Insights into functional modulation of catalytic RNA activity

IUBMB Life

Volumn 60, Issue 10, 2008, Pages 669-683

  Vourekas, Anastassios ^a   Stamatopoulou, Vassiliki ^a   Toumpeki, Chrisavgi ^a   Tsitlaidou, Marianthi ^a   Drainas, Denis ^a  

^a UNIVERSITY OF PATRAS   (Greece)

Author keywords

Antibiotics; Group I intron; Hairpin; Hammerhead; Modulators; Ribosome; Ribozymes; RNase P

Indexed keywords

ANTIBIOTIC AGENT; CATION; HAMMERHEAD RIBOZYME; ION; MICRORNA; NEOMYCIN; PEPTIDYLTRANSFERASE; POLYAMINE; RIBONUCLEASE P; RIBOZYME; RNA; SPERMIDINE; SPERMINE; SPIRAMYCIN; TUBERACTINOMYCIN; UNTRANSLATED RNA; VIOMYCIN; ANTIINFECTIVE AGENT; DIVALENT CATION;

CELL ACTIVITY; CELL STRUCTURE; CHEMICAL STRUCTURE; CYTOLOGY; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME SPECIFICITY; EVOLUTION; FUNCTIONAL ASSESSMENT; GENE ACTIVITY; GENE EXPRESSION REGULATION; GENE INTERACTION; INTRON; MODULATION; MOLECULAR EVOLUTION; MOLECULAR SIZE; PROTEIN SYNTHESIS; REVIEW; RIBOSOME; RIBOSWITCH; CHEMISTRY; CONFORMATION; ENZYME ACTIVATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION;

ANTI-BACTERIAL AGENTS; BASE SEQUENCE; CATIONS, DIVALENT; ENZYME ACTIVATION; GENE EXPRESSION REGULATION; INTRONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RIBONUCLEASE P; RIBOSOMES; RNA, CATALYTIC; RNA, UNTRANSLATED; SPERMIDINE; SPERMINE;

EID: 58149192812     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.105     Document Type: Review

References (164)

1. McGinness, K. E. and Joyce, G. F. (2003) In search for an RNA replicase enzyme. Chem. Biol. 10, 5-14.
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. Breaker, R. R. (2006) Riboswitches and the RNA world. In The RNA World, 3rd edn. (Gesteland, R. F., Cech, T. R., Atkins, J. F., eds.). CSHL Press, Cold Spring Harbor, NY.
5. Miller, S. L. (1953) A production of amino acids under possible primitive earth conditions. Science 117, 528-529.
6. Szathmáry, E. and Smith, J. M. (1997) From replicators to reproducers: the first major transitions leading to life. J. Theor. Biol. 187, 555-571.
7. Noller, H. F. (2004) The driving force for molecular evolution of translation. RNA 10, 1833-1837.
8. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857.
9. Pannucci, J. A., Haas, E. S., Hall, T. A., Harris, J. K., and Brown, J. W. (1999) RNase P RNAs from some Archaea are catalytically active. Proc. Natl. Acad. Sci. USA 6, 7803-7808.
10. Kikovska, E., Svard, S. G., and Kirsebom, L. A. (2007) Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc. Natl. Acad. Sci. USA 104, 2062-2067.
11. Ban, N., Nissen, P., Hansen, J., Moore, P.B., and Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289, 905-920.
12. Fedor, M. J. and Williamson, J. R. (2005) The catalytic diversity of RNAs. Nat. Rev. Mol. Cell. Biol. 6, 399-412.
13. Pley, H. W., Flaherty, K. M., and McKay, D. B. (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74.
14. Torres-Larios, A., Swinger, K. K., Krasilnikov, A. S., Pan, T., and Mondragon, A. (2005) Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437, 584-587.
15. Robertson, W. G. and Scott, M. P. (2007) The structural basis of ribozyme-catalyzed RNA assembly. Science 315, 1549-1553.
16. Fedor, M. J. (2002) The role of metal ions in RNA catalysis. Curr. Opin. Struct. Biol. 12, 289-295.
17. Kalavrizioti, D., Vourekas, A., Stamatopoulou, V., Toumpeki, C., Giannouli, S., Stathopoulos, C., and Drainas, D. (2006) RNA-mediated therapeutics: from gene inactivation to clinical application. Curr. Top. Med. Chem. 6, 1737-1758.
18. Vourekas, A., Kalavrizioti, D., Stathopoulos, C., and Drainas, D. (2006) Modulation of catalytic RNA biological activity by small molecule effectors. Mini Rev. Med. Chem. 6, 971-978.
19. Green, R. and Noller, H. F. (1997) Ribosomes and translation. Annu. Rev. Biochem. 66, 679-716.
20. Noller, H. F., Hoffarth, V., and Zimniak, L. (1992) Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416-1419.
21. Maguire, B. A., Beniaminov, A. D., Ramu, H., Mankin, A.S., and Zimmermann, R. A. (2005) A protein component at the heart of an RNA machine: the importance of protein L27 for the function of the bacterial ribosome. Mol. Cell. 20, 427-435.
22. Kalpaxis, D. L. and Drainas, D. (1992) Effect of spermine on peptide-bond formation, catalyzed by ribosomal peptidyltransferase. Mol. Cell Biochem. 115, 19-26.
23. Drainas, D. and Kalpaxis, D. L. (1994) Bimodal action of spermine on ribosomal peptidyl-transferase at low concentration of magnesium ions. Biochem. Biophys. Acta 1208, 55-64.
24. Xaplanteri, M. A., Petropoulos, A. D., Dinos, G. P., and Kalpaxis D. L. (2005) Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions. Nucleic Acids Res. 33, 2792-2805.
25. Kakegawa, T., Sato, E., Hirose, S., and Igarashi, K. (1986) Polyamine binding sites on Escherichia coli ribosomes. Arch. Biochem. Biophys. 251, 413-420.
26. Amarantos, I., Xaplanteri, M. A., Choli-Papadopoulou, T., and Kalpaxis, D. L. (2001) Effects of two photoreactive spermine analogues on peptide bond formation and their application for labeling proteins in Escherichia coli functional ribosomal complexes. Biochemistry 40, 7641-7650.
27. Kouvela, E. C., Gerbanas, G. V., Xaplanteri, M. A., Petropoulos, A. D., Dinos, G. P., and Kalpaxis D. L. (2007) Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine. Nucleic Acids Res. 35, 5108-5119.
28. Amarantos, I., Zarkadis, I. K., and Kalpaxis D. L. (2002) The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions. Nucleic Acids Res. 30, 2832-2843.
29. Spahn, C. M. and Prescott, C. D. (1996) Throwing a spanner in the works: antibiotics and the translation apparatus. J. Mol. Med. 74, 423-439.
30. Auerbach, T., Bashan, A., and Yonath, A. (2004) Ribosomal antibiotics: structural basis for resistance, synergism and selectivity. Trends Biotechnol. 22, 570-576.
31. Gale, E. F., Cundliffe, E., Reynolds, P. E., Richmond, M. H., and Waring, M. J. (1981) The Molecular Basis of Antibiotic Action, 2nd edn. Wiley, London.
32. Rodriguez-Fonseca, C., Phan, H., Long, K. S., Porse, B. T., Kirillov, S. V., Amils, R., and Garrett, R. A. (2000) Puromycin-rRNA interaction sites at the peptidyl transferase center. RNA 6, 744-754.
33. Hansen, J. L., Moore, P. B., and Steitz, T. A. (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol. 330, 1061-1075.
34. Petropoulos, A. D., Xaplanteri, M. A., Dinos, G. P., Wilson, D. N., and Kalpaxis, D. L. (2004) Polyamines affect diversely the antibiotic potency: insight gained from kinetic studies of the blasticidin S and spiramycin interactions with functional ribosomes. J. Biol. Chem. 279, 26518-26525.
35. Kallia-Raftopoulos, S., Synetos, D., Ottenheijm, H. C., van den Broek, L. A., and Coutsogeorgopoulos, C. (1996) Sparsomycin and its analogues: a new approach for evaluating their potency as inhibitors of peptide bond formation. Mol. Pharmacol. 49, 1085-1091.
36. Ioannou, M., Coutsogeorgopoulos, C., and Synetos, D. (1998) Kinetics of inhibition of rabbit reticulocyte peptidyltransferase by anisomycin and sparsomycin. Mol. Pharmacol. 53, 1089-1096.
37. Fredrick, K. and Noller, H. F. (2003) Catalysis of ribosomal translocation by sparsomycin. Science 300, 1159-1162.
38. Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., and Franceschi, F. (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413, 814-821.
39. Contreras, A. and Vazquez, D. (1977) Cooperative and antagonistic interactions of peptidyl-tRNA and antibiotics with bacterial ribosomes. Eur. J. Biochem. 74, 539-547.
40. Drainas, D., Kalpaxis, D. L., and Coutsogeorgopoulos, C. (1987) Inhibition of ribosomal peptidyltransferase by chloramphenicol. Kinetic studies. Eur. J. Biochem. 164, 53-58.
41. Xaplanteri, M. A., Andreou, A., Dinos, G. P., and Kalpaxis D. L. (2003) Effect of polyamines on the inhibition of peptidyltransferase by antibiotics: revisiting the mechanism of chloramphenicol action. Nucleic Acids Res. 31, 5074-5083.
42. Menniger, J. R. and Otto, D. P. (1982) Erythromycin, carbomycin, and spiramycin inhibit protein synthesis by stimulating the dissociation of peptidyl-tRNA from ribosomes. Antimicrob. Agents Chemother. 21, 811-818.
43. Champney, W. S. and Burdine, R. (1996) 50S ribosomal subunit synthesis and translation are equivalent targets for erythromycin inhibition in Staphylococcus aureus. Antimicrob. Agents Chemother. 40, 1301-1303.
44. Dinos, G. P., Synetos, D., and Coutsogeorgopoulos, C. (1993) Interaction between the antibiotic spiramycin and a ribosomal complex active in peptide bond formation. Biochemistry 32, 10638-10647.
45. Petropoulos, A. D., Kouvela, E. C., Dinos, G. P., and Kalpaxis, D. L. (2008) Stepwise binding of tylosin and erythromycin to Escherichia coli ribosomes, characterized by kinetic and footprinting analysis. J. Biol. Chem. 283, 4756-4765.
46. Hansen, J. L., Ippolito, J. A., Ban, N., Nissen, P., Moore, P. B., and Steitz, T. A. (2002) The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol. Cell. 10, 117-128.
47. Weisblum, B. (1995) Erythromycin resistance by ribosome modification. Antimicrob. Agents Chemother. 39, 577-585.
48. Pfister, P., Jenni, S., Poehlsgaard, J., Thomas, A., Douthwaite, S., Ban, N., and Bottger, E. C. (2004) The structural basis of macrolide-ribosome binding assessed using mutagenesis of 23S rRNA positions 2058 and 2059. J. Mol. Biol. 342, 1569-1581.
49. Schluenzen, F., Harms, J. M., Franceschi, F., Hansen, H. A., Bartels, H., Zarivach, R., and Yonath, A. (2003) Structural basis for the antibiotic activity of ketolides and azalides. Structure 11, 329-338.
50. Johnston, N. J., Mukhtar, T. A., and Wright, G. D. (2002) Streptogramin antibiotics: mode of action and resistance. Curr. Drug Targets 3, 335-344.
51. Harms, J. M., Schlunzen, F., Fucini, P., Bartels, H., and Yonath, A. (2004) Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin. BMC Biol. 2, 4.
52. Agmon, I., Amit, M., Auerbach, T., Bashan, A., Baram, D., Bartels, H., Berisio, R., Greenberg, I., Harms, J., Hansen, H. S. A., Kessler, M., Pyetan, E., Schluenzen, F., Sittner, A., Yonath, A., Zarivach, R. (2004) Ribosomal crystallography: a flexible nucleotide anchoring tRNA translocation, facilitates peptide-bond formation, chirality discrimination and antibiotics synergism. FEBS Lett. 567, 20-26.
53. Kazantsev, A. V. and Pace, N. R. (2006) Bacterial RNase P: a new view of an ancient enzyme. Nat. Rev. Microbiol. 4, 729-740.
54. Walker, S. C. and Engelke, D. R. (2006) Ribonuclease P: the evolution of an ancient RNA enzyme. Crit. Rev. Biochem. Mol. Biol. 41, 77-102.
55. Kurz, J. C. and Fierke, C. A. (2002) The affinity of magnesium binding sites in the Bacillus subtilis RNase P X pre-tRNA complex is enhanced by the protein subunit. Biochemistry 41, 9545-9558.
56. Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5, 587-595.
57. Tekos, A., Stathopoulos, C., and Drainas, D. (1998) Bimodal action of alkaline earth cations on Dictyostelium discoideum ribonuclease P activity. Biochemistry 37, 15474-15480.
58. Brännvall, M. and Kirsebom, L. A. (2001) Metal ion cooperativity in ribozyme cleavage of RNA. Proc. Natl. Acad. Sci. USA 98, 12943-12947.
59. Gopalan, V., Baxevanis, A. D., Landsman, D., and Altman, S. (1997) Analysis of the functional role of conserved residues in the protein subunit of ribonuclease P from Escherichia coli. J. Mol. Biol. 267, 818-829.
60. Niranjanakumari, S., Stams, T., Crary, S. M., Christianson, D. W., and Fierke, C. A. (1998) Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc. Natl. Acad. Sci. USA 95, 15212-15217.
61. Asp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry 44, 16130-16139.
62. Sun, L., Campbell, F. E., Zahler, N. H., and Harris, M. E. (2006) Evidence that substrate-specific effects of C5 protein lead to uniformity in binding and catalysis by RNase P. EMBO J. 25, 3998-4007.
63. Buck, A. H., Dalby, A. B., Poole, A. W., Kazantsev, A. V., and Pace, N. R. (2005) Protein activation of a ribozyme: the role of bacterial RNase P protein. EMBO J. 24, 3360-3368.
64. Westhof, E., Wesolowski, D., and Altman, S. (1996) Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent. J. Mol. Biol. 258, 600-613.
65. Fang, X. W., Yang, X. J., Littrell, K., Niranjanakumari, S., Thiyagarajan, P., Fierke, C. A., Sosnick, T. R., and Pan, T. (2001) The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA 7, 233-241.
66. Tekos, A., Tsagla, A., Stathopoulos, C., and Drainas, D. (2000) Inhibition of eukaryotic ribonuclease P activity by aminoglycosides: kinetic studies. FEBS Lett. 485, 71-75.
67. Mikkelsen, N. E., Brännvall, M., Virtanen, A., and Kirsebom, L. A. (1999) Inhibition of RNase P RNA cleavage by aminoglycosides. Proc. Natl. Acad. Sci. USA 96, 6155-6160.
68. Hermann T. (2005) Drugs targeting the ribosome. Curr. Opin. Struct. Biol. 15, 355-366.
69. Toumpeki, C., Vourekas, A., Kalavrizioti, D., Stamatopoulou, V., and Drainas, D. Activation of bacterial Ribonuclease P by macrolides. Biochemistry, 47, 4112-4118.
70. Vicens, Q. and Westhof, E. (2003) Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of X-ray crystal structures. Biopolymers 70, 42-57.
71. Eubank, T. D., Biswas, R., Jovanovic, M., Litovchick, A., Lapidot, A., and Gopalan, V. (2002) Inhibition of bacterial RNase P by aminoglycoside- arginine conjugates. FEBS Lett. 511, 107-112.
72. Kawamoto, S. A., Sudhahar, C. G., Hatfield, C. L., Sun, J., Behrman, E. J., and Gopalan, V. (2008) Studies on the mechanism of inhibition of bacterial ribonuclease P by aminoglycoside derivatives. Nucleic Acids Res. 36, 697-704.
73. Vioque, A. (1989) Protein synthesis inhibitors and catalytic RNA. Effect of puromycin on tRNA precursor processing by the RNA component of Escherichia coli RNase P. FEBS Lett. 246, 137-139.
74. Stathopoulos, C., Tsagla, A., Tekos, A., and Drainas, D. (2000) Effect of peptidyltransferase inhibitors on ribonuclease P activity from Dictyostelium discoideum. Effect of antibiotics on RNase P. Mol. Biol. Rep. 27, 107-111.
75. Kalavrizioti, D., Vourekas, A., Tekos, A., Tsagla, A., Stathopoulos, C., and Drainas, D. (2003) Kinetics of inhibition of ribonuclease P activity by peptidyl transferase inhibitors. Effect of antibiotics on RNase P. Mol. Biol. Rep. 30, 9-14.
76. Hori, Y., Rogert, M. C., Tanaka, T., Kikuchi, Y., Bichenkova, E. V., Wilton, A. N., Gbaj, A., and Douglas, K. T. (2005) Porphyrins and porphines bind strongly and specifically to tRNA, precursor tRNA and to M1 RNA and inhibit the ribonuclease P ribozyme reaction. Biochim. Biophys. Acta 1730, 47-55.
77. Papadimou, E., Georgiou, S., Tsambaos, D., and Drainas, D. (1998) Inhibition of ribonuclease P activity by retinoids. J. Biol. Chem. 273, 24375-24378.
78. Papadimou, E., Monastirli, A., Tsambaos, D., Merk, H. F., and Drainas, D. (2000) Inhibitory effects of arotinoids on tRNA biogenesis. Skin Pharmacol. Appl. Skin Physiol. 13, 345-351.
79. Papadimou, E., Monastirli, A., Stathopoulos, C., Tsambaos, D., and Drainas, D. (2000) Modulation of ribonuclease P activity by calcipotriol. Eur J Biochem. 267, 1173-1177.
80. Drainas, D., Papadimou, E., Monastirli, A., Tsambaos, D., and Merk, H. F. (2000) Dose-dependent inhibition of ribonuclease P activity by anthralin. Skin Pharmacol. Appl. Skin Physiol. 13, 128-132.
81. Papadimou, E., Monastirli, A., Tsambaos, D., and Drainas, D. (2000) Additive inhibitory effect of calcipotriol and anthralin on ribonuclease P activity. Biochem. Pharmacol. 60, 91-94.
82. Torres-Larios, A., Swinger, K. K., Krasilnikov, A. S., Pan, T., and Mondragón, A. (2005) Crystal structure of the RNA component of bacterial ribonuclease P. Nature 437, 584-587.
83. Kazantsev, A. V., Krivenko, A. A., Harrington, D. J., Holbrook, S. R., Adams, P. D., and Pace, N. R. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl. Acad. Sci. USA 102, 13392-13397.
84. Cech, T. R. (1990) Self-splicing of group I introns. Annu. Rev. Biochem. 59, 543-568.
85. Adams, P. L., Stahley, M. R., Gill, M. L., Kosek, A. B., Wang, J., and Strobel, S. A. (2004) Crystal structure of a group I intron splicing intermediate. RNA 10, 1867-1887. (Pubitemid 39557825)
86. 2+ stoichiometry for folding an RNA metal ion core. J. Am. Chem. Soc. 127, 8272-8273.
87. Travers, K. J., Boyd, N., and Hershlag, D. (2007) Low specificity of metal ion binding in the metal ion core of a folded RNA. RNA 13, 1205-1213.
88. Takamoto, K., Das R., He, Q., Doniach, S., Brenowitz, M., Herschlag, D., and Chance, M. R. (2004) Principles of RNA compaction: insights from the equilibrioum folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 343, 1195-1206.
89. Forconi, M., Piccirilli, J. A., and Herschlag, D. (2007) Modulation of individual steps in group I intron catalysis by a peripheral metal ion. RNA 13, 1656-1667.
90. Bass, B. and Cech, T. R. (1986) Ribozyme inhibitors: deoxyguanosine and dideoxygouanosine are competitive inhibitors of self-splicing of the Tetrahymena ribosomal RNA precursor. Biochemistry 25, 4473-4477.
91. Yarus, M. (1988) A specific amino acid binding site composed of RNA. Science 240, 1751-1758.
92. von Ahsen, U. and Schroeder R. (1991) Streptomycin inhibits splicing of group I introns by competition with the guanosine substrate. Nucleic Acids Res. 19, 2261-2265.
93. Wank, H., Rogers, J., Davies, J., and Schroeder, R. (1994) Peptide antibiotics of the tuberactinomycin family as inhibitors of group I intron RNA splicing. J. Mol. Biol. 236, 1001-1010.
94. Rogers, J. and Davies, J. (2001) The pseudodisaccharides: a novel class of group I intron splicing inhibitors. Nucleic Acids Res. 24, 4983-4988.
95. Wank, H. and Schroeder, R. (1996) Antibiotic-induced oligomerisation of group I intron RNA. J. Mol. Biol. 258, 53-61.
96. 2+ mimicry in the promotion of group I ribozyme activities by aminoglycoside antibiotics. Biochem. Biophys. Res. Commun. 344, 1246-1252.
97. Myers, C. A., Wallweber, G. J., Rennard, R., Kemel, Y., Caprara, M. G., Mohr, G., and Lambowitz, A. M. (1996) A tyrosyl-tRNA synthetase suppresses structural defects in the two major helical domains of the group I intron catalytic core. J. Mol. Biol. 262, 87-104.
98. von Ahsen, U., Danies, J., and Schroeder, R. (1991) Antibiotic inhibition of group I ribozyme function. Nature 353, 368-370.
99. Liu, Y., Tidwell, R. R., and Leibowitz, M. J. (1994) Inhibition of in vitro splicing of a group I intron of Pneumocystis carnii. J. Euk. Microbiol. 41, 31-38.
100. Park, I. K., Lim, E. H., and Shin, S. (2000) Spectinomycin inhibits the self-splicing of the group I intron RNA. Biochem. Biophys. Res. Commun. 269, 574-579.
101. 2+ ions promote the self-splicing of the td intron RNA inhibited by spectinomycin. Biochim. Biophys. Acta 1492, 94-99.
102. von Ahsen, U., Davies, J., and Schroeder, R. (1992) Non-competitive inhibition of group I intron RNA self-splicing by aminoglycoside antibiotics. J. Mol. Biol. 226, 935-941.
103. von Ahsen, U. and Noller, H. F. (1993) Footprinting the sites of interaction of antibiotics with catalytic group I intro RNA. Science 260, 1500-1503.
104. Davies, J., von Ahsen, U., and Schroeder, R. (1993) Antibiotics and the RNA world: a role for low molecular-weight effectors in biochemical evaluation. In The RNA World. pp. 185-204, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
105. Schroeder, R., Streicher, B., and Wank, H. (1993) Splice-site selection and decoding, are they related? Science 260, 1500-1503.
106. Kim, J. Y. and Park, I. K. (2000) The flavin coenzymes: a new class of group I intron inhibitors. Biochim. Biophys. Acta 1475, 56-61.
107. + inhibits the self-splicing of the group I introns. Biochem. Biophys. Res. Commun. 281, 206-211.
108. +. Mol. Cell. Biochem. 252, 285-293.
109. Ahn, S. J. and Park, I. K. (2001) The coenzyme thiamine pyrophosphate inhibits the self-splicing of the group I introns. Int. J. Biochem. Cell Biol. 35, 157-167.
110. Jung, C., Shin, S., and Park, I. K. (2005) Pyridoxal phosphate inhibits the group I intron splicing. Mol. Cell. Biochem. 280, 17-23.
111. Long, D. M. and Uhlenbeck, O. C. (1993) Self-cleaving catalytic RNA. FASEB J. 7, 25-30.
112. Forster, A. C. and Symons, R. H. (1987) Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site. Cell 50, 9-16.
113. Epstein, L. M. and Gall, J. G. (1987) Self-cleaving transcripts of satellite DNA from the newt. Cell 48, 535-543.
114. Uhlenbeck O. C. (1987) A small catalytic oligoribonucleotide. Nature 328, 596-600.
115. Haseloff, J. and Gerlach, W. L. (1988) Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334, 585-591.
116. Martick, M. and Scott, W. G. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126, 309-320.
117. Leclerc, F. and Karplus, M. (2006) Two-metal-ion mechanism for hammerhead-ribozyme catalysis. J. Phys. Chem. B 110, 3395-3409.
118. Dahm, S. C., Derrick, W. B., and Uhlenbeck, O. C. (1993) Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry 32, 13040-13045.
119. Schiemann, O., Fritscher, J., Kisseleva, N., Sigurdsson, S. T., and Prisner, T. F. (2003) Structural investigation of a high-affinity mnii binding site in the hammerhead ribozyme by epr spectroscopy and dft calculations. Effects of Neomycin B on metal-ion binding. ChemBioChem 4, 1057-1065.
120. Hansen, M. R., Simorre, J. P., Hanson, P., Mokler, V., Bellon, L., Beigelman, L., and Pardi, A. (1999) Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme. RNA 5, 1099-1104.
121. O'Rear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations. RNA 7, 537-545.
122. Curtis, E. A. and Bartel, D. P. (2001) The hammerhead cleavage reaction in monovalent cations. RNA 7, 546-552.
123. Markley, J. C., Godde, F., and Sigurdsson, S. T. (2001) Identification and characterization of a divalent metal ion-dependent cleavage site in the hammerhead ribozyme. Biochemistry 40, 13849-13856.
124. Borda, E. J., Markley, J. C., and Sigurdsson, S. T. (2003) Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change. Nucleic Acids Res. 31, 2595-2600.
125. Murray, J. B., Dunham, C. M., and Scott, W. G. (2002) A pH-dependent conformational change, rather than the chemical step, appears to be rate limiting in the hammerhead ribozyme cleavage reaction. J. Mol. Biol. 315, 121-130.
126. Hermann, T. and Westhof, E. (1998) Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J. Mol. Biol. 276, 903-912.
127. Jenne, A., Hartig, J. S., Piganeau, N., Tauer, A., Samarsky, D. A., Green, M. R., Davies, J., and Famulok, M. (2001) Rapid identification and characterization of hammerhead-ribozyme inhibitors using fluorescence-based technology. Nat. Biotechnol. 19, 56-61.
128. Stage, T. K., Hertel, K. J., and Uhlenbeck, O. C. (1995) Inhibition of the hammerhead ribozyme by neomycin. RNA 1, 95-101.
129. Tor, Y., Hermann, T., and Westhof, E. (1998) Deciphering RNA recognition: aminoglycoside binding to the hammerhead ribozyme. Chem. Biol. 5, R277-R283.
130. Dahm, S. C. and Uhlenbeck, O. C. (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30, 9464-9469.
131. Hammann, C., Hormes, R., Sczakiel, G., and Tabler, M. (1997) A spermidine-induced conformational change of long-armed hammerhead ribozymes: ionic requirements for fast cleavage kinetics. Nucleic Acids Res. 25, 4715-4722.
132. Murray, J. B. and Arnold, J. R. P. (1996) Antibiotic interactions with the hammerhead ribozyme: tetracyclines as a new class of hammerhead inhibitor. Biochem. J. 317, 855-860.
133. Goodchild, J. (1992) Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2′-O-methylation. Nucleic Acids Res. 20, 4607-4612.
134. Jankowsky, E. and Schwenzer, B. (1996) Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme. Nucleic Acids Res. 24, 423-429.
135. Herschlag, D., Khosla, M., Tsuchihashi, Z., and Karpel, R. L. (1994) An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 13, 2913-2924.
136. Müller, G., Strack, B., Danull, J., Sproat, B., Surovoy, A., Jung, G., and Moelling, K. (1994) Amino acid requirements of the nucleocapsid protein of HIV-1 for increasing catalytic activity of a Ki-ras ribozyme in vitro. J. Mol. Biol. 242, 422-429.
137. Tsuchihashi, Z., Khosla, M., and Herschlag, D. (1993) Protein enhancement of hammerhead ribozyme catalysis. Science 262, 99-102.
138. Bertand, E., and Rossi, J. J. (1994) Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein A1. EMBO J. 13, 2904-2912.
139. Stage-Zimmermann, T. K. and Uhlenbeck, O. C. (2001) A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase. Nat. Struct. Biol. 8, 863-867.
140. Buzayan, J. M., Gerlach, W. L., and Bruening, G. (1986) Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323, 349-353.
141. Buzayan, J. M., Gerlach, W. L., 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.
142. Ferré-D'Amaré, A. R. (2004) The hairpin ribozyme. Biopolymers 73, 71-78.
143. 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.
144. Anderson, P., Monforte, J., Tritz, R., Nesbitt, S., Hearst, J., and Hampel, A. (1994) Mutagenesis of the hairpin ribozyme. Nucleic Acids Res. 22, 1096-1100.
145. Rueda, D., Bokinsky, G., Rhodes, M. M., Rust, M. J., Zhuang, X., and Walter, N. G. (2004) Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proc. Natl. Acad. Sci. USA 101, 10066-10071.
146. Zhao, Z. Y., Wilson, T. J., Maxwell, K., Lilley, D. M. (2000) The folding of the hairpin ribozyme: dependence on the loops and the junction. RNA 6, 1833-1846.
147. Chowrira, B. M., Berzal-Herranz, A., and Burke, J. M. (1993). Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry 32, 1088-1095.
148. Walter, F., Murchie, A. I., Thomson, J. B., and Lilley, D. M. (1998). Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions. Biochemistry 37, 14195-14203.
149. Young, K. J., Gill, F., and Grasby, J. A. (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res. 25, 3760-3766.
150. Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol. 4, 619-630.
151. Hampel, A. and Cowan, J. A. (1997) A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem. Biol. 4, 513-517.
152. Fedor, M. J. (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry 38, 11040-11050.
153. Earnshaw, D. J. and Gait, M. J. (1998) Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acids Res. 26, 5551-5561.
154. Welz, R., Schmidt, C., and Müller, S. (2001) Spermine supports catalysis of hairpin ribozyme variants to differing extents. Biochem. Biophys. Res. Commun. 283, 648-654.
155. Stolze, K., Holmes, S. C., Earnshaw, D. J., Singh, M., Stetsenko, D., Williams, D., and Gait, M. J. (2001) Novel spermine-amino acid conjugates and basic tripeptides enhance cleavage of the hairpin ribozyme at low magnesium ion concentration. Bioorg. Med. Chem. Lett. 11, 3007-3010.
156. Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., and Breaker, R. R. (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281-286.
157. Yen, L., Svendsen, J., Lee, J. S., Gray, J. T., Magnier, M., Baba, T., D'Amato, R. J., and Mulligan, R. C. (2004) Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431, 471-476.
158. Breaker, R. R. (2002) Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31-39.
159. Silverman, S. K. (2003) Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377-383.
160. Wang, D. Y., Lai, B. H., and Sen, D. (2002) A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J. Mol. Biol. 318, 33-43.
161. Saito, H. and Inoue, T. (2007) RNA and RNP as new molecular parts in synthetic biology. J Biotechnol 132, 1-7.
162. Davies, J. (1990) What are antibiotics? Archaic functions for modern activities. Mol Moicrobiol. 4, 1227-1232.
163. Davies, J., von Ahsen, U., and Schroeder, R. (1993) Antibiotics and the RNA world: a role for low molecular - weight effectors in biochemical evaluation. In The RNA world, Cold Spring Harbor Laboratory Press, Cold Spring Harbor NY, pp. 185-204.
164. Müller, U. F. and Bartel, D.P. (2008) Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA 14, 552-562.