Ribozyme catalysis from the major groove of group II intron domain 5

Molecular Cell

Volumn 1, Issue 3, 1998, Pages 433-441

  Konforti, Boyana B ^a   Abramovitz, Dana L ^a   Duarte, Carlos M ^a   Karpeisky, Alex ^b   Beigelman, Leonid ^b   Pyle, Anna Marie ^a  

^a The New York Presbyterian Hospital   (United States)

^b Sirna Therapeutics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RIBOZYME;

ARTICLE; BINDING SITE; CHEMISTRY; CONFORMATION; GENETICS; INTRON; KINETICS; METABOLISM; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; RNA SPLICING;

BINDING SITES; INTRONS; KINETICS; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PROTEIN STRUCTURE, TERTIARY; RNA SPLICING; RNA, CATALYTIC;

EID: 0031991610     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(00)80043-X     Document Type: Article

References (65)

1. Abramovitz, D.L., Friedman, R.A., and Pyle, A.M. (1996). Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271, 1410-1413.
2. Abramovitz, D.L., and Pyle, A.M. (1997). Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J. Mol. Biol. 266, 493-506.
3. Allain, F.H.-T., and Varani, G. (1995). Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns. Nucleic Acids Res. 23, 341-350.
4. Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Mohandiram, D.R., Kay, L.E., Frankel, A., and Williamson, J.R. (1996). Alpha helix-RNA major groove recognition in an HIV-1 Rev peptide-RRE RNA complex. Science 273, 1547-1551.
5. Beebe, J.A., and Fierke, C.A. (1994). A kinetic mechanism for cleavage of pre-tRNA Asp catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry 33, 10294-10304.
6. Boulanger, S.C., Belcher, S.M., Schmidt, U., Dib-Hajj, S.D., Schmidt, T., and Perlman, P.S. (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.
7. Burgin, A.B., Gonzalez, C., Matulic-Adamic, J., Karpeisky, A.M., Usman, N., McSwiggen, J.A., and Beigelman, L. (1996). Chemically modified hammerhead ribozymes with improved catalytic rates. Biochemistry 35, 14090-14097.
8. Cate, J.H., and Doudna, J.A. (1996b). Metal-binding sites in the major groove of a large ribozyme domain. Structure 4, 1221-1229.
9. Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kundrot, C.E., Cech, T.R., and Doudna, J.A. (1996a). Crystal structure of a group I ribozyme domain reveals principles of higher order RNA folding. Science 273, 1678-1685.
10. Chanfreau, G., and Jacquier, A. (1994). Catalytic site components common to both splicing steps of a group II intron. Science 266, 1383-1387.
11. Conway, L., and Wickens, M. (1989). Modification interference analysis of reactions using RNA substrates. Meth. Enzymol. 180, 369-379.
12. Correll, C.C., Freeborn, B., Moore, P.B., and Steitz, T.A. (1997). Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91, 705-712.
13. Daniels, D., Michels, W.J., and Pyle, A.M. (1996). Two competing pathways forself-splicing by group II introns; a quantitative analysis of in-vitro reaction rates and products. J. Mol. Biol. 256, 31-49.
14. Doudna, J.A., and Cech, T.R. (1995). Self-assembly of a group I intron active site from its component tertiary structural domains. RNA 1, 36-45.
15. Doudna, J.A., Szostak, J.W., Rich, A., and Usman, N. (1990). Chemical synthesis of oligoribonucleotides containing 2-aminopurine: substrates for the investigation of ribozyme function. J. Org. Chem. 55, 5547-5549.
16. Fourmy, D., Recht, M.I., Blanchard, S.C., and Puglisi, J.D. (1996). Structure of the A site of E. coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274, 1367-1371.
17. Franzen, J.S., Zhang, M., and Peebles, C.L. (1993). Kinetic analysis of the 5′-splice junction hydrolysis of a group II intron promoted by Domain 5. Nucleic Acids Res. 21, 627-634.
18. Fu, D.-J., Rajur, S.B., and McLaughlin, L.W. (1993). Importance of specific guanosine N7-nitrogens and purine amino groups for efficient cleavage by hammerhead ribozyme. Biochemistry 32, 10629-10637.
19. Green, R., Szostak, J.W., Benner, S., Rich, A., and Usman, N. (1991). Synthesis of RNA containing inosine: analysis of the sequence requirements for the 5′ splice site of the Tetrahymena group I intron. Nucleic Acids Res. 15, 4161-4166.
20. Heus, H.A., and Pardi, A. (1991). Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253, 191-194.
21. Jacquier, A., and Michel, F. (1987). Multiple exon-binding sites in class II self-splicing introns. Cell 50, 17-29.
22. Jacquier, A., and Rosbash, M. (1986). Efficient trans-splicing of a yeast mitochondrial RNA group II intron implicates a strong 5′-exonintron interaction. Science 234, 1099-1104.
23. Jarrell, K.A., Dietrich, R.C., and Perlman, P.S. (1988b). Group II intron Domain 5 facilitates a trans-splicing reaction. Mol. Cell. Biol. 8, 2361-2366.
24. Jarrell, K.A., Peebles, C.L., Dietrich, R.C., Romiti, S.L., and Perlman, P.S. (1988a). Group II intron self-splicing: alternative reaction conditions yield novel products. J. Biol. Chem. 263, 3432-3439.
25. Kieft, J.S., and Tinoco, I. (1997). Solution structure of a metal binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure 5, 713-721.
26. Knitt, D.S., Narlikar, G.J., and Herschlag, D. (1994). Dissection of the role of the conserved G-U pair in group I RNA self-splicing. Biochemistry 33, 13864-13879.
27. Koch, J.L., Boulanger, S.C., Dib-Hajj, S.D., Hebbar, S.K., and Perlman, P.S. (1992). Group II introns deleted for multiple substructures retain self-splicing activity. Mol. Cell. Biol. 12, 1950-1958.
28. Kwakman, J.H., Konings, D.A., Hogeweg, P., Pel, H.J., and Grivell, L.A. (1990). Structural analysis of a group II intron by chemical modifications and minimal energy calculations. J. Biomol. Struct. Dyn. 8, 413-430.
29. Liu, Q., Green, J.B., Khodadadi, A., Haeberli, P., Beigelman, L., and Pyle, A.M. (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.
30. Madhani, H., and Guthrie, C. (1994). Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28, 1-26.
31. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E., and Cedergren, R. (1991). The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 253, 1255-1260.
32. McKay, D.B. (1996). Structure and function of the hammerhead ribozyme: an unfinished story. RNA 2, 395-403.
33. Michel, F., and Dujon, B. (1983). Conservation of RNA secondary structure in two intron families including mitochondrial-, chloroplast-, and nuclear-encoded members. EMBO J. 2, 33-38.
34. Michel, F., and Ferat, J.-L. (1995). Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435-461.
35. Michel, F., Umesono, K., and Ozeki, H. (1989). Comparative and functional anatomy of group II catalytic introns - a review. Gene 82, 5-30.
36. Michels, W.J., and Pyle, A.M. (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.
37. Musier-Forsyth, K., and Schimmel, P. (1992). Functional contacts of a transfer RNA synthetase with 2′-hydroxyl groups in the RNA minor groove. Nature 357, 513-515.
38. Musier-Forsyth, K., Usman, N., Scaringe, S., Doudna, J.A., Green, R., and Schimmel, P. (1991). Specificity for aminoacylation of an RNA helix: an unpaired, exocyclic amino group in the minor groove. Science 253, 784-786.
39. Neenhold, H.R., and Rana, T.M. (1995). Major groove opening at the HIV-1 Tat binding site of TAR RNA evidenced by a rhodium probe. Biochemistry 34, 6303-6309.
40. Nicholls, A., Sharp, K., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Prot. Struct. Funct. Genet. 11, 281-296.
41. Ott, G., Arnold, L., and Limmer, S. (1993). Proton NMR studies of manganese ion binding to tRNA-derived acceptor arm duplexes. Nucleic Acids Res. 21, 5859-5864.
42. Peattie, D.A. (1979). Direct chemical method for sequencing of RNA. Proc. Natl. Acad. Sci. USA 76, 1760-1764.
43. Peebles, C.L., Perlman, P.S., Mecklenburg, K.L., Petrillo, M.L., Tabor, J.H., Jarrell, K.A., and Cheng, H.-L. (1986). A self-splicing RNA excises an intron lariat. Cell 44, 213-223.
44. Peebles, C.L., Zhang, M., Perlman, P.S., and Franzen, J.F. (1995). Identification of a catalytically critical trinucleotide in Domain 5 of a group II intron. Proc. Natl. Acad. Sci. USA 92, 4422-4426.
45. Pley, H.W., Flaherty, K.M., and McKay, D.B. (1994a). Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
46. Pley, H.M., Flaherty, K.M., and McKay, D.B. (1994b). Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372, 111-113.
47. Podar, M., Perlman, P.S., and Padgett, R.A. (1995). Stereochemical selectivity of group II intron splicing, reverse-splicing and hydrolysis reactions. Mol. Cell. Biol. 15, 4466-4478.
48. Podar, M., Chu, V.T., Pyle, A.M., and Perlman, P.S. (1998). Group II intron splicing in-vivo by first step hydrolysis. Nature, in press.
49. Podar, M., Zhuo, J., Zhang, M., Franzen, J.S., Perlman, P.S., and Peebles, C.L. (1998). Domain 5 binds near a highly-conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron. RNA, 4, 151-166.
50. Pyle, A.M. (1993). Ribozymes: a distinct class of metalloenzymes. Science 261, 709-714.
51. Pyle, A.M. (1996). Catalytic reaction mechanisms and structural features of group II intron ribozymes. In Nucleic Acids and Molecular Biology (New York, Springer Verlag), pp. 75-107.
52. Pyle, A.M., and Green, J.B. (1994). Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry 33, 2716-2725.
53. Pyle, A.M., Moran, S., Strobel, S.A., Chapmen, T., Turner, D.H., and Cech, T.R. (1994). Replacement of the conserved G-U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity and fidelity. Biochem 33, 13856-13863.
54. Saenger, W. (1984). Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry. (New York, Springer-Verlag), pp. 242-252, 331-349.
55. Schmelzer, C., and Schweyen, R.J. (1986). Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell 46, 557-565.
56. Schmidt, U., Podar, M., Stahl, U., and Perlman, P.S. (1996). Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations. RNA 2, 1161-1172.
57. Scott, W.G., Finch, J.T., and Klug, A. (1995). The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81, 991-1002.
58. Steitz, T.A., and Steitz, J.A. (1993). A general two-metal ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA 90, 6498-6502.
59. Strobel, S.A., and Cech, T.R. (1995). Minor groove recognition of the conserved G-U pair at the Tetrahymena ribozyme reaction site. Science 267, 675-679.
60. Strobel, S.A., Cech, T.R., Usman, N., and Beigelman, L. (1994). The 2,6-diaminopurine riboside.5-methylisocytidine wobble base pair: an isoinergetic substitution for study of G-U pairs in RNA. Biochemistry 33, 13824-13835.
61. van der Veen, R., Arnberg, A.C., van der Horst, G., Bonen, L., Tabak, H.F., and Grivell, L.A. (1986). Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell 44, 225-234.
62. Weeks, K.M., and Crothers, D.M. (1993). Major groove accessibility of RNA. Science 261, 1574-1577.
63. Weiner, S.J., Kollman, P.A., Nguyen, D.T., and Case, D.A. (1986). A new forcefield for molecular mechanical simulation of nucleic acids and proteins (AMBER). J. Comp. Chem. 7, 230-252.
64. Westhof, E., Dumas, P., and Moras, D. (1985). Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184, 119-145.
65. Zimmerly, S., Guo, H., Eskes, R., Yang, J., Perlman, P.S., and Lambowitz, A.M. (1995). A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83, 529-538.