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General Introduction

  • Naohiro TerasakaEmail author
Chapter
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Part of the Springer Theses book series (Springer Theses)

Abstract

Transfer RNA (tRNA) is one of the most abundant and popular noncoding RNA (ncRNA), which works as an adaptor molecule linking a nucleotide to an amino acid in the translation step. The 3′-end of tRNA is universally conserved as CCA-3′ and forms base pairs with ribosomal RNA during the translation. If the easy method to prepare various aa-tRNA bearing mutations in the CCA-3′ end, it is usable for analyzing the role of CCA-3′ end during the translation and engineering the translation machinery. Recently, various small noncoding RNAs have been identified and the function of those RNAs have been studied. However, it is not easy to discover the small ncRNAs with very low abundance because tRNAs are too much abundant in small RNA fraction (less than 200 nt). To overcome this problem, easy method to remove tRNAs from small RNA fraction is required. In order to solve these problems, I focused on flexizymes that are aminoacylation ribozymes developed by in vitro selection. Flexizymes have following unique characteristics: (i) substrate RNA is recognized by two consecutive base pairs between 3′-end of substrate RNA and 3′-end of flexizyme, (ii) these base pairs can be substituted with other base pairs and (iii) various activated amino acids can be used as substrates including both canonical and noncanonical amino acids. Therefore, flexizymes enable to label all endogenous tRNAs bearing CCA-3′ end with ncAAs to be removed, and to aminoacylate CCA-3′ mutated tRNAs by compensatory mutations to engineer the translation machinery.

Keywords

Ribozyme MicroRNA SELEX tRNA Ribosome Translation 

References

  1. Agresti JJ, Kelly BT, Jaschke A, Griffiths AD (2005) Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc Natl Acad Sci USA 102(45):16170–16175. doi: 10.1073/pnas.0503733102 CrossRefGoogle Scholar
  2. Amaral PP, Mattick JS (2008) Noncoding RNA in development. Mamm Genome 19(7–8):454–492. doi: 10.1007/s00335-008-9136-7 CrossRefGoogle Scholar
  3. Ambrogelly A, Palioura S, Söll D (2006) Natural expansion of the genetic code. Nat Chem Biol 3(1):29–35. doi: 10.1038/nchembio847 CrossRefGoogle Scholar
  4. Cavarelli J, Moras D (1993) Recognition of tRNAs by aminoacyl-tRNA synthetases. FASEB J 7(1):79–86Google Scholar
  5. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey DK, Ganesh M, Ghosh S, Bell I, Gerhard DS, Gingeras TR (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308(5725):1149–1154. doi: 10.1126/science.1108625 CrossRefGoogle Scholar
  6. Chumachenko N, Novikov Y, Yarus M (2009) Rapid and simple ribozymic aminoacylation using three conserved nucleotides. J Am Chem Soc 131(14):5257–5263. doi: 10.1021/ja809419f CrossRefGoogle Scholar
  7. Collins FS, Lander ES, Rogers J, Waterston RH, Conso IHGS (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011):931–945. doi: 10.1038/Nature03001 CrossRefGoogle Scholar
  8. Doudna J, Cech T (2002) The chemical repertoire of natural ribozymes. Nature 418(6894):222–228. doi: 10.1038/418222a CrossRefGoogle Scholar
  9. Ellington A, Szostak J (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818–822. doi: 10.1038/346818a0 CrossRefGoogle Scholar
  10. Esteller M (2011) Noncoding RNAs in human disease. Nat Rev Genet 12(12):861–874. doi: 10.1038/Nrg3074 CrossRefGoogle Scholar
  11. Goto Y, Suga H (2009) Translation initiation with initiator tRNA charged with exotic peptides. J Am Chem Soc 131(14):5040–5041. doi: 10.1021/ja900597d CrossRefGoogle Scholar
  12. Goto Y, Murakami H, Suga H (2008a) Initiating translation with d-amino acids. RNA 14(7):1390–1398. doi: 10.1261/rna.1020708 CrossRefGoogle Scholar
  13. Goto Y, Ohta A, Sako Y, Yamagishi Y, Murakami H, Suga H (2008b) Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem Biol 3(2):120–129. doi: 10.1021/cb700233t CrossRefGoogle Scholar
  14. 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(3 Pt 2):849–857. doi: 10.1016/0092-8674(83)90117-4 CrossRefGoogle Scholar
  15. Hecht SM, Alford BL, Kuroda Y, Kitano S (1978) “Chemical aminoacylation” of tRNA’s. J Biol Chem 253(10):4517–4520Google Scholar
  16. Huang Y, Zhang JL, Yu XL, Xu TS, Wang ZB, Cheng XC (2013) Molecular functions of small regulatory noncoding RNA. Biochemistry 78(3):221–230. doi: 10.1134/S0006297913030024 Google Scholar
  17. Illangasekare M, Yarus M (1999) A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5(11):1482–1489. doi: 10.1017/S1355838299991264 CrossRefGoogle Scholar
  18. Illangasekare M, Sanchez G, Nickles T, Yarus M (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267(5198):643–647. doi: 10.1126/science.7530860 CrossRefGoogle Scholar
  19. Illangasekare M, Kovalchuke O, Yarus M (1997) Essential structures of a self-aminoacylating RNA. J Mol Biol 274(4):519–529. doi: 10.1006/jmbi.1997.1414 CrossRefGoogle Scholar
  20. Johnston W, Unrau P, Lawrence M, Glasner M, Bartel D (2001) RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292(5520):1319–1325. doi: 10.1126/science.1060786 CrossRefGoogle Scholar
  21. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484–1488. doi: 10.1126/science.1138341 CrossRefGoogle Scholar
  22. Kawakami T, Ishizawa T, Murakami H (2013) Extensive Reprogramming of the genetic code for genetically encoded synthesis of highly N-Alkylated polycyclic peptidomimetics. J Am Chem Soc 135(33):12297–12304. doi: 10.1021/Ja405044k CrossRefGoogle Scholar
  23. Kawakami T, Murakami H, Suga H (2008a) Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem Biol 15(1):32–42. doi: 10.1016/j.chembiol.2007.12.008 CrossRefGoogle Scholar
  24. Kawakami T, Murakami H, Suga H (2008b) Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J Am Chem Soc 130(50):16861–16863. doi: 10.1021/ja806998v CrossRefGoogle 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(12):888–890. doi: 10.1038/nchembio.259 CrossRefGoogle Scholar
  26. Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42(D1):D68–D73. doi: 10.1093/Nar/Gkt1181 CrossRefGoogle Scholar
  27. Kruger K, Grabowski P, Zaug A, Sands J, Gottschling D, Cech T (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1):147–157. doi: 10.1016/0092-8674(82)90414-7 CrossRefGoogle Scholar
  28. Kumar R, Yarus M (2001) RNA-catalyzed amino acid activation. Biochemistry 40(24):6998–7004. doi: 10.1021/bi010710x CrossRefGoogle Scholar
  29. Lee N, Bessho Y, Wei K, Szostak J, Suga H (2000) Ribozyme-catalyzed tRNA aminoacylation. Nat Struct Biol 7(1):28–33. doi: 10.1038/71225 CrossRefGoogle Scholar
  30. Lindberg J, Lundeberg J (2010) The plasticity of the mammalian transcriptome. Genomics 95(1):1–6. doi: 10.1016/j.ygeno.2009.08.010 CrossRefGoogle Scholar
  31. Liu M, Horowitz J (1994) Functional transfer RNAs with modifications in the 3′-CCA end: differential effects on aminoacylation and polypeptide synthesis. Proc Natl Acad Sci USA 91(22):10389–10393. doi: 10.2307/2366033 CrossRefGoogle Scholar
  32. Lodder M, Wang BX, Hecht SM (2005) The N-pentenoyl protecting group for aminoacyl-tRNAs. Methods 36(3):245–251. doi: 10.1016/j.ymeth.2005.04.002 CrossRefGoogle Scholar
  33. Marck C, Grosjean H (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8(10):1189–1232. doi: 10.1017/S1355838202022021 CrossRefGoogle Scholar
  34. Matera AG, Terns RM, Terns MP (2007) Noncoding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat Rev Mol Cell Biol 8(3):209–220. doi: 10.1038/Nrm2124 CrossRefGoogle Scholar
  35. Mattick JS, Makunin IV (2006) Noncoding RNA. Hum Mol Genet 15:R17–R29. doi: 10.1093/Hmg/Ddl046 CrossRefGoogle Scholar
  36. Mercer TR, Dinger ME, Mattick JS (2009) Long noncoding RNAs: insights into functions. Nat Rev Genet 10(3):155–159. doi: 10.1038/Nrg2521 CrossRefGoogle Scholar
  37. Murakami H, Ohta A, Ashigai H, Suga H (2006) A highly flexible tRNA acylation method for nonnatural polypeptide synthesis. Nat Methods 3(5):357–359. doi: 10.1038/nmeth877 CrossRefGoogle Scholar
  38. 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(14):3892–3894. doi: 10.1016/j.bmcl.2009.03.114 CrossRefGoogle Scholar
  39. Ohta A, Murakami H, Higashimura E, Suga H (2007) Synthesis of polyester by means of genetic code reprogramming. Chem Biol 14(12):1315–1322. doi: 10.1016/j.chembiol.2007.10.015 CrossRefGoogle Scholar
  40. Perona JJ, Rould MA, Steitz TA (1993) Structural basis for transfer RNA aminoacylation by Escherichia Coli glutaminyl-tRNA synthetase. Biochemistry 32(34):8758–8771. doi: 10.1021/Bi00085a006 CrossRefGoogle Scholar
  41. Robertson D, Joyce G (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344(6265):467–468. doi: 10.1038/344467a0 CrossRefGoogle Scholar
  42. Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252(5013):1682–1689. doi: 10.1126/science.2047877 CrossRefGoogle Scholar
  43. Saito H, Kourouklis D, Suga H (2001a) An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J 20(7):1797–1806. doi: 10.1093/emboj/20.7.1797 CrossRefGoogle Scholar
  44. Saito H, Watanabe K, Suga H (2001b) Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA 7(12):1867–1878Google Scholar
  45. Schulman LH, Pelka H (1977) Structural requirements for aminoacylation of Escherichia coli formylmethionine transfer RNA. Biochemistry 16(19):4256–4265. doi: 10.1021/bi00638a020 CrossRefGoogle Scholar
  46. Sczepanski JT, Joyce GF (2014) A cross-chiral RNA polymerase ribozyme. Nature 515(7527):440–442. doi: 10.1038/nature13900 Google Scholar
  47. Shi HJ, Moore PB (2000) The crystal structure of yeast phenylalanine tRNA at 1.93 angstrom resolution: a classic structure revisited. RNA 6(8):1091–1105. doi: 10.1017/S1355838200000364 CrossRefGoogle Scholar
  48. Snead NM, Rossi JJ (2010) Biogenesis and function of endogenous and exogenous siRNAs. Wires RNA 1(1):117–131. doi: 10.1002/Wrna.14 Google Scholar
  49. Suga H, Hayashi G, Terasaka N (2011) The RNA origin of transfer RNA aminoacylation and beyond. Phil Trans R Soc B 366(1580):2959–2964. doi: 10.1098/rstb.2011.0137 CrossRefGoogle Scholar
  50. Terasaka N, Suga H (2014) Flexizymes-facilitated genetic code reprogramming leading to the discovery of drug-like peptides. Chem Lett 43(1):11–19. doi: 10.1246/Cl.130910 CrossRefGoogle Scholar
  51. Tsukiji S, Pattnaik S, Suga H (2003) An alcohol dehydrogenase ribozyme. Nat Struct Biol 10(9):713–717. doi: 10.1038/nsb964 CrossRefGoogle Scholar
  52. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249(4968):505–510. doi: 10.1126/science.2200121 CrossRefGoogle Scholar
  53. Walter G (1986) Origin of life: the RNA world. Nature 319. doi: 10.1038/319618a0
  54. Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332(6026):209–212. doi: 10.1126/science.1200752 CrossRefGoogle Scholar
  55. Xiao H, Murakami H, Suga H, Ferré-D’Amaré AR (2008) Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 454(7202):358–361. doi: 10.1038/nature07033 CrossRefGoogle Scholar
  56. 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(12):1562–1570. doi: 10.1016/j.chembiol.2011.09.013 CrossRefGoogle Scholar
  57. Yang F, Moss LG, Phillips GN (1996) The molecular structure of green fluorescent protein. Nat Biotechnol 14(10):1246–1251. doi: 10.1038/Nbt1096-1246 CrossRefGoogle Scholar
  58. Yarus M (2011) The meaning of a minuscule ribozyme. Phil Trans R Soc B 366(1580):2902–2909. doi: 10.1098/rstb.2011.0139 CrossRefGoogle Scholar
  59. Zhou XL, Du DH, Tan M, Lei HY, Ruan LL, Eriani G, Wang ED (2011) Role of tRNA amino acid-accepting end in aminoacylation and its quality control. Nucleic Acids Res 39(20):8857–8868. doi: 10.1093/nar/gkr595 CrossRefGoogle Scholar

Copyright information

© Springer Japan KK 2017

Authors and Affiliations

  1. 1.ETH ZurichZurichSwitzerland

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