Building a Kinetic Framework for Group II Intron Ribozyme Activity: Quantitation of Interdomain Binding and Reaction Rate (original) (raw)

ArticleMarch 1, 1994

Building a Kinetic Framework for Group II Intron Ribozyme Activity: Quantitation of Interdomain Binding and Reaction Rate

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Biochemistry

Cite this: Biochemistry 1994, 33, 9

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  2. Olga Fedorova, Grace Arhin, Anna Marie Pyle, Aaron T. Frank. In Silico Discovery of Group II Intron RNA Splicing Inhibitors. ACS Chemical Biology 2023, 18 (9) , 1968-1975. https://doi.org/10.1021/acschembio.3c00160
  3. Rhiju Das, Rick Russell. How to Kinetically Dissect an RNA Machine. Biochemistry 2021, 60 (46) , 3485-3490. https://doi.org/10.1021/acs.biochem.1c00392
  4. Yun Fang,, Qi Cai, and, Peter Z. Qin. The Procapsid Binding Domain of φ29 Packaging RNA Has a Modular Architecture and Requires 2‘-Hydroxyl Groups in Packaging RNA Interaction. Biochemistry 2005, 44 (26) , 9348-9358. https://doi.org/10.1021/bi0475020
  5. Yangming Wang and, Scott K. Silverman. Characterization of Deoxyribozymes That Synthesize Branched RNA. Biochemistry 2003, 42 (51) , 15252-15263. https://doi.org/10.1021/bi0355847
  6. Qusay Q Omran, Olga Fedorova, Tianshuo Liu, Anna M Pyle. A molecular beacon assay for monitoring RNA splicing. Nucleic Acids Research 2022, 50 (13) , e74-e74. https://doi.org/10.1093/nar/gkac242
  7. Susann Zelger-Paulus, Mélodie C. A. S. Hadzic, Roland K. O. Sigel, Richard Börner. Encapsulation of Fluorescently Labeled RNAs into Surface-Tethered Vesicles for Single-Molecule FRET Studies in TIRF Microscopy. 2020, 1-16. https://doi.org/10.1007/978-1-0716-0278-2_1
  8. Olga Fedorova, G. Erik Jagdmann, Rebecca L. Adams, Lin Yuan, Michael C. Van Zandt, Anna Marie Pyle. Small molecules that target group II introns are potent antifungal agents. Nature Chemical Biology 2018, 14 (12) , 1073-1078. https://doi.org/10.1038/s41589-018-0142-0
  9. Lorraine Ling, Sherwin P. Montaño, Robert T. Sauer, Phoebe A. Rice, Tania A. Baker. Deciphering the Roles of Multicomponent Recognition Signals by the AAA + Unfoldase ClpX. Journal of Molecular Biology 2015, 427 (18) , 2966-2982. https://doi.org/10.1016/j.jmb.2015.03.008
  10. Isabel Chillón, María Dolores Molina-Sánchez, Olga Fedorova, Fernando Manuel García-Rodríguez, Francisco Martínez-Abarca, Nicolás Toro. In vitro characterization of the splicing efficiency and fidelity of the RmInt1 group II intron as a means of controlling the dispersion of its host mobile element. RNA 2014, 20 (12) , 2000-2010. https://doi.org/10.1261/rna.047407.114
  11. Srinivas Somarowthu, Michal Legiewicz, Kevin S. Keating, Anna Marie Pyle. Visualizing the ai5γ group IIB intron. Nucleic Acids Research 2014, 42 (3) , 1947-1958. https://doi.org/10.1093/nar/gkt1051
  12. Nora Zingler. The Kinetics of Ribozyme Cleavage: A Tool to Analyze RNA Folding as a Function of Catalysis. 2014, 209-224. https://doi.org/10.1007/978-1-62703-667-2_12
  13. Marco Marcia, Anna Marie Pyle. Visualizing Group II Intron Catalysis through the Stages of Splicing. Cell 2012, 151 (3) , 497-507. https://doi.org/10.1016/j.cell.2012.09.033
  14. Olga Fedorova, Anna Marie Pyle. The Brace for a Growing Scaffold: Mss116 Protein Promotes RNA Folding by Stabilizing an Early Assembly Intermediate. Journal of Molecular Biology 2012, 422 (3) , 347-365. https://doi.org/10.1016/j.jmb.2012.05.037
  15. Olga Fedorova. Kinetic Characterization of Group II Intron Folding and Splicing. 2012, 91-111. https://doi.org/10.1007/978-1-61779-545-9_7
  16. Jeffrey P. Potratz, Rick Russell. RNA Catalysis as a Probe for Chaperone Activity of DEAD-Box Helicases. 2012, 111-130. https://doi.org/10.1016/B978-0-12-396546-2.00005-X
  17. Todd C. Appleby, Robert Anderson, Olga Fedorova, Anna M. Pyle, Ruth Wang, Xiaohong Liu, Katherine M. Brendza, John R. Somoza. Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV. Journal of Molecular Biology 2011, 405 (5) , 1139-1153. https://doi.org/10.1016/j.jmb.2010.11.034
  18. Caroline Lee, Yasaman Jaladat, Afshin Mohammadi, Armin Sharifi, Sarah Geisler, Saba Valadkhan. Metal binding and substrate positioning by evolutionarily invariant U6 sequences in catalytically active protein-free snRNAs. RNA 2010, 16 (11) , 2226-2238. https://doi.org/10.1261/rna.2170910
  19. Olga Fedorova, Amanda Solem, Anna Marie Pyle. Protein-Facilitated Folding of Group II Intron Ribozymes. Journal of Molecular Biology 2010, 397 (3) , 799-813. https://doi.org/10.1016/j.jmb.2010.02.001
  20. Lei Sun, Frank E. Campbell, Lindsay E. Yandek, Michael E. Harris. Binding of C5 Protein to P RNA Enhances the Rate Constant for Catalysis for P RNA Processing of Pre-tRNAs Lacking a Consensus G(+1)/C(+72) Pair. Journal of Molecular Biology 2010, 395 (5) , 1019-1037. https://doi.org/10.1016/j.jmb.2009.11.027
  21. Navtej Toor, Kevin S. Keating, Olga Fedorova, Kanagalaghatta Rajashankar, Jimin Wang, Anna Marie Pyle. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 2010, 16 (1) , 57-69. https://doi.org/10.1261/rna.1844010
  22. Michèle C. Erat, Roland K. O. Sigel. Divalent metal ions tune the self-splicing reaction of the yeast mitochondrial group II intron Sc.ai5γ. JBIC Journal of Biological Inorganic Chemistry 2008, 13 (6) , 1025-1036. https://doi.org/10.1007/s00775-008-0390-7
  23. P. Patrick Dotson II, Joy Sinha, Stephen M. Testa. Kinetic characterization of the first step of the ribozyme‐catalyzed trans excision‐splicing reaction. The FEBS Journal 2008, 275 (12) , 3110-3122. https://doi.org/10.1111/j.1742-4658.2008.06464.x
  24. Olga Fedorova, Anna Marie Pyle. A conserved element that stabilizes the group II intron active site. RNA 2008, 14 (6) , 1048-1056. https://doi.org/10.1261/rna.942308
  25. Aliaa H. Abdelhakim, Elizabeth C. Oakes, Robert T. Sauer, Tania A. Baker. Unique Contacts Direct High-Priority Recognition of the Tetrameric Mu Transposase-DNA Complex by the AAA+ Unfoldase ClpX. Molecular Cell 2008, 30 (1) , 39-50. https://doi.org/10.1016/j.molcel.2008.02.013
  26. Alexandre de Lencastre, Anna Marie Pyle. Three essential and conserved regions of the group II intron are proximal to the 5′-splice site. RNA 2008, 14 (1) , 11-24. https://doi.org/10.1261/rna.774008
  27. Anna Marie Pyle. Group II Introns: Catalysts for Splicing, Genomic Change and Evolution. 2007, 201-228. https://doi.org/10.1039/9781847557988-00201
  28. Olga Fedorova, Christina Waldsich, Anna Marie Pyle. Group II Intron Folding under Near-physiological Conditions: Collapsing to the Near-native State. Journal of Molecular Biology 2007, 366 (4) , 1099-1114. https://doi.org/10.1016/j.jmb.2006.12.003
  29. Hani S. Zaher, R. Ammon Watkins, Peter J. Unrau. Two independently selected capping ribozymes share similar substrate requirements. RNA 2006, 12 (11) , 1949-1958. https://doi.org/10.1261/rna.131306
  30. Stephanie Glanz, Astrid Bunse, Andrea Wimbert, Carsten Balczun, Ulrich Kück. A nucleosome assembly protein-like polypeptide binds to chloroplast group II intron RNA in Chlamydomonas reinhardtii. Nucleic Acids Research 2006, 34 (18) , 5337-5351. https://doi.org/10.1093/nar/gkl611
  31. Stephanie Hamill, Anna Marie Pyle. The Receptor for Branch-Site Docking within a Group II Intron Active Site. Molecular Cell 2006, 23 (6) , 831-840. https://doi.org/10.1016/j.molcel.2006.07.017
  32. Orlando H. Gumbs, Richard A. Padgett, Kwaku T. Dayie. Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme. RNA 2006, 12 (9) , 1693-1707. https://doi.org/10.1261/rna.137006
  33. Souta Horie, Yoshiya Ikawa, Tan Inoue. Structural and biochemical characterization of DSL ribozyme. Biochemical and Biophysical Research Communications 2006, 339 (1) , 115-121. https://doi.org/10.1016/j.bbrc.2005.11.007
  34. Olga Fedorova, Anna Marie Pyle. Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. The EMBO Journal 2005, 24 (22) , 3906-3916. https://doi.org/10.1038/sj.emboj.7600852
  35. Roland K. O. Sigel. Group II Intron Ribozymes and Metal Ions – A Delicate Relationship. European Journal of Inorganic Chemistry 2005, 2005 (12) , 2281-2292. https://doi.org/10.1002/ejic.200401007
  36. R. L. Katona, I. Cserpán, K. Fátyol, Erika Csonka, G. Hadlaczky. Transgenic mice, carrying an expressed anti-HIV ribozyme in their genome, show no sign of phenotypic alterations. Acta Biologica Hungarica 2005, 56 (1-2) , 67-74. https://doi.org/10.1556/ABiol.56.2005.1-2.7
  37. Eric L. Christian. Identification and Characterization of Metal Ion Binding by Thiophilic Metal Ion Rescue. 2005, 319-344. https://doi.org/10.1002/9783527619504.ch19
  38. Peter M. Gordon, Robert Fong, Shirshendu K. Deb, Nan-Sheng Li, Jason P. Schwans, Jing-Dong Ye, Joseph A. Piccirilli. New Strategies for Exploring RNA's 2′-OH Expose the Importance of Solvent during Group II Intron Catalysis. Chemistry & Biology 2004, 11 (2) , 237-246. https://doi.org/10.1016/j.chembiol.2004.02.011
  39. Bruno Sargueil, Ken J. Hampel, Dominic Lambert, John M. Burke. In Vitro Selection of Second Site Revertants Analysis of the Hairpin Ribozyme Active Site. Journal of Biological Chemistry 2003, 278 (52) , 52783-52791. https://doi.org/10.1074/jbc.M306703200
  40. Olga Fedorova, Therese Mitros, Anna Marie Pyle. Domains 2 and 3 Interact to Form Critical Elements of the Group II Intron Active Site. Journal of Molecular Biology 2003, 330 (2) , 197-209. https://doi.org/10.1016/S0022-2836(03)00594-1
  41. Olga Fedorova, Linhui Julie Su, Anna Marie Pyle. Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods 2002, 28 (3) , 323-335. https://doi.org/10.1016/S1046-2023(02)00239-6
  42. Lan Zhang, Jennifer A. Doudna. Structural Insights into Group II Intron Catalysis and Branch-Site Selection. Science 2002, 295 (5562) , 2084-2088. https://doi.org/10.1126/science.1069268
  43. Scott A. Strobel. Self‐Splicing Introns. 2002https://doi.org/10.1002/047120918X.emb1395
  44. Linhui Julie Su, Peter Z Qin, William J Michels, Anna Marie Pyle. Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group II intron ribozyme. Journal of Molecular Biology 2001, 306 (4) , 655-668. https://doi.org/10.1006/jmbi.2000.4323
  45. Marc Boudvillain, Alexandre de Lencastre, Anna Marie Pyle. A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron. Nature 2000, 406 (6793) , 315-318. https://doi.org/10.1038/35018589
  46. Martha J Fedor. Structure and function of the hairpin ribozyme. Journal of Molecular Biology 2000, 297 (2) , 269-291. https://doi.org/10.1006/jmbi.2000.3560
  47. Peter Zhifeng Qin, Anna Marie Pyle. Antagonistic substrate binding by a group II intron ribozyme. Journal of Molecular Biology 1999, 291 (1) , 15-27. https://doi.org/10.1006/jmbi.1999.2922
  48. Marc Boudvillain, Anna Marie Pyle. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. The EMBO Journal 1998, 17 (23) , 7091-7104. https://doi.org/10.1093/emboj/17.23.7091
  49. Boyana B. Konforti, Qiaolian Liu, Anna Marie Pyle. A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme. The EMBO Journal 1998, 17 (23) , 7105-7117. https://doi.org/10.1093/emboj/17.23.7105
  50. Adrian R Ferré-D’Amaré, Kaihong Zhou, Jennifer A Doudna. A general module for RNA crystallization. Journal of Molecular Biology 1998, 279 (3) , 621-631. https://doi.org/10.1006/jmbi.1998.1789
  51. Peter Zhifeng Qin, Anna Marie Pyle. The architectural organization and mechanistic function of group II intron structural elements. Current Opinion in Structural Biology 1998, 8 (3) , 301-308. https://doi.org/10.1016/S0959-440X(98)80062-6
  52. Boyana B Konforti, Dana L Abramovitz, Carlos M Duarte, Alex Karpeisky, Leonid Beigelman, Anna Marie Pyle. Ribozyme Catalysis from the Major Groove of Group II Intron Domain 5. Molecular Cell 1998, 1 (3) , 433-441. https://doi.org/10.1016/S1097-2765(00)80043-X
  53. Joshua T. Jones, Bruce A. Sullenger. Evaluating and enhancing ribozyme reaction efficiency in mammalian cells. Nature Biotechnology 1997, 15 (9) , 902-905. https://doi.org/10.1038/nbt0997-902
  54. Geeta J. Narlikar, Daniel Herschlag. MECHANISTIC ASPECTS OF ENZYMATIC CATALYSIS: Lessons from Comparison of RNA and Protein Enzymes. Annual Review of Biochemistry 1997, 66 (1) , 19-59. https://doi.org/10.1146/annurev.biochem.66.1.19
  55. Philippe Brion, Eric Westhof. HIERARCHY AND DYNAMICS OF RNA FOLDING. Annual Review of Biophysics and Biomolecular Structure 1997, 26 (1) , 113-137. https://doi.org/10.1146/annurev.biophys.26.1.113
  56. José A. Esteban, Aloke Raj Banerjee, John M. Burke. Kinetic Mechanism of the Hairpin Ribozyme. Journal of Biological Chemistry 1997, 272 (21) , 13629-13639. https://doi.org/10.1074/jbc.272.21.13629
  57. M. Hetzer, R. J. Schweyen, M. W. Mueller. DNA polymerization catalysed by a group II intron RNA in vitro. Nucleic Acids Research 1997, 25 (9) , 1825-1829. https://doi.org/10.1093/nar/25.9.1825
  58. Maria Costa, Elise Dème, Alain Jacquier, François Michel. Multiple tertiary interactions involving domain II of group II self-splicing introns 1 1Edited by M. Yaniv. Journal of Molecular Biology 1997, 267 (3) , 520-536. https://doi.org/10.1006/jmbi.1996.0882
  59. Michael A. Tanner, Thomas R. Cech. Joining the Two Domains of a Group I Ribozyme to Form the Catalytic Core. Science 1997, 275 (5301) , 847-849. https://doi.org/10.1126/science.275.5301.847
  60. Dana L Abramovitz, Anna Marie Pyle. Remarkable morphological variability of a common RNA folding motif: the GNRATetraloop-receptor interaction. Journal of Molecular Biology 1997, 266 (3) , 493-506. https://doi.org/10.1006/jmbi.1996.0810
  61. Scott C. Boulanger, Peggy Ho Faix, Haiyan Yang, Jin Zhuo, James S. Franzen, Craig L. Peebles, Philip S. Perlman. Length Changes in the Joining Segment between Domains 5 and 6 of a Group II Intron Inhibit Self-Splicing and Alter 3′ Splice Site Selection. Molecular and Cellular Biology 1996, 16 (10) , 5896-5904. https://doi.org/10.1128/MCB.16.10.5896
  62. Dana L. Abramovitz, Richard A. Friedman, Anna Marie Pyle. Catalytic Role of 2′-Hydroxyl Groups Within a Group II Intron Active Site. Science 1996, 271 (5254) , 1410-1413. https://doi.org/10.1126/science.271.5254.1410
  63. A. M. Pyle. Catalytic Reaction Mechanisms and Structural Features of Group II Intron Ribozymes. 1996, 75-107. https://doi.org/10.1007/978-3-642-61202-2_5
  64. A. Jacquier. Group II introns: Elaborate ribozymes. Biochimie 1996, 78 (6) , 474-487. https://doi.org/10.1016/0300-9084(96)84754-7
  65. Philip S. Perlman, Mircea Podar. [8] Reactions catalyzed by group II introns in Vitro. 1996, 66-86. https://doi.org/10.1016/S0076-6879(96)64010-5
  66. Samuel E. Butcher, Joyce E. Heckman, John M. Burke. Reconstitution of Hairpin Ribozyme Activity following Separation of Functional Domains. Journal of Biological Chemistry 1995, 270 (50) , 29648-29651. https://doi.org/10.1074/jbc.270.50.29648
  67. Edmund A. Griffiin, Zhifeng Qin, William J. Michels, Anna Marie Pyle. Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups. Chemistry & Biology 1995, 2 (11) , 761-770. https://doi.org/10.1016/1074-5521(95)90104-3
  68. Scott C. Boulanger, Scott M. Belcher, Udo Schmidt, Sulayman D. Dib-Hajj, Troy Schmidt, Philip S. Perlman. Studies of Point Mutants Define Three Essential Paired Nucleotides in the Domain 5 Substructure of a Group II Intron. Molecular and Cellular Biology 1995, 15 (8) , 4479-4488. https://doi.org/10.1128/MCB.15.8.4479
  69. Anna Marie Pyle, Justin B Green. RNA folding. Current Opinion in Structural Biology 1995, 5 (3) , 303-310. https://doi.org/10.1016/0959-440X(95)80091-3
  70. Guillaume Chanfreau, Alain Jacquier. Catalytic Site Components Common to Both Splicing Steps of a Group II Intron. Science 1994, 266 (5189) , 1383-1387. https://doi.org/10.1126/science.7973729
  71. Jon R. Lorsch, Jack W. Szostak. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 1994, 371 (6492) , 31-36. https://doi.org/10.1038/371031a0

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