RNA Structure, Not Sequence, Determines the 5' Splice-site Specificity of a Group I Intron

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1989 Oct 1

PMID 2678103

Citations 51

Authors

J A Doudna

B P Cormack

J W Szostak

Affiliations

Soon will be listed here.

Abstract

The group I self-splicing introns act at exon-intron junctions without recognizing a particular sequence. In order to understand splice-site selection, we have developed an assay system based on the Tetrahymena ribozyme to allow the study of numerous 5'-splice-site variants. Cleavage at the correct site requires formation of the correct secondary structure and occurs most efficiently within a 3-base-pair window centered on base pair 5 from the bottom of the P1 stem. Within this window the ribozyme recognizes and cleaves at a "wobble" base pair; the base pair above the cleavage site also influences splicing efficiency. The recognition of RNA structure rather than sequence explains the ability of these transposable introns to splice out of a variety of sequence contexts.

Citing Articles

Programmable trans-splicing riboregulators for complex cellular logic computation.

Gao Y, Mardian R, Ma J, Li Y, French C, Wang B Nat Chem Biol. 2025; .

PMID: 39747656 DOI: 10.1038/s41589-024-01781-4.

Efficient circular RNA synthesis for potent rolling circle translation.

Du Y, Zuber P, Xiao H, Li X, Gordiyenko Y, Ramakrishnan V Nat Biomed Eng. 2024; .

PMID: 39672985 DOI: 10.1038/s41551-024-01306-3.

Efficient circularization of protein-encoding RNAs via a novel cis-splicing system.

Qi S, Wang H, Liu G, Qin Q, Gao P, Ying B Nucleic Acids Res. 2024; 52(17):10400-10415.

PMID: 39162233 PMC: 11417360. DOI: 10.1093/nar/gkae711.

Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species.

Chen L, Yan W, Wang T, Wang Y, Liu J, Yu Z PLoS One. 2021; 16(3):e0245714.

PMID: 33720962 PMC: 7959364. DOI: 10.1371/journal.pone.0245714.

Fitness landscape of a dynamic RNA structure.

Soo V, Swadling J, Faure A, Warnecke T PLoS Genet. 2021; 17(2):e1009353.

PMID: 33524037 PMC: 7877785. DOI: 10.1371/journal.pgen.1009353.

References

Szostak J . Enzymatic activity of the conserved core of a group I self-splicing intron. Nature. 1986; 322(6074):83-6. DOI: 10.1038/322083a0. View

Waring R, Scazzocchio C, Brown T, Davies R . Close relationship between certain nuclear and mitochondrial introns. Implications for the mechanism of RNA splicing. J Mol Biol. 1983; 167(3):595-605. DOI: 10.1016/s0022-2836(83)80100-4. View

Cech T . The chemistry of self-splicing RNA and RNA enzymes. Science. 1987; 236(4808):1532-9. DOI: 10.1126/science.2438771. View

Burke J, Belfort M, Cech T, Davies R, Schweyen R, Shub D . Structural conventions for group I introns. Nucleic Acids Res. 1987; 15(18):7217-21. PMC: 306243. DOI: 10.1093/nar/15.18.7217. View

Milligan J, Groebe D, Witherell G, Uhlenbeck O . Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987; 15(21):8783-98. PMC: 306405. DOI: 10.1093/nar/15.21.8783. View

Been M, Barfod E, Burke J, Price J, Tanner N, Zaug A . Structures involved in Tetrahymena rRNA self-splicing and RNA enzyme activity. Cold Spring Harb Symp Quant Biol. 1987; 52:147-57. DOI: 10.1101/sqb.1987.052.01.019. View

Doudna J, Gerber A, Cherry J, Szostak J . Genetic dissection of an RNA enzyme. Cold Spring Harb Symp Quant Biol. 1987; 52:173-80. DOI: 10.1101/sqb.1987.052.01.022. View

Woodson S, Cech T . Reverse self-splicing of the tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell. 1989; 57(2):335-45. DOI: 10.1016/0092-8674(89)90971-9. View

McSwiggen J, Cech T . Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate-limiting. Science. 1989; 244(4905):679-83. DOI: 10.1126/science.2470150. View

10.

Rajagopal J, Doudna J, Szostak J . Stereochemical course of catalysis by the Tetrahymena ribozyme. Science. 1989; 244(4905):692-4. DOI: 10.1126/science.2470151. View

11.

Michel F, Dujon B . Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members. EMBO J. 1983; 2(1):33-8. PMC: 555082. DOI: 10.1002/j.1460-2075.1983.tb01376.x. View

12.

SANGER F, Nicklen S, Coulson A . DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977; 74(12):5463-7. PMC: 431765. DOI: 10.1073/pnas.74.12.5463. View

13.

Davies R, Waring R, Ray J, Brown T, Scazzocchio C . Making ends meet: a model for RNA splicing in fungal mitochondria. Nature. 1982; 300(5894):719-24. DOI: 10.1038/300719a0. View

14.

Zaug A, Grabowski P, Cech T . Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature. 1983; 301(5901):578-83. DOI: 10.1038/301578a0. View

15.

Cech T, Tanner N, Tinoco Jr I, Weir B, Zuker M, Perlman P . Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Proc Natl Acad Sci U S A. 1983; 80(13):3903-7. PMC: 394167. DOI: 10.1073/pnas.80.13.3903. View

16.

Been M, Cech T . One binding site determines sequence specificity of Tetrahymena pre-rRNA self-splicing, trans-splicing, and RNA enzyme activity. Cell. 1986; 47(2):207-16. DOI: 10.1016/0092-8674(86)90443-5. View