The RNA origin of transfer RNA aminoacylation and beyond

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 366, Issue 1580, 2011, Pages 2959-2964

  Suga, Hiroaki ^a   Hayashi, Gosuke ^a   Terasaka, Naohiro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Flexizyme; Genetic code reprogramming; Ribozyme; RNA world; Translation

Indexed keywords

AMINO ACID; ENZYME ACTIVITY; LABORATORY METHOD; PROTEIN; RNA;

EID: 80052928027     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2011.0137     Document Type: Review

References (40)

1. Nissen, P., Hansen, J., Ban, N., Moore, P. & Steitz, T. 2000 The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930. (doi:10.1126/science.289.5481.920)
2. Illangasekare, M., Sanchez, G., Nickles, T. & Yarus, M. 1995 Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267, 643-647. (doi:10.1126/science.7530860)
3. Schimmel, P., Giegé, R., Moras, D. & Yokoyama, S. 1993 An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl Acad. Sci. USA 90, 8763-8768. (doi:10.1073/pnas.90.19.8763)
4. Piccirilli, J., McConnell, T., Zaug, A., Noller, H. & Cech, T. 1992 Aminoacyl esterase activity of the Tetrahymena ribozyme. Science 256, 1420-1424. (doi:10.1126/science.1604316)
5. DePouplana, L., Turner, R., Steer, B. & Schimmel, P. 1998 Genetic code origins: tRNAs older than their synthetases? Proc. Natl Acad. Sci. USA 95, 11295-11300. (doi:10.1073/pnas.95.19.11295)
6. Illangasekare, M. & Yarus, M. 1999 Specific, rapid synthesis of Phe-RNA by RNA. Proc. Natl Acad. Sci. USA 96, 5470-5475. (doi:10.1073/pnas.96.10.5470)
7. Jenne, A. & Famulok, M. 1998 A novel ribozyme with ester transferase activity. Chem. Biol. 5, 23-34. (doi:10.1016/S1074-5521(98)90084-9)
8. Lee, N., Bessho, Y., Wei, K., Szostak, J. & Suga, H. 2000 Ribozyme-catalyzed tRNA aminoacylation. Nat. Struct. Biol. 7, 28-33. (doi:10.1038/71225)
9. Saito, H., Kourouklis, D. & Suga, H. 2001 An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J. 20, 1797-1806. (doi:10.1093/emboj/20.7.1797)
10. Murakami, H., Saito, H. & Suga, H. 2003 A versatile tRNA aminoacylation catalyst based on RNA. Chem. Biol. 10, 655-662. (doi:10.1016/S1074-5521(03)00145-5)
11. Murakami, H., Ohta, A., Ashigai, H. & Suga, H. 2006 A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat. Methods 3, 357-359. (doi:10.1038/nmeth877)
12. Forster, A., Tan, Z., Nalam, M., Lin, H., Qu, H., Cornish, V. & Blacklow, S. 2003 Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc. Natl Acad. Sci. USA 100, 6353-6357. (doi:10.1073/pnas.1132122100)
13. Josephson, K., Hartman, M. & Szostak, J. 2005 Ribosomal synthesis of unnatural peptides. J. Am. Chem. Soc. 127, 11 727-11 735. (doi:10.1021/ja0515809)
14. Goto, Y., Katoh, T. & Suga, H. 2011 Flexizymes for genetic code reprogramming. Nat. Protoc. 6, 779-790. (doi:10.1038/nprot.2011.331)
15. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. & Ueda, T. 2001 Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751-755. (doi:10.1038/90802)
16. Kumar, R. K. & Yarus, M. 2001 RNA-catalyzed amino acid activation. Biochemistry 40, 6998-7004. (doi:10.1021/bi010710x)
17. Suga, H., Lohse, P. & Szostak, J. 1998 Structural and kinetic characterization of an acyl transferase ribozyme. J. Am. Chem. Soc. 120, 1151-1156. (doi:10.1021/ja972472s)
18. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. 1983 The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857. (doi:10.1016/0092-8674(83)90117-4)
19. Frank, D. & Pace, N. 1998 Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67, 153-180. (doi:10.1146/annurev.biochem.67.1.153)
20. Saito, H., Watanabe, K. & Suga, H. 2001 Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA 7, 1867-1878. (doi:10.1017/S1355838201013164)
21. Saito, H. & Suga, H. 2002 Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme. Nucleic Acids Res. 30, 5151-5159. (doi:10.1093/nar/gkf641)
22. Murakami, H., Kourouklis, D. & Suga, H. 2003 Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code. Chem. Biol. 10, 1077-1084. (doi:10.1016/j.chembiol.2003.10.010)
23. Niwa, N., Yamagishi, Y., Murakami, H. & Suga, H. 2009 A flexizyme that selectively charges amino acids activated by a water-friendly leaving group. Bioorg. Med. Chem. Lett. 19, 3892-3894. (doi:10.1016/j.bmcl.2009.03.114)
24. Goto, Y., Murakami, H. & Suga, H. 2008 Initiating translation with D-amino acids. RNA 14, 1390-1398. (doi:10.1261/rna.1020708)
25. Kawakami, T., Murakami, H. & Suga, H. 2008 Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem. Biol. 15, 32-42. (doi:10.1016/j.chembiol.2007.12.008)
26. Goto, Y., Ohta, A., Sako, Y., Yamagishi, Y., Murakami, H. & Suga, H. 2008 Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem. Biol. 3, 120-129. (doi:10.1021/cb700233t)
27. Noren, C., Anthony-Cahill, S., Griffith, M. & Schultz, P. 1989 A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244, 182-188. (doi:10.1126/science.2649980)
28. Bain, J., Diala, E., Glabe, C., Dix, T. & Chamberlin, A. 1989 Biosynthetic site-specific incorporation of a nonnatural amino acid into a polypeptide. J. Am. Chem. Soc. 111, 8013-8014. (doi:10.1021/ja00202a052)
29. Frankel, A., Millward, S. & Roberts, R. 2003 Encodamers: unnatural peptide oligomers encoded in RNA. Chem. Biol. 10, 1043-1050. (doi:10.1016/j.chembiol.2003.11.004)
30. Tan, Z., Forster, A., Blacklow, S. & Cornish, V. 2004 Amino acid backbone specificity of the Escherichia coli translation machinery. J. Am. Chem. Soc. 126, 12 752-12 753. (doi:10.1021/ja0472174)
31. Heckler, T., Chang, L., Zama, Y., Naka, T., Chorghade, M. & Hecht, S. 1984 T4 RNA ligase mediated preparation of novel 'chemically misacylated' tRNAPheS. Biochemistry 23, 1468-1473. (doi:10.1021/bi00302a020)
32. Robertson, S., Ellman, J. & Schultz, P. 1991 A general and efficient route for chemical aminoacylation of transfer RNAs. J. Am. Chem. Soc. 113, 2722-2729. (doi:10.1021/ja00007a055)
33. Hendrickson, T., de Crecy-Lagard, V. & Schimmel, P. 2004 Incorporation of nonnatural amino acids into proteins. Annu. Rev. Biochem. 73, 147-176. (doi:10.1146/annurev.biochem.73.012803.092429)
34. Wang, L. & Schultz, P. 2005 Expanding the genetic code. Angew. Chem. Int. Ed. 44, 34-66. (doi:10.1002/anie.200460627)
35. Santoro, S., Wang, L., Herberich, B., King, D. & Schultz, P. 2002 An efficient system for the evolution of aminoacyltRNA synthetase specificity. Nat. Biotechnol. 20, 1044-1048. (doi:10.1038/nbt742)
36. Kiga, D. et al. 2002 An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system. Proc. Natl Acad. Sci. USA 99, 9715-9720. (doi:10.1073/pnas.142220099)
37. Link, A. & Tirrell, D. 2005 Reassignment of sense codons in vivo. Methods 36, 291-298. (doi:10.1016/j.ymeth.2005.04.005)
38. Kawakami, T., Ohta, A., Ohuchi, M., Ashigai, H., Murakami, H. & Suga, H. 2009 Diverse backbonecyclized peptides via codon reprogramming. Nat. Chem. Biol. 5, 888-890. (doi:10.1038/nchembio.259)
39. Kawakami, T., Murakami, H. & Suga, H. 2008 Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J. Am. Chem. Soc. 130, 16 861-16 863. (doi:10.1021/ja806998v)
40. Ohta, A., Murakami, H., Higashimura, E. & Suga, H. 2007 Synthesis of polyester by means of genetic code reprogramming. Chem. Biol. 14, 1315-1322. (doi:10.1016/j.chembiol.2007.10.015)