 14194–14195 (2009).
  Article CAS Google Scholar
• 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 Google Scholar
• Mukai, T. et al. Codon reassignment in the Escherichia coli genetic code. Nucleic Acids Res. 38, 8188–8195 (2010).
  Article CAS Google Scholar
• Lajoie, M.J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).
  Article CAS Google Scholar
• Kondapalli, C. et al. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates parkin E3 ligase activity by phosphorylating serine 65. Open Biol 2, 120080 (2012).
  Article Google Scholar
• Valente, E.M. et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 304, 1158–1160 (2004).
  Article CAS Google Scholar
• Wauer, T. et al. Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. EMBO J. 34, 307–325 (2015).
  Article CAS Google Scholar
• Belham, C. et al. A mitotic cascade of NIMA family kinases. Nercc1/Nek9 activates the Nek6 and Nek7 kinases. J. Biol. Chem. 278, 34897–34909 (2003).
  Article CAS Google Scholar
• O'Regan, L. & Fry, A.M. The Nek6 and Nek7 protein kinases are required for robust mitotic spindle formation and cytokinesis. Mol. Cell. Biol. 29, 3975–3990 (2009).
  Article CAS Google Scholar
• Richards, M.W. et al. An autoinhibitory tyrosine motif in the cell-cycle-regulated Nek7 kinase is released through binding of Nek9. Mol. Cell 36, 560–570 (2009).
  Article CAS Google Scholar
• Liu, F. et al. Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat. Chem. Biol. 7, 595–601 (2011).
  Article CAS Google Scholar
• Klingberg, R. et al. Analysis of phosphorylation-dependent protein-protein interactions of histone H3. ACS Chem. Biol. 10, 138–145 (2015).
  Article CAS Google Scholar
• Neumann, H., Slusarczyk, A.L. & Chin, J.W. De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA Pairs. J. Am. Chem. Soc. 132, 2142–2144 (2010).
  Article CAS Google Scholar
• Hohn, M.J., Park, H.S., O'Donoghue, P., Schnitzbauer, M. & Soll, D. Emergence of the universal genetic code imprinted in an RNA record. Proc. Natl. Acad. Sci. USA 103, 18095–18100 (2006).
  Article CAS Google Scholar
• Stemmer, W.P. & Morris, S.K. Enzymatic inverse PCR: a restriction site independent, single-fragment method for high-efficiency, site-directed mutagenesis. Biotechniques 13, 214–220 (1992).
  CAS PubMed Google Scholar