Abstract
We have previously proposed a hierarchical model for the folding mechanism of the Tetrahymena ribozyme that may illustrate general features of the folding pathways of large RNAs. While the role of elements in the conserved catalytic core of this ribozyme during the folding process is beginning to emerge, the participation of non-conserved peripheral extensions in the kinetic folding mechanism has not yet been addressed. We now show that the 3'-terminal P9.1-P9.2 extension of the Tetrahymena ribozyme plays an important role during the folding process and appears to guide formation of the catalytic core.
Full Text
The Full Text of this article is available as a PDF (65.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure. Biochemistry. 1993 Jan 12;32(1):153–163. doi: 10.1021/bi00052a021. [DOI] [PubMed] [Google Scholar]
- Beaudry A. A., Joyce G. F. Minimum secondary structure requirements for catalytic activity of a self-splicing group I intron. Biochemistry. 1990 Jul 10;29(27):6534–6539. doi: 10.1021/bi00479a027. [DOI] [PubMed] [Google Scholar]
- Cech T. R., Damberger S. H., Gutell R. R. Representation of the secondary and tertiary structure of group I introns. Nat Struct Biol. 1994 May;1(5):273–280. doi: 10.1038/nsb0594-273. [DOI] [PubMed] [Google Scholar]
- Celander D. W., Cech T. R. Visualizing the higher order folding of a catalytic RNA molecule. Science. 1991 Jan 25;251(4992):401–407. doi: 10.1126/science.1989074. [DOI] [PubMed] [Google Scholar]
- Darr S. C., Brown J. W., Pace N. R. The varieties of ribonuclease P. Trends Biochem Sci. 1992 May;17(5):178–182. doi: 10.1016/0968-0004(92)90262-8. [DOI] [PubMed] [Google Scholar]
- De Rijk P., Van de Peer Y., Chapelle S., De Wachter R. Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 1994 Sep;22(17):3495–3501. doi: 10.1093/nar/22.17.3495. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doudna J. A., Cech T. R. Self-assembly of a group I intron active site from its component tertiary structural domains. RNA. 1995 Mar;1(1):36–45. [PMC free article] [PubMed] [Google Scholar]
- Doudna J. A., Szostak J. W. Miniribozymes, small derivatives of the sunY intron, are catalytically active. Mol Cell Biol. 1989 Dec;9(12):5480–5483. doi: 10.1128/mcb.9.12.5480. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jaeger L., Westhof E., Michel F. Function of P11, a tertiary base pairing in self-splicing introns of subgroup IA. J Mol Biol. 1991 Oct 20;221(4):1153–1164. doi: 10.1016/0022-2836(91)90925-v. [DOI] [PubMed] [Google Scholar]
- Jaeger L., Westhof E., Michel F. Monitoring of the cooperative unfolding of the sunY group I intron of bacteriophage T4. The active form of the sunY ribozyme is stabilized by multiple interactions with 3' terminal intron components. J Mol Biol. 1993 Nov 20;234(2):331–346. doi: 10.1006/jmbi.1993.1590. [DOI] [PubMed] [Google Scholar]
- Laggerbauer B., Murphy F. L., Cech T. R. Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J. 1994 Jun 1;13(11):2669–2676. doi: 10.1002/j.1460-2075.1994.tb06557.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Michel F., Ellington A. D., Couture S., Szostak J. W. Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature. 1990 Oct 11;347(6293):578–580. doi: 10.1038/347578a0. [DOI] [PubMed] [Google Scholar]
- Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns--a review. Gene. 1989 Oct 15;82(1):5–30. doi: 10.1016/0378-1119(89)90026-7. [DOI] [PubMed] [Google Scholar]
- Michel F., Westhof E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J Mol Biol. 1990 Dec 5;216(3):585–610. doi: 10.1016/0022-2836(90)90386-Z. [DOI] [PubMed] [Google Scholar]
- Mohr G., Caprara M. G., Guo Q., Lambowitz A. M. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature. 1994 Jul 14;370(6485):147–150. doi: 10.1038/370147a0. [DOI] [PubMed] [Google Scholar]
- Murphy F. L., Cech T. R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry. 1993 May 25;32(20):5291–5300. doi: 10.1021/bi00071a003. [DOI] [PubMed] [Google Scholar]
- Nakamura T. M., Wang Y. H., Zaug A. J., Griffith J. D., Cech T. R. Relative orientation of RNA helices in a group 1 ribozyme determined by helix extension electron microscopy. EMBO J. 1995 Oct 2;14(19):4849–4859. doi: 10.1002/j.1460-2075.1995.tb00166.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Neefs J. M., Van de Peer Y., De Rijk P., Chapelle S., De Wachter R. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 1993 Jul 1;21(13):3025–3049. doi: 10.1093/nar/21.13.3025. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Y. H., Murphy F. L., Cech T. R., Griffith J. D. Visualization of a tertiary structural domain of the Tetrahymena group I intron by electron microscopy. J Mol Biol. 1994 Feb 11;236(1):64–71. doi: 10.1006/jmbi.1994.1118. [DOI] [PubMed] [Google Scholar]
- Zarrinkar P. P., Williamson J. R. Kinetic intermediates in RNA folding. Science. 1994 Aug 12;265(5174):918–924. doi: 10.1126/science.8052848. [DOI] [PubMed] [Google Scholar]
- Zaug A. J., Grosshans C. A., Cech T. R. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry. 1988 Dec 13;27(25):8924–8931. doi: 10.1021/bi00425a008. [DOI] [PubMed] [Google Scholar]
- van der Horst G., Christian A., Inoue T. Reconstitution of a group I intron self-splicing reaction with an activator RNA. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):184–188. doi: 10.1073/pnas.88.1.184. [DOI] [PMC free article] [PubMed] [Google Scholar]