Skip to main content
NCBI home page
RNA logoLink to RNA
. 2000 Nov;6(11):1509–1515. doi: 10.1017/s1355838200000972

Deletion of a conserved dinucleotide inhibits the second step of group II intron splicing.

S Mikheeva 1, H L Murray 1, H Zhou 1, B M Turczyk 1, K A Jarrell 1
PMCID: PMC1370021  PMID: 11105751

Abstract

Few point mutations have been described that specifically inhibit the second step of group II intron splicing. Furthermore, the effects of such mutations are typically not apparent unless the mutations are studied in the context of a substrate that harbors a very short 5' exon. Truncation of the 5' exon slows the second step of splicing. Once the second step has been slowed, the effects of point mutations can be seen. We report the unexpected observation that the deletion of a conserved GA dinucleotide dramatically inhibits the second step of splicing, even when the mutation is studied in the context of a full-length substrate. In contrast, we find that this mutation does not significantly affect the first step of splicing, unless the mutation is studied in combination with a second point mutation that is known to inhibit the first step. Even in that context, the effect of the GA deletion mutation on the first step is modest. These observations, together with the inferred location of the GA dinucleotide in the three-dimensional structure of the intron, suggest that this dinucleotide plays a particularly important role in the second step of splicing.

Full Text

The Full Text of this article is available as a PDF (1.2 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Boulanger S. C., Belcher S. M., Schmidt U., Dib-Hajj S. D., Schmidt T., Perlman P. S. Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Mol Cell Biol. 1995 Aug;15(8):4479–4488. doi: 10.1128/mcb.15.8.4479. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chanfreau G., Jacquier A. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J. 1996 Jul 1;15(13):3466–3476. [PMC free article] [PubMed] [Google Scholar]
  3. Chanfreau G., Jacquier A. Catalytic site components common to both splicing steps of a group II intron. Science. 1994 Nov 25;266(5189):1383–1387. doi: 10.1126/science.7973729. [DOI] [PubMed] [Google Scholar]
  4. Chanfreau G., Jacquier A. Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron. EMBO J. 1993 Dec 15;12(13):5173–5180. doi: 10.1002/j.1460-2075.1993.tb06212.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Chin K., Pyle A. M. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection. RNA. 1995 Jun;1(4):391–406. [PMC free article] [PubMed] [Google Scholar]
  6. Jacquier A., Jacquesson-Breuleux N. Splice site selection and role of the lariat in a group II intron. J Mol Biol. 1991 Jun 5;219(3):415–428. doi: 10.1016/0022-2836(91)90183-7. [DOI] [PubMed] [Google Scholar]
  7. Jacquier A., Michel F. Base-pairing interactions involving the 5' and 3'-terminal nucleotides of group II self-splicing introns. J Mol Biol. 1990 Jun 5;213(3):437–447. doi: 10.1016/S0022-2836(05)80206-2. [DOI] [PubMed] [Google Scholar]
  8. Jarrell K. A., Dietrich R. C., Perlman P. S. Group II intron domain 5 facilitates a trans-splicing reaction. Mol Cell Biol. 1988 Jun;8(6):2361–2366. doi: 10.1128/mcb.8.6.2361. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Jarrell K. A., Peebles C. L., Dietrich R. C., Romiti S. L., Perlman P. S. Group II intron self-splicing. Alternative reaction conditions yield novel products. J Biol Chem. 1988 Mar 5;263(7):3432–3439. [PubMed] [Google Scholar]
  10. Koch J. L., Boulanger S. C., Dib-Hajj S. D., Hebbar S. K., Perlman P. S. Group II introns deleted for multiple substructures retain self-splicing activity. Mol Cell Biol. 1992 May;12(5):1950–1958. doi: 10.1128/mcb.12.5.1950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Michel F., Ferat J. L. Structure and activities of group II introns. Annu Rev Biochem. 1995;64:435–461. doi: 10.1146/annurev.bi.64.070195.002251. [DOI] [PubMed] [Google Scholar]
  12. Michel F., Jacquier A. Long-range intron-exon and intron-intron pairings involved in self-splicing of class II catalytic introns. Cold Spring Harb Symp Quant Biol. 1987;52:201–212. doi: 10.1101/sqb.1987.052.01.025. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Peebles C. L., Benatan E. J., Jarrell K. A., Perlman P. S. Group II intron self-splicing: development of alternative reaction conditions and identification of a predicted intermediate. Cold Spring Harb Symp Quant Biol. 1987;52:223–232. doi: 10.1101/sqb.1987.052.01.027. [DOI] [PubMed] [Google Scholar]
  15. Peebles C. L., Zhang M., Perlman P. S., Franzen J. S. Catalytically critical nucleotide in domain 5 of a group II intron. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4422–4426. doi: 10.1073/pnas.92.10.4422. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Podar M., Perlman P. S., Padgett R. A. Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions. Mol Cell Biol. 1995 Aug;15(8):4466–4478. doi: 10.1128/mcb.15.8.4466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Podar M., Zhuo J., Zhang M., Franzen J. S., Perlman P. S., Peebles C. L. Domain 5 binds near a highly conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron. RNA. 1998 Feb;4(2):151–166. [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES