Abstract
The RNA-world hypothesis proposes that, before the advent of DNA and protein, life was based on RNA, with RNA serving as both the repository of genetic information and the chief agent of catalytic function1. An argument against an RNA world is that the components of RNA lack the chemical diversity necessary to sustain life. Unlike proteins, which contain 20 different amino-acid subunits, nucleic acids are composed of only four subunits which have very similar chemical properties. Yet RNA is capable of a broad range of catalytic functions2,3,4,5,6,7. Here we show that even three nucleic-acid subunits are sufficient to provide a substantial increase in the catalytic rate. Starting from a molecule that contained roughly equal proportions of all four nucleosides, we used in vitro evolution to obtain an RNA ligase ribozyme that lacks cytidine. This ribozyme folds into a defined structure and has a catalytic rate that is about 105-fold faster than the uncatalysed rate of template-directed RNA ligation.
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References
Gesteland,R. F., Cech,T. R. & Atkins,J. F. (eds) The RNA World 2nd edn (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1999).
Kruger,K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31, 147–157 (1982).
Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. & Altman,S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849–857 (1983).
Lorsch,J. R. & Szostak,J. W. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 371, 31–36 (1994).
Ekland,E. H. & Bartel,D. P. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382, 373–376 (1996).
Zhang,B. & Cech,T. R. Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. Chem. Biol. 5, 539–553 (1998).
Unrau,P. J. & Bartel,D. P. RNA-catalysed nucleotide synthesis. Nature 395, 260–263 (1998).
Levy,M. & Miller,S. L. The stability of the RNA bases: implications for the origin of life. Proc. Natl Acad. Sci. USA 95, 7933–7938 (1998).
Bartel,D. P. & Szostak,J. W. Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411–1418 (1993).
Ekland,E. H., Szostak,J. W. & Bartel,D. P. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269, 364–370 (1995).
Wright,M. C. & Joyce,G. F. Continuous in vitro evolution of catalytic function. Science 276, 614–617 (1997).
Hayatsu,H., Wataya,Y. & Kai,K. The addition of sodium bisulfite to uracil and to cytosine. J. Am. Chem. Soc. 92, 724–726 (1970).
Rohatgi,R., Bartel,D. P. & Szostak,J. W. Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc. 118, 3332–3339 (1996).
Yoshida,H., Kumimoto,H. & Okamoto,K. dutA RNA functions as an untranslatable RNA in the development of Dictyostelium discoideum. Nucleic Acids Res. 22, 41–46 (1994).
Shu,H., Wise,C. A., Clark-Walker,G. D. & Martin,N. C. A gene required for RNase P activity in Candida (Torulopsis) glabrata mitochondria codes for a 227-nucleotide RNA with homology to bacterial RNase P RNA. Mol. Cell. Biol. 11, 1662–1667 (1991).
Goodall,G. J. & Filipowicz,W. The A-U rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell 58, 473–483 (1989).
Crick,F. H. C. The origin of the genetic code. J. Mol. Biol. 38, 367–379 (1968).
Vassylyev,D. G. & Morikawa,K. Precluding uracil from DNA. Structure 4, 1381–1385 (1996).
Vartanian,J., Henry,M. & Wain-Hobson,S. Hypermutagenic PCR involving all four transitions and a sizeable portion of transversions. Nucleic Acids Res. 24, 2627–2631 (1996).
Cadwell,R. C. & Joyce,G. F. Randomization of genes by PCR mutagenesis. PCR Methods Applic. 2, 28–33 (1992).
Stern,S., Moazed,D. & Noller,H. F. Analysis of RNA structure using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164, 481–489 (1988).
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This work was supported by a grant from NASA.
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Rogers, J., Joyce, G. A ribozyme that lacks cytidine. Nature 402, 323–325 (1999). https://doi.org/10.1038/46335
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DOI: https://doi.org/10.1038/46335
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