More than one way to splice an RNA: Branching without a bulge and splicing without branching in group II introns

RNA

Volumn 4, Issue 10, 1998, Pages 1186-1202

  Chu, Vi T ^a   Liu, Qiaolian ^a   Podar, Mircea ^b   Perlman, Philip S ^b   Pyle, Anna Marie ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

Base flipping; Catalysis; Conformation; Evolution; Mismatch; Ribozyme; Self splicing

Indexed keywords

ARTICLE; CATALYSIS; DNA STRUCTURE; INTRON; POINT MUTATION; PRIORITY JOURNAL; RNA CONFORMATION; RNA SPLICING;

ADENOSINE; BASE SEQUENCE; ENDORIBONUCLEASES; INTRONS; KINETICS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; POINT MUTATION; RNA; RNA SPLICING; SEQUENCE ANALYSIS, RNA; SEQUENCE DELETION;

EID: 0031671299     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298980724     Document Type: Article

References (46)

1. Borer PN, Lin Y, Wang S, Roggenbuck MW, Gott JM, Uhlenbeck OC, Pelczar I. 1995. Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry 34:6488-6503.
2. Boulanger SC, Belcher SM, Schmidt U, Dib-Hajj SD, Schmidt T, Perlman PS. 1995. Studies of point mutants define three essential paired nucleotides in the domain 5 substructure of a group II intron. Mol Cell Biol 15:4479-4488.
3. Chanfreau G, Jacquier A. 1994. Catalytic site components common to both splicing steps of a group II intron. Science 266:1383-1387.
4. Chanfreau G, Jacquier A. 1996. An RNA conformational change between the two chemical steps of group II self-splicing. EMBO J 15:3466-3476.
5. Cheng X, Blumenthal RM. 1996. Finding a basis for flipping bases. Structure 4:639-645.
6. Costa M, Deme E, Jacquier A, Michel F. 1997. Multiple tertiary interactions involving domain II of group II self-splicing introns. J Mol Biol 267:520-536.
7. Daniels D, 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.
8. Davanloo P, Rosenburg AH, Dunn JJ, Studier FW. 1984. Cloning and expression of the gene for bacteriophage T7 DNA. Proc Natl Acad Sci USA 81:2035-2039.
9. Donis-Keller H, Maxam AM, Gilbert W. 1977. Sequencing RNA with endonucleases (SIC). Nucleic Acids Res 4:2527-2538.
10. Fersht A. 1985. Enzyme structure and mechanism. New York: W.H. Freeman.
11. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MA, Neilson T, Turner DH. 1986. Improved free energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83:9373-9377.
12. Gaur RK, Mclaughlin LW, Green MR. 1997. Functional group substitutions of the branchpoint adenosine in a nuclear pre-mRNA and a group II intron. RNA 3:861-869.
13. Hornig H, Aebi M, Weissman C. 1986. Effect of mutations at the lariat branch acceptor site on β-globin pre-mRNA splicing in vitro. Nature 324:589-591.
14. Jacquier A, Michel F. 1987. Multiple exon-binding sites in class II self-splicing introns. Cell 50:17-29.
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. Jencks WP. 1987. Catalysis in chemistry and enzymology. New York: Dover. pp 569-574.
17. Klimasauskas S, Roberts RJ. 1995. M Hhal binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res 23:1388-1395.
18. Koch JL, Boulanger SC, Dib-Hajj SD, Hebbar SK, Perlman PS. 1992. Group II Introns deleted for multiple substructures retain self-splicing activity. Mol Cell Biol 12:1950-1958.
19. Kuchino Y, Nishimura S. 1989. Enzymatic RNA sequencing. Methods Enzymol 180:154-163.
20. Kunkel TA, Bebenek K, McClary J. 1991. Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol 204: 125-139.
21. Leroy JL, Bolo N, Figueroa N, Plateau P, Gueron M. 1985a. Internal motions of transfer RNA: A study of exchanging protons by magnetic resonance. J Biomol Struct Dyn 2:915-939.
22. Leroy JL, Broseta D, Gueron M. 1985b. Proton exchange and base-pair kinetics of poly(rA).poly(rU) and poly(rl).poly(rC). J Mol Biol 184:165-178.
23. Liu Q, Green JB, Khodadadi A, Haeberli P, Beigelman L, Pyle AM. 1997. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. J Mol Biol 267:163-171.
24. 2. Biochemistry 32: 3583-3595.
25. Michel F, Ferat JL. 1995. Structure and activities of group II introns. Annu Rev Biochem 64:435-461.
26. Michel F, Umesono K, Ozeki H. 1989. Comparative and functional anatomy of group II catalytic introns - A review. Gene 82:5-30.
27. Padgett RA, Konarska MM, Grabowski PJ, Hardy SF, Sharp PA. 1984. Lariat RNAs as intermediates and products in the splicing of messenger RNA precursors. Science 225:898-903.
28. Pardi A, Morden KM, Patel DJ, Tinoco I. 1982. Kinetics for exchange of imino protons in the d(CGCAATTCGCG) double helix and in two similar helices that contain a G-T base pair and an extra adenine. Biochemistry 21:6567-6574.
29. Peebles CL, Benatan EJ, Jarrell KA, Perlman PS. 1987. Group II intron self-splicing: Development of alternative reaction conditions and identification of a predicted intermediate. Cold Spring Harbor Symp Quant Biol 52:223-232.
30. Peebles CL, Perlman PS, Mecklenburg KL, Petrillo ML, Tabor JH, Jarrell KA, Cheng HL. 1986. A self-splicing RNA excises an intron lariat. Cell 44:213-223.
31. Podar M, Chu VT, Pyle AM, Perlman PS. 1998. Group II intron splicing in-vivo by first step hydrolysis. Nature 391:915-918.
32. 2+-dependent crosslink traps an active form of domain 3 of a self-splicing group II intron. RNA 1:828-840.
33. Portmann S, Grimm S, Workman C, Usman N, Egli M. 1996. Crystal structures of an A-form duplex with single-adenosine bulges an a conformational basis for site-specific RNA self-cleavage. Chemistry and Biology 3:173-184.
34. Pyle AM, Green JB. 1994. Building a kinetic framework for group II intron ribozyme activity: Quantitation of interdomain binding and reaction rate. Biochemistry 33:2716-2725.
35. Qin PZ, Pyle AM. 1997. Stopped-flow fluorescence spectroscopy reveals that domain 1 of a group II intron is an independent folding unit. Biochemistry 36:4718-4730.
36. Query CC, Strobel SA, Sharp PA. 1996. Three recognition events at the branch-site adenine. EMBO J 15:1392-1402.
37. Roberts RJ. 1995. On base flipping. Cell 82:9-12.
38. Ruskin B, Krainer AR, Maniatis T, Green MR. 1984. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell 38:317-331.
39. Santoro SW, Joyce GF. 1997. A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262-4266.
40. Schmelzer C, Müller MW. 1987. Self-splicing of group II introns in vitro: Lariat formation and 3′-splice site selection in mutant RNAs. Cell 51:753-762.
41. Schmelzer C, Schweyen RJ. 1986. Self-splicing of group II introns in vitro: Mapping of the branch point and mutational inhibition of lariat formation. Cell 46:557-565.
42. Valegard K, Murray JB, Stockley PG, Stonehouse NJ, Liljas L. 1994. Crystal structure of an RNA bacteriophage protein-operator complex. Nature 371:623-626.
43. van der Veen R, Arnberg AC, van der Horst G, Bonen L, Tabak HF, Grivell LA. 1986. Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell 44:225-234.
44. van der Veen R, Kwakman JHJM, Grivell LA. 1987. Mutations at the lariat acceptor site allow self-splicing of a group II intron without lariat formation. EMBO J 6:3827-3831.
45. Vijayraghavan U, Parker R, Tamm J, Iimura Y, Rossi J, Abelson J, Guthrie C. 1986. Mutations in conserved intron sequences affect multiple steps in the yeast splicing pathway, particularly assembly of the spliceosome. EMBO J 5:1683-1695.
46. Yang AS, Shen JC, Zingg JM, Mi S, Jones PA. 1995. Hha1 and Hpall DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. Nucleic Acids Res 23:1380-1387.