Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1993 Nov 15;90(22):10658–10662. doi: 10.1073/pnas.90.22.10658

The phylogenetically predicted base-pairing interaction between alpha and alpha' is required for group II splicing in vitro.

C L Harris-Kerr 1, M Zhang 1, C L Peebles 1
PMCID: PMC47836  PMID: 7504276

Abstract

The correct folding of group II introns apparently depends on multiple tertiary base-pairing interactions. Understanding the relationship between spliceosome and group II splicing systems ultimately requires a three-dimensional model for both structures. In turn, successful modeling depends at least in part on identifying tertiary base pairings. Sequence elements alpha and alpha' are partners in a potential interaction of approximately 6 base pairs that can be identified within domain 1 of most group II introns. In comparisons between related introns, alpha and alpha' maintain their potential for Watson-Crick base pairing, even though their primary sequences can vary [Michel, F., Umesono, K. & Ozeki, H. (1989) Gene 82, 5-30]. Substitutions were constructed at alpha and alpha' for a block of 6 bases each in the group II intron a5 gamma, the last intron of the COXI gene from the mitochondrial DNA of Saccharomyces cerevisiae. Each substitution was defective for self-splicing, while the compensatory double derivative was restored to active splicing. The alpha-alpha' interaction is required for the first step of splicing--that is, recognition of the 5' splice junction and transesterification with the branch site--since the derivative transcripts displayed little or no activity. The compensatory double derivative produced lariat introns and spliced exons with normal structures, showing that splicing activity and precise recognition were restored. We conclude that the alpha-alpha' base pairing is necessary for efficient self-splicing by intron a5 gamma under several conditions. This result also provides an additional constraint for any three-dimensional model of group II intron structure.

Full text

PDF
10658

Images in this article

10661Fig. 2
on p.10661
10661Fig. 3
on p.10661
10662Fig. 4
on p.10662

Selected References

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

  1. Bonitz S. G., Coruzzi G., Thalenfeld B. E., Tzagoloff A., Macino G. Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrme oxidase. J Biol Chem. 1980 Dec 25;255(24):11927–11941. [PubMed] [Google Scholar]
  2. Cech T. R. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543–568. doi: 10.1146/annurev.bi.59.070190.002551. [DOI] [PubMed] [Google Scholar]
  3. Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science. 1991 Jul 12;253(5016):157–163. doi: 10.1126/science.1853200. [DOI] [PubMed] [Google Scholar]
  4. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Jacquier A., Michel F. Multiple exon-binding sites in class II self-splicing introns. Cell. 1987 Jul 3;50(1):17–29. doi: 10.1016/0092-8674(87)90658-1. [DOI] [PubMed] [Google Scholar]
  7. Jacquier A. Self-splicing group II and nuclear pre-mRNA introns: how similar are they? Trends Biochem Sci. 1990 Sep;15(9):351–354. doi: 10.1016/0968-0004(90)90075-m. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Madhani H. D., Guthrie C. A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell. 1992 Nov 27;71(5):803–817. doi: 10.1016/0092-8674(92)90556-r. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. 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]
  14. Peebles C. L., Perlman P. S., Mecklenburg K. L., Petrillo M. L., Tabor J. H., Jarrell K. A., Cheng H. L. A self-splicing RNA excises an intron lariat. Cell. 1986 Jan 31;44(2):213–223. doi: 10.1016/0092-8674(86)90755-5. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES