Now on Display: a Gallery of Group II Intron Structures at Different Stages of Catalysis

Overview

Journal Mob DNA

Publisher Biomed Central

Specialty Genetics

Date 2013 May 3

PMID 23634971

Citations 23

Authors

Marco Marcia

Srinivas Somarowthu

Anna Marie Pyle

Affiliations

Soon will be listed here.

Abstract

Group II introns are mobile genetic elements that self-splice and retrotranspose into DNA and RNA. They are considered evolutionary ancestors of the spliceosome, the ribonucleoprotein complex essential for pre-mRNA processing in higher eukaryotes. Over a 20-year period, group II introns have been characterized first genetically, then biochemically, and finally by means of X-ray crystallography. To date, 17 crystal structures of a group II intron are available, representing five different stages of the splicing cycle. This review provides a framework for classifying and understanding these new structures in the context of the splicing cycle. Structural and functional implications for the spliceosome are also discussed.

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References

Tseng C, Cheng S . Both catalytic steps of nuclear pre-mRNA splicing are reversible. Science. 2008; 320(5884):1782-4. DOI: 10.1126/science.1158993. View

Wolff T, Menssen R, Hammel J, Bindereif A . Splicing function of mammalian U6 small nuclear RNA: conserved positions in central domain and helix I are essential during the first and second step of pre-mRNA splicing. Proc Natl Acad Sci U S A. 1994; 91(3):903-7. PMC: 521421. DOI: 10.1073/pnas.91.3.903. View

Eldho N, Dayie K . Internal bulge and tetraloop of the catalytic domain 5 of a group II intron ribozyme are flexible: implications for catalysis. J Mol Biol. 2006; 365(4):930-44. DOI: 10.1016/j.jmb.2006.10.037. View

Chanfreau G, Jacquier A . Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron. EMBO J. 1993; 12(13):5173-80. PMC: 413780. DOI: 10.1002/j.1460-2075.1993.tb06212.x. View

Zimmerly S, Hausner G, Wu Xc . Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 2001; 29(5):1238-50. PMC: 29734. DOI: 10.1093/nar/29.5.1238. View

Chu V, Adamidi C, Liu Q, Perlman P, Pyle A . Control of branch-site choice by a group II intron. EMBO J. 2001; 20(23):6866-76. PMC: 125754. DOI: 10.1093/emboj/20.23.6866. View

Query C, Strobel S, Sharp P . Three recognition events at the branch-site adenine. EMBO J. 1996; 15(6):1392-402. PMC: 450044. View

Costa M, Deme E, Jacquier A, Michel F . Multiple tertiary interactions involving domain II of group II self-splicing introns. J Mol Biol. 1997; 267(3):520-36. DOI: 10.1006/jmbi.1996.0882. View

Garcia-Rodriguez F, Barrientos-Duran A, Diaz-Prado V, Fernandez-Lopez M, Toro N . Use of RmInt1, a group IIB intron lacking the intron-encoded protein endonuclease domain, in gene targeting. Appl Environ Microbiol. 2010; 77(3):854-61. PMC: 3028726. DOI: 10.1128/AEM.02319-10. View

10.

Fabrizio P, Abelson J . Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing. Science. 1990; 250(4979):404-9. DOI: 10.1126/science.2145630. View

11.

Dai L, Chai D, Gu S, Gabel J, Noskov S, Blocker F . A three-dimensional model of a group II intron RNA and its interaction with the intron-encoded reverse transcriptase. Mol Cell. 2008; 30(4):472-85. PMC: 2724966. DOI: 10.1016/j.molcel.2008.04.001. View

12.

Jacquier A, Michel F . Base-pairing interactions involving the 5' and 3'-terminal nucleotides of group II self-splicing introns. J Mol Biol. 1990; 213(3):437-47. DOI: 10.1016/S0022-2836(05)80206-2. View

13.

Viadiu H, Aggarwal A . The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol. 1998; 5(10):910-6. DOI: 10.1038/2352. View

14.

Vipond I, Baldwin G, Halford S . Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases. Biochemistry. 1995; 34(2):697-704. DOI: 10.1021/bi00002a037. View

15.

Schlatterer J, Crayton S, Greenbaum N . Conformation of the Group II intron branch site in solution. J Am Chem Soc. 2006; 128(12):3866-7. DOI: 10.1021/ja0578754. View

16.

de Lencastre A, Hamill S, Pyle A . A single active-site region for a group II intron. Nat Struct Mol Biol. 2005; 12(7):626-7. DOI: 10.1038/nsmb957. View

17.

Mattick J . Introns: evolution and function. Curr Opin Genet Dev. 1994; 4(6):823-31. DOI: 10.1016/0959-437x(94)90066-3. View

18.

Chillon I, Martinez-Abarca F, Toro N . Splicing of the Sinorhizobium meliloti RmInt1 group II intron provides evidence of retroelement behavior. Nucleic Acids Res. 2010; 39(3):1095-104. PMC: 3035460. DOI: 10.1093/nar/gkq847. View

19.

Yu Y, Maroney P, Darzynkiwicz E, Nilsen T . U6 snRNA function in nuclear pre-mRNA splicing: a phosphorothioate interference analysis of the U6 phosphate backbone. RNA. 1995; 1(1):46-54. PMC: 1369059. View

20.

Steitz T, Steitz J . A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci U S A. 1993; 90(14):6498-502. PMC: 46959. DOI: 10.1073/pnas.90.14.6498. View