The two steps of group II intron self-splicing are mechanistically distinguishable

RNA

Volumn 4, Issue 8, 1998, Pages 890-900

  Podar, Mircea ^a,c   Perlman, Philip S ^a   Padgett, Richard A ^b  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b LERNER RESEARCH INSTITUTE   (United States)

^c WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

Author keywords

Kinetics; Metal ions; Phosphorothioate; Ribozyme; Transesterification

Indexed keywords

PHOSPHOROTHIOIC ACID;

ARTICLE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME KINETICS; ESTERIFICATION; METAL BINDING; PRIORITY JOURNAL; REACTION ANALYSIS; RNA SPLICING; SPLICEOSOME;

BINDING SITES; INTRONS; MANGANESE; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; OLIGORIBONUCLEOTIDES; RNA; RNA SPLICING; STEREOISOMERISM; THIONUCLEOTIDES;

EID: 0031857783     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298971643     Document Type: Article

References (39)

1. Bass BL, Cech TR. 1984. Specific interactions between the self-splicing RNA of Tetrahymena and its guanosine substrate: Implications for biological catalysis by RNA. Nature 303:820-826.
2. Chanfreau G, Jacquier A. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266:1383-1387.
3. Chanfreau G, Jacquier A. 1996. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J 15:3466-3476.
4. Chin K, Pyle AM. 1995. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proof-reading mechanism for 5′-splice site selection. RNA 1:391-406.
5. Dahm SC, Uhlenbeck OC. 1991. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30:9464-9469.
6. Daniels DL, Michels WJ, Pyle AM. 1996. Two competing pathways for self-splicing by group II introns: A quantitative analysis of in vitro reaction rates and products. J Mol Biol 256:31-49.
7. Eckstein F. 1985. Nucleoside phosphorothioates. Annu Rev Biochem 54:367-402.
8. + on an equilibrium between alternative conformations of an RNA pseudoknot. J Mol Biol 270:451-463.
9. Griffin EA, Qin Z, Michels WJ, Pyle AM. 1995. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups. Chem & Biol 2:761-770.
10. Herschlag D, Eckstein F, Cech TR. 1993a. Contributions of 2′-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA. Biochemistry 32:8299-8311.
11. Herschlag D, Eckstein F, Cech TR. 1993b. The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction. Biochemistry 32:8312-8321.
12. Herschlag D, Khosla M. 1994. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2′-substituted and phosphorothioate substrates reveals a rate-limiting conformational step. Biochemistry 33:5291-5297.
13. Herschlag D, Piccirilli JA, Cech TR. 1991. Ribozyme-catalyzed and nonenzymatic reactions of phosphate diesters: Rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom. Biochemistry 30:4844-4854.
14. Jacquier A. 1996. Group II introns: Elaborate ribozymes. Biochemie 78:474-487.
15. Jarrell KA, Peebles CL, Dietrich RC, Romiti SL, Perlman PS. 1988. Group II intron self-splicing: Alternative reaction conditions yield novel products. J Biol Chem 263:3432-3439.
16. Kao TH, Crothers DM. 1980. A proton-coupled conformational switch of Escherichia coli 5S ribosomal RNA. Proc Natl Acad Sci USA 77:3360-3364.
17. a. Biochemistry 35:1560-1570.
18. Koizumi M, Ohtsuka E. 1991. Effects of phosphorothioate and 2-amino groups in hammerhead ribozymes on cleavage rates and Mg2+ binding. Biochemistry 30:5145-5150.
19. Konforti BB, Abramovitz DL, Duarte CM, Karpeisky A, Beigelman L, Pyle AM. 1998. Ribozyme catalysis from the major groove of group II intron domain 5. Mol Cell 1:433-441.
20. Macaya R, Wang E, Schultze P, Sklenar V, Feigon J. 1992. Proton nuclear magnetic resonance assignments and structural characterization of an intramolecular DNA triplex. J Mol Biol 225:755-773.
21. Maschhoff KL, Padgett RA. 1993. The stereochemical course of the first step of pre-mRNA splicing. Nucleic Acids Res 21:5456-5462.
22. McSwiggen JA, Cech TR. 1989. Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate limiting. Science 244:679-683.
23. Michel F, Ferat JL. 1995. Structure and activities of group II introns. Annu Rev Biochem 64:435-461.
24. Michels WJ, Pyle AM. 1995. Conversion of a Group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/function relationships. Biochemistry 34:2965-2977.
25. Moore MJ, Sharp PA. 1992. Site-specific modification of pre-mRNA: The 2′ hydroxyl groups at the splice sites. Science 256:992-997.
26. Moore MJ, Sharp PA. 1993. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 365:364-368.
27. Narlikar GJ, Herschlag D. 1997. Mechanistic aspects of enzymatic catalysis: Lessons from comparison of RNA and protein enzymes. Annu Rev Biochem 66:19-59.
28. Nilsen TW. 1998. RNA-RNA interactions in nuclear pre-mRNA splicing. In: Simons RW, Grunberg-Manago M, eds. RNA structure and function. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. pp 279-307.
29. Padgett RA, Podar M, Boulanger SC, Perlman PS. 1994. The stereochemical course of group II intron self-splicing. Science 266: 1685-1688.
30. Pecoraro VL, Hermes JD, Cleland WW. 1984. Stability constants of Mg2+ and Cd2+ complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of MgATP and MgADP. Biochemistry 23:5262-5271.
31. Podar M, Perlman PS, Padgett RA. 1995. Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions. Mol Cell Biol 15:4466-4478.
32. Puglisi JD, Wyatt JD, Tinoco I. 1990. Solution conformation of an RNA hairpin loop. Biochemistry 29:4215-4226.
33. Rajagopal J, Doudna JA, Szostak JW. 1989. Stereochemical course of catalysis by the Tetrahymena ribozyme. Science 244:692-694.
34. Slim G, Gait MJ. 1991. Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes. Nucleic Acids Res 19:1183-1188.
35. Smith D, Pace NR. 1993. Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry 32:5273-5281.
36. Sontheimer EJ, Sun S, Piccirilli JA. 1997. Metal ion catalysis during splicing of premessenger RNA. Nature 380:801-805.
37. Steitz TA, Steitz JA. 1993. A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90:6498-6502.
38. Suh E, Waring RB. 1992. A phosphorothioate at the 3′ splice-site inhibits the second step in a group I intron. Nucleic Acids Res 20:6303-6309.
39. leu. Biochemistry 33:14935-14947.