Journal of Molecular Evolution

, Volume 86, Issue 7, pp 431–442 | Cite as

Oligomerization of a Bimolecular Ribozyme Modestly Rescues its Structural Defects that Disturb Interdomain Assembly to Form the Catalytic Site

  • Md. Motiar Rahman
  • Shigeyoshi Matsumura
  • Yoshiya IkawaEmail author
Original Article


The emergence of cellular compartmentalization was a crucial step in the hypothetical RNA world and its evolution because it would not only prevent the extinction of RNA self-replication systems due to dispersion/diffusion of their components but also facilitate ribozyme reactions by molecular crowding effects. Here, we proposed and examined self-assembly of RNA components as a primitive cellular-like environment, which may have the ability to mimic cellular compartmentalization and crowding effects. We engineered a bimolecular group I ribozyme to form a one-dimensional (1D)-ribozyme assembly. In the 1D assembly form, severe mutations that inactivated the parent bimolecular ribozyme were modestly rescued resulting in weak catalytic ability.


Cellular compartmentalization Self-assembly Ribozyme RNA nanostructure RNA world 



This work was supported by MEXT KAKENHI Grant Number JP15K05561 (to Y.I.). This work was also supported partly by University of Toyama Discretionary Funds of the President “Toyama RNA Research Alliance” (to Y.I and S.M.).

Supplementary material

239_2018_9862_MOESM1_ESM.pdf (1.1 mb)
Supplementary material 1 (PDF 1127 KB)


  1. Adamala KP, Engelhart AE, Szostak JW (2016) Collaboration between primitive cell membranes and soluble catalysts. Nat Commun 7:11041CrossRefPubMedPubMedCentralGoogle Scholar
  2. Anella F, Danelon C (2017) Prebiotic factors influencing the activity of a ligase ribozyme. Life 7:E17CrossRefPubMedGoogle Scholar
  3. Attwater J, Wochner A, Pinheiro VB, Coulson A, Holliger P (2010) Ice as a protocellular medium for RNA replication. Nat Commun 1:76CrossRefPubMedGoogle Scholar
  4. Attwater J, Wochner A, Holliger P (2013) In-ice evolution of RNA polymerase ribozyme activity. Nat Chem 5:1011–1018CrossRefPubMedPubMedCentralGoogle Scholar
  5. Benz-Moy TL, Herschlag D (2011) Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry 50:8733–8755CrossRefPubMedPubMedCentralGoogle Scholar
  6. Biondi E, Branciamore S, Fusi L, Gago S, Gallori E (2007a) Catalytic activity of hammerhead ribozymes in a clay mineral environment: implications for the RNA world. Gene 389:10–18CrossRefPubMedGoogle Scholar
  7. Biondi E, Branciamore S, Maurel MC, Gallori E (2007b) Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment. BMC Evol Biol 7:S2CrossRefPubMedPubMedCentralGoogle Scholar
  8. Chen IA, Salehi-Ashtiani K, Szostak JW (2005) RNA catalysis in model protocell vesicles. J Am Chem Soc 127:13213–13219CrossRefPubMedPubMedCentralGoogle Scholar
  9. Cheng LK, Unrau PJ (2010) Closing the circle: replicating RNA with RNA. Cold Spring Harb Perspect Biol 2:a002204CrossRefPubMedPubMedCentralGoogle Scholar
  10. Costa M, Michel F (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J 14:1276–1285PubMedPubMedCentralCrossRefGoogle Scholar
  11. Desai R, Kilburn D, Lee HT, Woodson SA (2014) Increased ribozyme activity in crowded solutions. J Biol Chem 289:2972–2977CrossRefPubMedGoogle Scholar
  12. Doudna JA, Cech TR (1995) Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1:36–45PubMedPubMedCentralGoogle Scholar
  13. Ertem G, Ferris JP (1996) Synthesis of RNA oligomers on heterogeneous templates. Nature 379:238–240CrossRefPubMedGoogle Scholar
  14. Fiammengo R, Crego-Calama M, Reinhoudt DN (2001) Synthetic self-assembled models with biomimetic functions. Curr Opin Chem Biol 5:660–673CrossRefPubMedGoogle Scholar
  15. Geary C, Rothemund PW, Andersen ES (2014) RNA nanostructures. A single-stranded architecture for cotranscriptional folding of RNAnanostructures. Science 345:799–804CrossRefPubMedGoogle Scholar
  16. Gillams RJ, Jia TZ (2018) Mineral surface-templated self-assembling systems: case studies from nanoscience and aurface acience towards origins of life research. Life 8:E10CrossRefPubMedGoogle Scholar
  17. Glasgow J, Tullman-Ercek D (2014) Production and applications of engineered viral capsids. Appl Microbiol Biotechnol 98:5847–5858CrossRefPubMedGoogle Scholar
  18. Grabow WW, Jaeger L (2014) RNA self-assembly and RNA nanotechnology. Acc Chem Res 47:1871–1880CrossRefPubMedGoogle Scholar
  19. Guo F, Gooding AR, Cech TR (2004) Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 16:351–362PubMedGoogle Scholar
  20. Hanczyc MM, Fujikawa SM, Szostak JW (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302:618–622CrossRefPubMedPubMedCentralGoogle Scholar
  21. Higgs PG, Lehman N (2015) The RNA World: molecular cooperation at the origins of life. Nat Rev Genet 16:7–17CrossRefPubMedGoogle Scholar
  22. Ikawa Y, Inoue T (2003) Designed structural-rearrangement of an active group I ribozyme. J Biochem 133:189–195CrossRefPubMedGoogle Scholar
  23. Ikawa Y, Shiraishi H, Inoue T (2000) A small structural element, Pc-J5/5a, plays dual roles in a group IC1 intron RNA. Biochem Biophys Res Commun 274:259–265CrossRefPubMedGoogle Scholar
  24. Ikawa Y, Yoshimura T, Hara H, Shiraishi H, Inoue T (2002) Two conserved structural components, A-rich bulge and P4 XJ6/7 base-triples, in activating the group I ribozymes. Genes Cells 7:1205–1215CrossRefPubMedGoogle Scholar
  25. Ikawa Y, Moriyama S, Furuta H (2008) Facile syntheses of BODIPY derivatives for fluorescent labeling of the 3′ and 5′ ends of RNAs. Anal Biochem 378:166–170CrossRefPubMedGoogle Scholar
  26. Ishikawa J, Furuta H, Ikawa Y (2013) RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology. Wiley Interdiscip Rev RNA 4:651–664CrossRefPubMedGoogle Scholar
  27. Jheeta S, Joshi PC (2014) Prebiotic RNA synthesis by montmorillonite catalysis. Life 4:318–330CrossRefPubMedPubMedCentralGoogle Scholar
  28. Joshi PC, Aldersley MF, Delano JW, Ferris JP (2009) Mechanism of montmorillonite catalysis in the formation of RNA oligomers. J Am Chem Soc 131:13369–13374CrossRefPubMedGoogle Scholar
  29. Joyce GF (2009) Evolution in an RNA world. Cold Spring Harb Symp Quant Biol 74:17–23CrossRefPubMedPubMedCentralGoogle Scholar
  30. Kurihara K, Matsuo M, Yamaguchi T, Sato S (2018) Synthetic approach to biomolecular science by cyborg supramolecular chemistry. Biochim Biophys Acta 1862:358–364CrossRefPubMedGoogle Scholar
  31. Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC (2016) Bridging the gap between in vitro and in vivo RNA folding. Q Rev Biophys 49:e10CrossRefPubMedPubMedCentralGoogle Scholar
  32. Lee HT, Kilburn D, Behrouzi R, Briber RM, Woodson SA (2015) Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme. Nucleic Acids Res 43:1170–1176CrossRefPubMedGoogle Scholar
  33. Lehnert V, Jaeger L, Michel F, Westhof E (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem Biol 3:993–1009CrossRefPubMedGoogle Scholar
  34. Lincoln TA, Joyce GF (2009) Self-sustained replication of an RNA enzyme. Science 323:1229–1232CrossRefPubMedPubMedCentralGoogle Scholar
  35. Liu Z, Qiao J, Niu Z, Wang Q (2012) Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles. Chem Soc Rev 41:6178–6194CrossRefPubMedGoogle Scholar
  36. Loria A, Pan T (1996) Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2:551–563PubMedPubMedCentralGoogle Scholar
  37. Mansy SS, Szostak JW (2009) Reconstructing the emergence of cellular life through the synthesis of model protocells. Cold Spring Harb Symp Quant Biol 74:47–54CrossRefPubMedGoogle Scholar
  38. McGinness KE, Joyce GF (2003) In search of an RNA replicase ribozyme. Chem Biol 10:5–14CrossRefPubMedGoogle Scholar
  39. Minton AP (2005) Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations. J Pharm Sci 94:1668–1675CrossRefPubMedGoogle Scholar
  40. Mittal S, Chowhan RK, Singh LR (2015) Macromolecular crowding: macromolecules friend or foe. Biochim Biophys Acta 1850:1822–1831CrossRefPubMedGoogle Scholar
  41. Mondragón A (2013) Structural studies of RNase P. Annu Rev Biophys 42:537–557CrossRefPubMedGoogle Scholar
  42. Monnard PA, Ziock H (2008) Eutectic phase in water-ice: a self-assembled environment conducive to metal-catalyzed non-enzymatic RNA polymerization. Chem Biodivers 5:1521–1539CrossRefPubMedGoogle Scholar
  43. Murphy FL, Wang YH, Griffith JD, Cech TR (1994) Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265:1709–1712CrossRefPubMedGoogle Scholar
  44. Mutschler H, Wochner A, Holliger P (2015) Freeze-thaw cycles as drivers of complex ribozyme assembly. Nat Chem 7:502–508CrossRefPubMedPubMedCentralGoogle Scholar
  45. Nakano SI, Sugimoto N (2016) Model studies of the effects of intracellular crowding on nucleic acid interactions. Mol Biosyst 13:32–41CrossRefPubMedGoogle Scholar
  46. Oi H, Fujita D, Suzuki Y, Sugiyama H, Endo M, Matsumura S, Ikawa Y (2017) Programmable formation of catalytic RNA triangles and squares by assembling modular RNA enzymes. J Biochem 161:451–462PubMedGoogle Scholar
  47. Pan T (1995) Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P. Biochemistry 34:902–909CrossRefPubMedGoogle Scholar
  48. Pressman A, Blanco C, Chen IA (2015) The RNA World as a model system to study the origin of life. Curr Biol 25:R953–R963CrossRefPubMedGoogle Scholar
  49. Pyle AM (2016) Group II intron self-splicing. Annu Rev Biophys 45:183–205CrossRefPubMedGoogle Scholar
  50. Rahman MM, Matsumura S, Ikawa Y (2017) Artificial RNA motifs expand the programmable assembly between RNA modules of a bimolecular ribozyme leading to application to RNA nanostructure design. Biology 6:E37CrossRefPubMedGoogle Scholar
  51. Saha R, Pohorille A, Chen IA (2014) Molecular crowding and early evolution. Orig Life Evol Biosph 44:319–324CrossRefPubMedGoogle Scholar
  52. Saha R, Verbanic S, Chen IA (2018) Lipid vesicles chaperone an encapsulated RNA aptamer. Nat Commun 9:2313CrossRefPubMedPubMedCentralGoogle Scholar
  53. Sczepanski JT, Joyce GF (2014) A cross-chiral RNA polymerase ribozyme. Nature 515:440–442CrossRefPubMedPubMedCentralGoogle Scholar
  54. Shu D, Huang LP, Hoeprich S, Guo P (2003) Construction of phi29 DNA-packaging RNA monomers, dimers, and trimers with variable sizes and shapes as potential parts for nanodevices. J Nanosci Nanotechnol 3:295–302CrossRefPubMedGoogle Scholar
  55. Shu Y, Cinier M, Shu D, Guo P (2011) Assembly of multifunctional phi29 pRNA nanoparticles for specific delivery of siRNA and other therapeutics to targeted cells. Methods 54:204–214CrossRefPubMedPubMedCentralGoogle Scholar
  56. Stephenson JD, Popović M, Bristow TF, Ditzler MA (2016) Evolution of ribozymes in the presence of a mineral surface. RNA 22:1893–1901PubMedPubMedCentralCrossRefGoogle Scholar
  57. Szilágyi A, Zachar I, Scheuring I, Kun Á, Könnyű B, Czárán T (2017) Ecology and evolution in the RNA world dynamics and stability of prebiotic replicator systems. Life 7:E48CrossRefPubMedGoogle Scholar
  58. Szostak JW, Bartel DP, Luisi PL (2001) Synthesizing life. Nature 409:387–390CrossRefPubMedGoogle Scholar
  59. Tanaka T, Matsumura S, Furuta H, Ikawa Y (2016) Tecto-GIRz: engineered Group I ribozyme the catalytic ability of which can be controlled by self-dimerization. ChemBioChem 17:1448–1455CrossRefPubMedGoogle Scholar
  60. Tanner M, Cech T (1996) Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus. RNA 2:74–83PubMedPubMedCentralGoogle Scholar
  61. Vaidya N, Manapat ML, Chen IA, Xulvi-Brunet R, Hayden EJ, Lehman N (2012) Spontaneous network formation among cooperative RNA replicators. Nature 491:72–77CrossRefPubMedGoogle Scholar
  62. Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332:209–212CrossRefPubMedGoogle Scholar
  63. Wu Q, Huang L, Zhang Y (2009) The structure and function of catalytic RNAs. Sci China C 52:232–244CrossRefGoogle Scholar
  64. Zhu TF, Szostak JW (2009) Coupled growth and division of model protocell membranes. J Am Chem Soc 131:5705–5713CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Chemistry, Graduate School of Science and EngineeringUniversity of ToyamaToyamaJapan
  2. 2.Graduate School of Innovative Life ScienceUniversity of ToyamaToyamaJapan

Personalised recommendations