The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

Nucleic Acids Research

Volumn 33, Issue 8, 2005, Pages 2557-2564

  Tobé, Sylvia ^b   Heams, Thomas ^b   Vergne, Jacques ^b   Hervé, Guy ^a   Maurel, Marie Christine ^b  

^a CNRS   (France)

^b INSTITUT JACQUES MONOD   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HAIRPIN RIBOZYME; RIBOZYME; RNA; UNCLASSIFIED DRUG; SOLVENT;

ARTICLE; CALCULATION; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ANALYSIS; ENZYME DEGRADATION; ENZYME KINETICS; ENZYME MECHANISM; ENZYME STRUCTURE; HYDROSTATIC PRESSURE; HYPERBARISM; OSMOTIC PRESSURE; PHASE TRANSITION; PRIORITY JOURNAL; STRUCTURE ANALYSIS; WATER TRANSPORT; CHEMISTRY; KINETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CATALYSIS; HYDROSTATIC PRESSURE; KINETICS; MOLECULAR SEQUENCE DATA; OSMOTIC PRESSURE; RNA, CATALYTIC; SOLVENTS;

EID: 18744411284     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki552     Document Type: Article

References (55)

1. Woese, C.R. (1965) On the evolution of the genetic code. Proc. Natl Acad. Sci. USA, 54, 1546-1551
2. Crick, F.H.C. (1968) The origin of the genetic code. J. Mol. Biol., 38, 367-379.
3. Orgel, L.E. (1968) Evolution of the genetic apparatus. J. Mol. Biol., 38, 381-393.
4. Gilbert, W. (1986) Origin of life: The RNA world. Nature, 319, 618.
5. Maurel, M.-C. (1992) RNA in evolution: A review. J. Evol. Biol., 2, 173-188.
6. Paul, N. and Joyce, G.F. (2002) A self-replicating ligase ribozyme. Proc. Natl Acad. Sci. USA, 99, 12733-12740.
7. Benner, S.A., Ellington, A.D. and Tauer, A. (1989) Modern metabolism as a palimpsest of the RNA world. Proc. Natl Acad. Sci. USA, 86, 7054-7058.
8. Joyce, G.F. (2002) Molecular evolution: Booting up life. Nature, 418, 214-221.
9. Doudna, J.A. and Cech, T.R. (2002) The chemical repetoire of natural ribozymes. Nature, 418, 222-228.
10. Bartel, D.P. and Unrau, P.J. (1999) Constructing an RNA world. Trends Cell. Biol., 9, M9-M13.
11. Nissen, P., Hansen, J., Ban, N., Moore, P.B. and Steitz, T.A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
12. Muth, G.W., Ortoleva-Donnelly, L. and Strobel, S.A. (2000) A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center. Science, 289, 947-950.
13. Lilley, D.M. (2001) The ribosome functions as a ribozyme. Chembiochem, 2, 31-35.
14. Wilson, D.S. and Szostak, J.W. (1999) In vitro selection of functional nucleic acids. Annu. Rev. Biochem., 68, 611-647.
15. Joyce, G.F. (2004) Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem., 73, 791-836.
16. Buzavan, J.M., Hampel, A. and Bruening, G. (1986) Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res., 14, 9729-9743.
17. Buzayan, J.M., Feldstein, P.A., Segrelles, C. and Bruening, G. (1988) Autolytic processing of a phosphorothioate diester bond. Nucleic Acids Res., 16, 4009-4023.
18. van Tol, H., Buzayan, J.M., Feldstein, P.A., Eckstein, F. and Bruening, G. (1990) Two autolytic processing reactions of a satellite RNA proceed with inversion of configuration. Nucleic Acids Res., 18, 1971-1975.
19. Walter, N.G. and Burke, J.M. (1998) The hairpin ribozyme: Structure. assembly and catalysis. Curr. Opin. Chem. Biol.. 2, 24-30.
20. Rupert, P.B. and Ferré-D'Amaré, A.R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature, 410, 780-786.
21. Rupert, P.B., Massey, A.P., Sigurdsson, S.T. and Ferré-D'Amaré, A.R. (2002) Transition state stabilization by a catalytic RNA. Science, 298, 1421-1424.
22. Ferré-D'Amaré, A.R. (2004) The hairpin ribozyme. Biopolymers, 73, 71-78.
23. Ryder, S.P., Oyelere, A.K., Padilla, J.L., Klostermeier, D., Millar, D.P. and Strobel, S.A. (2001) Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA, 7, 1454-1463.
24. Feldstein, P.A. and Bruening, G. (1993) Catalytically active geometry in the reversible circularization of 'mini-monomer' RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucleic Acids Res., 21, 1991-1998.
25. Komatsu, Y., Kanzaki, I., Koizumi, M. and Ohtsuka, E. (1995) Construction of new hairpin ribozymes with replaced domain. Nucleic Acids Symp. Ser., 34, 223-224.
26. Hegg, L.A. and Fedor, M.J. (1995) Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry, 34, 15813-15828.
27. Nesbitt, S.M., Erlacher, H.A. and Fedor, M.J. (1999) The internal equilibrium of the hairpin ribozyme: Temperature, ion and pH effects. J. Mol. Biol., 286, 1009-1024.
28. Fedor, M.J. (2002) The catalytic mechanism of the hairpin ribozyme. Biochem. Soc. Trans., 30. 1109-1115.
29. Bevilacqua, P.C. (2003) Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of the hairpin ribozyme. Biochemistry, 42, 2259-2265.
30. Wilson, T.J. and Lilley, D.M.J. (2002) Metal ion binding and the folding of the hairpin ribozyme. RNA, 8, 587-600.
31. Heremans, K. (1982) High pressure effects on proteins and other biomolecules. Annu. Rev. Biophys. Bioeng., 11, 1-21.
32. Weber, G, and Drickamer, H.G. (1983) The effect of high pressure upon proteins and other biomolecules. Q. Rev. Biophys., 16, 89-112.
33. Konisky, J., Michels, P. and Clark, D. (1995) Pressure stabilization is not a general property of thermophilic enzymes: The adenylate kinases of Methanococcus voltae, Methanococcus maripaludis, Methanococcus thermolithotrophicus, and Methanococcus jannaschii. Appl. Environ. Microbiol., 13, 263-269.
34. Zaccai, G., Cendrin, F. Haik, Y., Borochov, N. and Eisenberg, H. (1989) Stabilization of halophilic malate dehydrogenase. J. Mol. Biol., 208. 491-500.
35. Gounot, A.-M. (1991) Bacterial life at low temperature: Physiological aspects and biotechnological implications. J. Appl. Bacteriol., 71, 386-397.
36. Adams, M. (1993) Enzymes and proteins from organisms that grow near and above 100°C. Annu. Rev. Microbiol., 47, 627-658.
37. Balny, C., Masson, P. and Heremans, K. (2002) High pressure effects on biological macromolecules: From structural changes to alteration of cellular processes. Biochim. Biophys. Acta, 1595, 3-10.
38. Komblatt, J.A. and Komblatt, J. (2002) The effects of osmotic and hydrostatic pressures on macromolecular systems. Biochim. Biophys. Acta, 1595, 30-47.
39. The effect of high pressure on biological processes (2004) Cell. Mol. Biol., 50, 309-500 (All the articles of this issue).
40. Parsegian, V.A., Rand, R.P., Fuller, N.L. and Rau, D.C. (1986) Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol., 127, 400-416.
41. LiCata, V.J. and Allewell, N.M. (1997) Functionally linked hydration changes in Escherichia coli aspartate transcarbamylase and its catalytic subunit. Biochemistry, 36, 10161-10167.
42. Macgregor, R.B., Jr (1998) Effect of hydrostatic pressure on nucleic acids. Biopolymers, 48, 253-263.
43. Macgregor, R.B.,Jr (2002) The interactions of nucleic acids at elevated hydrostatic pressure. Biochim. Biophys. Acta, 1595, 266-276.
44. Barciszewski, J., Jurczak, J., Porowski, S., Specht, T. and Erdmann, V.A. (1999) The role of water structure in conformational changes of nucleic acids in ambient and high-pressure conditions. Eur. J. Biochem,. 260, 293-307.
45. Hoa, G.H., Hamel, G., Else, A., Weill, G. and Hervé, G. (1990) A reactor permitting injection and sampling for steady state studies of enzymatic reactions at high pressure: Tests with aspartate transcarbamylase. Anal. Biochem., 187, 258-261.
46. Colombo, M.F., Rau, D.C. and Parsegian, V.A. (1992) Protein solvation in allosteric regulation: A water effect on hemoglobin. Science, 256, 655-659.
47. Rand, R.P., Fuller, N.L., Butko, P., Francis, G. and Nicholls, P. (1993) Measured change in protein solvation with substrate binding and turnover. Biochemistry, 32, 5925-5929.
48. Parsegian, V.A., Rand, R.P. and Rau, D.C. (1995) Macromolecules and water: Probing with osmotic stress. Methods Enzymol., 259. 43-94.
49. Arnold, K., Herrmann, A., Pratsch, L. and Gawrisch, K. (1985) The dielectric properties of aqueous solutions of poly (ethylene glycol) and their influence on membrane structure. Biochim. Biophys. Acta, 815, 515-518.
50. Tan, E., Wilson, T.J., Nahas, M.K., Clegg, R.M., Lilley, D.M. and Ha, T. (2003) A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl Acad. Sci. USA, 100. 9308-9313.
51. Nahas, M.K., Wilson, T.J.. Hohng, S., Jarvie, K., Lilley, D.M. and Ha, T. (2004) Observation of internal cleavage and ligation reactions of a ribozyme. Nature Struct. Mol. Biol., 11, 1107-1113.
52. Cai, Z. and Tinoco, I., Jr (1996) Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry, 35. 6026-6036.
53. Butcher, S.E., Allain, F.H. and Feigon, J. (1999) Comparative analysis of hairpin ribozyme structures and interference data. Nature Struct. Biol.. 6, 212-216.
54. Ryder, S.P. and Strobel, S.A. (2002) Comparative analysis of hairpin ribozyme structures and interference data. Nucleic Acids Res., 30, 1287-1291.
55. Meli, M.. Vergne, J. and Maurel, M.-C. (2003) In vitro selection of adenine-dependent hairpin ribozymes. J. Biol. Chem., 278, 9835-9843.