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. 1991 Aug 25;19(16):4429–4436. doi: 10.1093/nar/19.16.4429

A self-splicing group I intron in the nuclear pre-rRNA of the green alga, Ankistrodesmus stipitatus.

J A Dávila-Aponte 1, V A Huss 1, M L Sogin 1, T R Cech 1
PMCID: PMC328630  PMID: 1886767

Abstract

The nuclear small subunit ribosomal RNA gene of the unicellular green alga Ankistrodesmus stipitatus contains a group I intron, the first of its kind to be found in the nucleus of a member of the plant kingdom. The intron RNA closely resembles the group I intron found in the large subunit rRNA precursor of Tetrahymena thermophila, differing by only eight nucleotides of 48 in the catalytic core and having the same peripheral secondary structure elements. The Ankistrodesmus RNA self-splices in vitro, yielding the typical group I intron splicing intermediates and products. Unlike the Tetrahymena intron, however, splicing is accelerated by high concentrations of monovalent cations and is rate-limited by the exon ligation step. This system provides an opportunity to understand how limited changes in intron sequence and structure alter the properties of an RNA catalytic center.

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Selected References

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  1. Bass B. L., Cech T. R. Ribozyme inhibitors: deoxyguanosine and dideoxyguanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal ribonucleic acid precursor. Biochemistry. 1986 Aug 12;25(16):4473–4477. doi: 10.1021/bi00364a001. [DOI] [PubMed] [Google Scholar]
  2. Been M. D., Cech T. R. One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell. 1986 Oct 24;47(2):207–216. doi: 10.1016/0092-8674(86)90443-5. [DOI] [PubMed] [Google Scholar]
  3. Been M. D., Perrotta A. T. Group I intron self-splicing with adenosine: evidence for a single nucleoside-binding site. Science. 1991 Apr 19;252(5004):434–437. doi: 10.1126/science.2017681. [DOI] [PubMed] [Google Scholar]
  4. Burke J. M., Belfort M., Cech T. R., Davies R. W., Schweyen R. J., Shub D. A., Szostak J. W., Tabak H. F. Structural conventions for group I introns. Nucleic Acids Res. 1987 Sep 25;15(18):7217–7221. doi: 10.1093/nar/15.18.7217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burke J. M., Irvine K. D., Kaneko K. J., Kerker B. J., Oettgen A. B., Tierney W. M., Williamson C. L., Zaug A. J., Cech T. R. Role of conserved sequence elements 9L and 2 in self-splicing of the Tetrahymena ribosomal RNA precursor. Cell. 1986 Apr 25;45(2):167–176. doi: 10.1016/0092-8674(86)90380-6. [DOI] [PubMed] [Google Scholar]
  6. Cech T. R. Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene. 1988 Dec 20;73(2):259–271. doi: 10.1016/0378-1119(88)90492-1. [DOI] [PubMed] [Google Scholar]
  7. Cech T. R., Zaug A. J., Grabowski P. J. In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence. Cell. 1981 Dec;27(3 Pt 2):487–496. doi: 10.1016/0092-8674(81)90390-1. [DOI] [PubMed] [Google Scholar]
  8. Couture S., Ellington A. D., Gerber A. S., Cherry J. M., Doudna J. A., Green R., Hanna M., Pace U., Rajagopal J., Szostak J. W. Mutational analysis of conserved nucleotides in a self-splicing group I intron. J Mol Biol. 1990 Oct 5;215(3):345–358. doi: 10.1016/s0022-2836(05)80356-0. [DOI] [PubMed] [Google Scholar]
  9. Dams E., Hendriks L., Van de Peer Y., Neefs J. M., Smits G., Vandenbempt I., De Wachter R. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 1988;16 (Suppl):r87–173. doi: 10.1093/nar/16.suppl.r87. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Davies R. W., Waring R. B., Ray J. A., Brown T. A., Scazzocchio C. Making ends meet: a model for RNA splicing in fungal mitochondria. Nature. 1982 Dec 23;300(5894):719–724. doi: 10.1038/300719a0. [DOI] [PubMed] [Google Scholar]
  11. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dujon B. Group I introns as mobile genetic elements: facts and mechanistic speculations--a review. Gene. 1989 Oct 15;82(1):91–114. doi: 10.1016/0378-1119(89)90034-6. [DOI] [PubMed] [Google Scholar]
  13. Ehrenman K., Schroeder R., Chandry P. S., Hall D. H., Belfort M. Sequence specificity of the P6 pairing for splicing of the group I td intron of phage T4. Nucleic Acids Res. 1989 Nov 25;17(22):9147–9163. doi: 10.1093/nar/17.22.9147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Flor P. J., Flanegan J. B., Cech T. R. A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing. EMBO J. 1989 Nov;8(11):3391–3399. doi: 10.1002/j.1460-2075.1989.tb08503.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Godson G. N., Vapnek D. A simple method of preparing large amounts of phiX174 RF 1 supercoiled DNA. Biochim Biophys Acta. 1973 Apr 11;299(4):516–520. doi: 10.1016/0005-2787(73)90223-2. [DOI] [PubMed] [Google Scholar]
  16. Hicke B. J., Christian E. L., Yarus M. Stereoselective arginine binding is a phylogenetically conserved property of group I self-splicing RNAs. EMBO J. 1989 Dec 1;8(12):3843–3851. doi: 10.1002/j.1460-2075.1989.tb08562.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Huss V. A., Sogin M. L. Phylogenetic position of some Chlorella species within the chlorococcales based upon complete small-subunit ribosomal RNA sequences. J Mol Evol. 1990 Nov;31(5):432–442. doi: 10.1007/BF02106057. [DOI] [PubMed] [Google Scholar]
  18. Inoue T., Sullivan F. X., Cech T. R. New reactions of the ribosomal RNA precursor of Tetrahymena and the mechanism of self-splicing. J Mol Biol. 1986 May 5;189(1):143–165. doi: 10.1016/0022-2836(86)90387-6. [DOI] [PubMed] [Google Scholar]
  19. Kruger K., Grabowski P. J., Zaug A. J., Sands J., Gottschling D. E., Cech T. R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell. 1982 Nov;31(1):147–157. doi: 10.1016/0092-8674(82)90414-7. [DOI] [PubMed] [Google Scholar]
  20. Kuhsel M. G., Strickland R., Palmer J. D. An ancient group I intron shared by eubacteria and chloroplasts. Science. 1990 Dec 14;250(4987):1570–1573. doi: 10.1126/science.2125748. [DOI] [PubMed] [Google Scholar]
  21. Kück U., Godehardt I., Schmidt U. A self-splicing group II intron in the mitochondrial large subunit rRNA (LSUrRNA) gene of the eukaryotic alga Scenedesmus obliquus. Nucleic Acids Res. 1990 May 11;18(9):2691–2697. doi: 10.1093/nar/18.9.2691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Long E. O., Dawid I. B. Repeated genes in eukaryotes. Annu Rev Biochem. 1980;49:727–764. doi: 10.1146/annurev.bi.49.070180.003455. [DOI] [PubMed] [Google Scholar]
  23. Medlin L., Elwood H. J., Stickel S., Sogin M. L. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene. 1988 Nov 30;71(2):491–499. doi: 10.1016/0378-1119(88)90066-2. [DOI] [PubMed] [Google Scholar]
  24. Michel F., Hanna M., Green R., Bartel D. P., Szostak J. W. The guanosine binding site of the Tetrahymena ribozyme. Nature. 1989 Nov 23;342(6248):391–395. doi: 10.1038/342391a0. [DOI] [PubMed] [Google Scholar]
  25. Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982 Oct;64(10):867–881. doi: 10.1016/s0300-9084(82)80349-0. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Murphy F. L., Cech T. R. Alteration of substrate specificity for the endoribonucleolytic cleavage of RNA by the Tetrahymena ribozyme. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9218–9222. doi: 10.1073/pnas.86.23.9218. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Muscarella D. E., Vogt V. M. A mobile group I intron in the nuclear rDNA of Physarum polycephalum. Cell. 1989 Feb 10;56(3):443–454. doi: 10.1016/0092-8674(89)90247-x. [DOI] [PubMed] [Google Scholar]
  29. Perea J., Jacq C. Role of the 5' hairpin structure in the splicing accuracy of the fourth intron of the yeast cob-box gene. EMBO J. 1985 Dec 1;4(12):3281–3288. doi: 10.1002/j.1460-2075.1985.tb04078.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Quirk S. M., Bell-Pedersen D., Belfort M. Intron mobility in the T-even phages: high frequency inheritance of group I introns promoted by intron open reading frames. Cell. 1989 Feb 10;56(3):455–465. doi: 10.1016/0092-8674(89)90248-1. [DOI] [PubMed] [Google Scholar]
  31. Sogin M. L., Edman J. C. A self-splicing intron in the small subunit rRNA gene of Pneumocystis carinii. Nucleic Acids Res. 1989 Jul 11;17(13):5349–5359. doi: 10.1093/nar/17.13.5349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Weiss-Brummer B., Holl J., Schweyen R. J., Rödel G., Kaudewitz F. Processing of yeast mitochondrial RNA: involvement of intramolecular hybrids in splicing of cob intron 4 RNA by mutation and reversion. Cell. 1983 May;33(1):195–202. doi: 10.1016/0092-8674(83)90348-3. [DOI] [PubMed] [Google Scholar]
  33. Williamson C. L., Desai N. M., Burke J. M. Compensatory mutations demonstrate that P8 and P6 are RNA secondary structure elements important for processing of a group I intron. Nucleic Acids Res. 1989 Jan 25;17(2):675–689. doi: 10.1093/nar/17.2.675. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Williamson C. L., Tierney W. M., Kerker B. J., Burke J. M. Site-directed mutagenesis of core sequence elements 9R', 9L, 9R, and 2 in self-splicing Tetrahymena pre-rRNA. J Biol Chem. 1987 Oct 25;262(30):14672–14682. [PubMed] [Google Scholar]
  35. Woodson S. A., Cech T. R. Reverse self-splicing of the tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell. 1989 Apr 21;57(2):335–345. doi: 10.1016/0092-8674(89)90971-9. [DOI] [PubMed] [Google Scholar]
  36. Xu M. Q., Kathe S. D., Goodrich-Blair H., Nierzwicki-Bauer S. A., Shub D. A. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science. 1990 Dec 14;250(4987):1566–1570. doi: 10.1126/science.2125747. [DOI] [PubMed] [Google Scholar]
  37. Zaug A. J., Kent J. R., Cech T. R. A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA. Science. 1984 May 11;224(4649):574–578. doi: 10.1126/science.6200938. [DOI] [PubMed] [Google Scholar]

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