Skip to main content
SpringerLink
Log in

Flexizymes, Their Evolutionary History and Diverse Utilities

  • Chapter
  • First Online:
Aminoacyl-tRNA Synthetases in Biology and Medicine

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 344))

Abstract

In contemporary organisms the aminoacylation of tRNAs is performed exclusively by protein aminoacyl-tRNA synthetases. However, in vitro selection experiments have identified RNA enzymes that exhibit the necessary characteristics to charge tRNA molecules with acyl groups in a way that is compatible with ribosomal translation, suggesting that such ribozymes may have fulfilled this function prior to the evolution of proteinaceous life. The current chapter provides a review of the history, structure, and function of these RNA aminoacyl synthetases, and discusses their practical application to “genetic reprogramming” and other biotechnologies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 299.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 379.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

ABT:

2-Aminoethyl)amidocarboxybenzyl thioester

AMP:

Adenosine monophosphate

ARS:

Aminoacyl-RNA synthetase

cab:

2-Amino-4-(2-chloroacetamido)butanoic acid

CBT:

Chlorobenzyl thioester

CME:

Cyanomethyl ester

DBE:

3,5-Dinitro-benzyl ester

FIT:

Flexible in vitro translation

Gln:

Glutamine

Phe:

Phenylalanine

PheEE:

Phenylalanine ethyl ester

RNase:

Ribonuclease

tRNA:

Transfer RNA

Tyr:

Tyrosine

References

  1. Cech TR (2009) Evolution of biological catalysis: ribozyme to RNP enzyme. Cold Spring Harb Symp Quant Biol 74:11–16

    Article  CAS  Google Scholar 

  2. Illangasekare M, Sanchez G, Nickles T, Yarus M (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267:643–647

    Article  CAS  Google Scholar 

  3. Jenne A, Famulok M (1998) A novel ribozyme with ester transferase activity. Chem Biol 5:23–34

    Article  CAS  Google Scholar 

  4. Lee N, Bessho Y, Wei K, Szostak JW, Suga H (2000) Ribozyme-catalyzed tRNA aminoacylation. Nat Struct Biol 7:28–33

    Article  CAS  Google Scholar 

  5. Saito H, Kourouklis D, Suga H (2001) An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J 20:1797–1806

    Article  CAS  Google Scholar 

  6. Lohse PA, Szostak JW (1996) Ribozyme-catalysed amino-acid transfer reactions. Nature 381:442–444

    Article  CAS  Google Scholar 

  7. Bessho Y, Hodgson DR, Suga H (2002) A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme. Nat Biotechnol 20:723–728

    Article  CAS  Google Scholar 

  8. 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

    Article  CAS  Google Scholar 

  9. Saito H, Watanabe K, Suga H (2001) Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA 7:1867–1878

    CAS  Google Scholar 

  10. Saito H, Suga H (2002) Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme. Nucleic Acids Res 30:5151–5159

    Article  CAS  Google Scholar 

  11. Saito H, Suga H (2001) A ribozyme exclusively aminoacylates the 3′-hydroxyl group of the tRNA terminal adenosine. J Am Chem Soc 123:7178–7179

    Article  CAS  Google Scholar 

  12. Murakami H, Saito H, Suga H (2003) A versatile tRNA aminoacylation catalyst based on RNA. Chem Biol 10:655–662

    Article  CAS  Google Scholar 

  13. 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

    Article  CAS  Google Scholar 

  14. Goto Y, Murakami H, Suga H (2008) Initiating translation with d-amino acids. RNA 14:1390–1398

    Article  CAS  Google Scholar 

  15. 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

    Article  CAS  Google Scholar 

  16. 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

    Article  CAS  Google Scholar 

  17. Kawakami T, Murakami H, Suga H (2008) Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J Am Chem Soc 130:16861–16863

    Article  CAS  Google Scholar 

  18. Ohta A, Murakami H, Higashimura E, Suga H (2007) Synthesis of polyester by means of genetic code reprogramming. Chem Biol 14:1315–1322

    Article  CAS  Google Scholar 

  19. 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

    Article  CAS  Google Scholar 

  20. Xiao H, Murakami H, Suga H, Ferre-D'Amare AR (2008) Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454:358–361

    Article  CAS  Google Scholar 

  21. Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203–206

    Article  CAS  Google Scholar 

  22. Goto Y, Iwasaki K, Torikai K, Murakami H, Suga H (2009) Ribosomal synthesis of dehydrobutyrine- and methyllanthionine-containing peptides. Chem Commun (Camb) 3419–3421

    Google Scholar 

  23. Goto Y, Suga H (2009) Translation initiation with initiator tRNA charged with exotic peptides. J Am Chem Soc 131:5040–5041

    Article  CAS  Google Scholar 

  24. Hayashi Y, Morimoto J, Suga H (2012) In vitro selection of anti-Akt2 thioether-macrocyclic peptides leading to isoform-selective inhibitors. ACS Chem Biol 7:607–613

    Article  CAS  Google Scholar 

  25. Kawakami T, Ohta A, Ohuchi M, Ashigai H, Murakami H, Suga H (2009) Diverse backbone-cyclized peptides via codon reprogramming. Nat Chem Biol 5:888–890

    Article  CAS  Google Scholar 

  26. Morimoto J, Hayashi Y, Suga H (2012) Discovery of macrocyclic peptides armed with a mechanism-based warhead: isoform-selective inhibition of human deacetylase SIRT2. Angew Chem Int Ed Engl 51:3423–3427

    Article  CAS  Google Scholar 

  27. Nakajima E, Goto Y, Sako Y, Murakami H, Suga H (2009) Ribosomal synthesis of peptides with C-terminal lactams, thiolactones, and alkylamides. Chembiochem 10:1186–1192

    Article  CAS  Google Scholar 

  28. Ohshiro Y, Nakajima E, Goto Y, Fuse S, Takahashi T, Doi T, Suga H (2011) Ribosomal synthesis of backbone-macrocyclic peptides containing gamma-amino acids. Chembiochem 12:1183–1187

    Article  CAS  Google Scholar 

  29. Ohta A, Murakami H, Suga H (2008) Polymerization of alpha-hydroxy acids by ribosomes. Chembiochem 9:2773–2778

    Article  CAS  Google Scholar 

  30. Sako Y, Goto Y, Murakami H, Suga H (2008) Ribosomal synthesis of peptidase-resistant peptides closed by a nonreducible inter-side-chain bond. ACS Chem Biol 3:241–249

    Article  CAS  Google Scholar 

  31. Sako Y, Morimoto J, Murakami H, Suga H (2008) Ribosomal synthesis of bicyclic peptides via two orthogonal inter-side-chain reactions. J Am Chem Soc 130:7232–7234

    Article  CAS  Google Scholar 

  32. Yamagishi Y, Ashigai H, Goto Y, Murakami H, Suga H (2009) Ribosomal synthesis of cyclic peptides with a fluorogenic oxidative coupling reaction. Chembiochem 10:1469–1472

    Article  CAS  Google Scholar 

  33. Yamagishi Y, Shoji I, Miyagawa S, Kawakami T, Katoh T, Goto Y, Suga H (2011) Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library. Chem Biol 18:1562–1570

    Article  CAS  Google Scholar 

  34. Goto Y, Katoh T, Suga H (2011) Flexizymes for genetic code reprogramming. Nat Protoc 6:779–790

    Article  CAS  Google Scholar 

  35. Forster AC, Tan Z, Nalam MN, Lin H, Qu H, Cornish VW, Blacklow SC (2003) Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc Natl Acad Sci U S A 100:6353–6357

    Article  CAS  Google Scholar 

  36. Hartman MC, Josephson K, Lin CW, Szostak JW (2007) An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2:e972

    Article  CAS  Google Scholar 

  37. Johnson JA, Lu YY, van Deventer JA, Tirrell DA (2010) Residue-specific incorporation of non-canonical amino acids into proteins: recent developments and applications. Curr Opin Chem Biol 14:774–780

    Article  CAS  Google Scholar 

  38. Datta D, Wang P, Carrico IS, Mayo SL, Tirrell DA (2002) A designed phenylalanyl-tRNA synthetase variant allows efficient in vivo incorporation of aryl ketone functionality into proteins. J Am Chem Soc 124:5652–5653

    Article  CAS  Google Scholar 

  39. Hipolito CJ, Suga H (2012) Ribosomal production and in vitro selection of natural product-like peptidomimetics: the FIT and RaPID systems. Curr Opin Chem Biol 16:196–203

    Article  CAS  Google Scholar 

  40. Reid PC, Goto Y, Katoh T, Suga H (2012) Charging of tRNAs using ribozymes and selection of cyclic peptides containing thioethers. Methods Mol Biol 805:335–348

    Article  CAS  Google Scholar 

  41. Ojemalm K, Higuchi T, Jiang Y, Langel U, Nilsson I, White SH, Suga H, von Heijne G (2011) Apolar surface area determines the efficiency of translocon-mediated membrane-protein integration into the endoplasmic reticulum. Proc Natl Acad Sci U S A 108:E359–E364

    Article  Google Scholar 

  42. Goto Y, Ashigai H, Sako Y, Murakami H, Suga H (2006) Translation initiation by using various N-acylaminoacyl tRNAs. Nucleic Acids Symp Ser (Oxf) 293–294

    Google Scholar 

  43. 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 464:441–444

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the JSPS Grant-in-Aid for the Specially Promoted Research (21000005) and the NRF (R31-2008-000-10103-0) to H.S. and partly supported by JST-CREST, Molecular Technologies.

Author information

Authors and Affiliations

  1. Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo, 113-0033, Japan

    Toby Passioura & Hiroaki Suga

  2. Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Saitama, 332-0012, Japan

    Hiroaki Suga

Authors
  1. Toby Passioura
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hiroaki Suga
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hiroaki Suga .

Editor information

Editors and Affiliations

  1. Department of Molecular Medicine and Biopharmaceutical Sciences, Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Korea, Republic of (South Korea)

    Sunghoon Kim

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Passioura, T., Suga, H. (2013). Flexizymes, Their Evolutionary History and Diverse Utilities. In: Kim, S. (eds) Aminoacyl-tRNA Synthetases in Biology and Medicine. Topics in Current Chemistry, vol 344. Springer, Dordrecht. https://doi.org/10.1007/128_2013_421

Download citation

Publish with us

Policies and ethics

Search

Navigation