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. 1996 Oct 1;24(19):3722–3727. doi: 10.1093/nar/24.19.3722

Conserved thermochemistry of guanosine nucleophile binding for structurally distinct group I ribozymes.

L Y Kuo 1, T R Cech 1
PMCID: PMC146156  PMID: 8871550

Abstract

We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is similar for the two ribozymes. The delta(H)degrees' and delta(S)degrees' for pG binding to the Anabaena ribozyme--RNA substrate complex (E x S) are 3.4 +/- 4 kcal/mol and 27 +/- 10 e.u., respectively. The negligible enthalpic contribution and positive entropy change were found previously for the Tetrahymena ribozyme, and are considered remarkable for a hydrogen-bonding interaction between a nucleotide and a nucleic acid. These thermodynamic values may reflect conformational changes or water release upon pG binding that are comparable for the two ribozymes. In addition, the apparent chemical steps of the two ribozyme reactions share similar activation energies and a positive deltaS++. It now appears that such thermochemical values for guanosine binding and activation may be intrinsic properties of the group I intron catalytic center.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bevilacqua P. C., Johnson K. A., Turner D. H. Cooperative and anticooperative binding to a ribozyme. Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8357–8361. doi: 10.1073/pnas.90.18.8357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bevilacqua P. C., Kierzek R., Johnson K. A., Turner D. H. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science. 1992 Nov 20;258(5086):1355–1358. doi: 10.1126/science.1455230. [DOI] [PubMed] [Google Scholar]
  3. Burz D. S., Allewell N. M. Interactions of ionizable groups in Escherichia coli aspartate transcarbamylase with adenosine and cytidine 5'-triphosphates. Biochemistry. 1982 Dec 21;21(26):6647–6655. doi: 10.1021/bi00269a006. [DOI] [PubMed] [Google Scholar]
  4. Cech T. R., Herschlag D., Piccirilli J. A., Pyle A. M. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. J Biol Chem. 1992 Sep 5;267(25):17479–17482. [PubMed] [Google Scholar]
  5. Cech T. R. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543–568. doi: 10.1146/annurev.bi.59.070190.002551. [DOI] [PubMed] [Google Scholar]
  6. Davies R. W., Waring R. B., Ray J. A., Brown T. A., Scazzocchio C. Making ends meet: a model for RNA splicing in fungal mitochondria. Nature. 1982 Dec 23;300(5894):719–724. doi: 10.1038/300719a0. [DOI] [PubMed] [Google Scholar]
  7. Dieckmann T., Suzuki E., Nakamura G. K., Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA. 1996 Jul;2(7):628–640. [PMC free article] [PubMed] [Google Scholar]
  8. Doudna J. A., Szostak J. W. RNA-catalysed synthesis of complementary-strand RNA. Nature. 1989 Jun 15;339(6225):519–522. doi: 10.1038/339519a0. [DOI] [PubMed] [Google Scholar]
  9. Gutierrez Merino C., Menendez M., Laynez J., Garcia Blanco F. Thermodynamics of nucleotides binding to phosphorylase b. Biophys Chem. 1979 Mar;9(3):263–271. doi: 10.1016/0301-4622(79)85009-7. [DOI] [PubMed] [Google Scholar]
  10. Ha J. H., Spolar R. S., Record M. T., Jr Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J Mol Biol. 1989 Oct 20;209(4):801–816. doi: 10.1016/0022-2836(89)90608-6. [DOI] [PubMed] [Google Scholar]
  11. Herschlag D., Cech T. R. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 1990 Nov 6;29(44):10159–10171. doi: 10.1021/bi00496a003. [DOI] [PubMed] [Google Scholar]
  12. Herschlag D., Eckstein F., Cech T. R. Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA. Biochemistry. 1993 Aug 17;32(32):8299–8311. doi: 10.1021/bi00083a034. [DOI] [PubMed] [Google Scholar]
  13. Herschlag D., Khosla M. Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step. Biochemistry. 1994 May 3;33(17):5291–5297. doi: 10.1021/bi00183a036. [DOI] [PubMed] [Google Scholar]
  14. Hu C. Q., Sturtevant J. M. Thermodynamic study of yeast phosphoglycerate kinase. Biochemistry. 1987 Jan 13;26(1):178–182. doi: 10.1021/bi00375a025. [DOI] [PubMed] [Google Scholar]
  15. Jin R. Z., Breslauer K. J., Jones R. A., Gaffney B. L. Tetraplex formation of a guanine-containing nonameric DNA fragment. Science. 1990 Oct 26;250(4980):543–546. doi: 10.1126/science.2237404. [DOI] [PubMed] [Google Scholar]
  16. Jobe A., Sadler J. R., Bourgeois S. lac Repressor-operator interaction. IX. The binding of lac repressor to operators containing Oc mutations. J Mol Biol. 1974 May 15;85(2):231–248. doi: 10.1016/0022-2836(74)90362-3. [DOI] [PubMed] [Google Scholar]
  17. Kuhsel M. G., Strickland R., Palmer J. D. An ancient group I intron shared by eubacteria and chloroplasts. Science. 1990 Dec 14;250(4987):1570–1573. doi: 10.1126/science.2125748. [DOI] [PubMed] [Google Scholar]
  18. Mascotti D. P., Lohman T. M. Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition. Biochemistry. 1993 Oct 12;32(40):10568–10579. doi: 10.1021/bi00091a006. [DOI] [PubMed] [Google Scholar]
  19. Mascotti D. P., Lohman T. M. Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan. Biochemistry. 1992 Sep 22;31(37):8932–8946. doi: 10.1021/bi00152a033. [DOI] [PubMed] [Google Scholar]
  20. Mateo P. L., González J. F., Barón C., López-Mayorga O., Cortijo M. Thermodynamics of the binding of AMP to glycogen phosphorylase a. J Biol Chem. 1986 Dec 25;261(36):17067–17072. [PubMed] [Google Scholar]
  21. McConnell T. S., Cech T. R. A positive entropy change for guanosine binding and for the chemical step in the Tetrahymena ribozyme reaction. Biochemistry. 1995 Mar 28;34(12):4056–4067. doi: 10.1021/bi00012a024. [DOI] [PubMed] [Google Scholar]
  22. McConnell T. S., Cech T. R., Herschlag D. Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding. Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8362–8366. doi: 10.1073/pnas.90.18.8362. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. McSwiggen J. A., Cech T. R. Stereochemistry of RNA cleavage by the Tetrahymena ribozyme and evidence that the chemical step is not rate-limiting. Science. 1989 May 12;244(4905):679–683. doi: 10.1126/science.2470150. [DOI] [PubMed] [Google Scholar]
  24. Michel F., Dujon B. Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear-encoded members. EMBO J. 1983;2(1):33–38. doi: 10.1002/j.1460-2075.1983.tb01376.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Michel F., Hanna M., Green R., Bartel D. P., Szostak J. W. The guanosine binding site of the Tetrahymena ribozyme. Nature. 1989 Nov 23;342(6248):391–395. doi: 10.1038/342391a0. [DOI] [PubMed] [Google Scholar]
  26. Michel F., Jacquier A., Dujon B. Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie. 1982 Oct;64(10):867–881. doi: 10.1016/s0300-9084(82)80349-0. [DOI] [PubMed] [Google Scholar]
  27. Plum G. E., Park Y. W., Singleton S. F., Dervan P. B., Breslauer K. J. Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9436–9440. doi: 10.1073/pnas.87.23.9436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pyle A. M., Murphy F. L., Cech T. R. RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme. Nature. 1992 Jul 9;358(6382):123–128. doi: 10.1038/358123a0. [DOI] [PubMed] [Google Scholar]
  29. Record M. T., Jr, deHaseth P. L., Lohman T. M. Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry. 1977 Nov 1;16(22):4791–4796. doi: 10.1021/bi00641a005. [DOI] [PubMed] [Google Scholar]
  30. Riggs A. D., Bourgeois S., Cohn M. The lac repressor-operator interaction. 3. Kinetic studies. J Mol Biol. 1970 Nov 14;53(3):401–417. doi: 10.1016/0022-2836(70)90074-4. [DOI] [PubMed] [Google Scholar]
  31. Sassanfar M., Szostak J. W. An RNA motif that binds ATP. Nature. 1993 Aug 5;364(6437):550–553. doi: 10.1038/364550a0. [DOI] [PubMed] [Google Scholar]
  32. Strobel S. A., Cech T. R. Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site. Science. 1995 Feb 3;267(5198):675–679. doi: 10.1126/science.7839142. [DOI] [PubMed] [Google Scholar]
  33. Strobel S. A., Cech T. R. Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry. 1993 Dec 14;32(49):13593–13604. doi: 10.1021/bi00212a027. [DOI] [PubMed] [Google Scholar]
  34. Thierfelder W. E., van Deursen J. M., Yamamoto K., Tripp R. A., Sarawar S. R., Carson R. T., Sangster M. Y., Vignali D. A., Doherty P. C., Grosveld G. C. Requirement for Stat4 in interleukin-12-mediated responses of natural killer and T cells. Nature. 1996 Jul 11;382(6587):171–174. doi: 10.1038/382171a0. [DOI] [PubMed] [Google Scholar]
  35. Wang J. F., Downs W. D., Cech T. R. Movement of the guide sequence during RNA catalysis by a group I ribozyme. Science. 1993 Apr 23;260(5107):504–508. doi: 10.1126/science.7682726. [DOI] [PubMed] [Google Scholar]
  36. Waring R. B., Scazzocchio C., Brown T. A., Davies R. W. Close relationship between certain nuclear and mitochondrial introns. Implications for the mechanism of RNA splicing. J Mol Biol. 1983 Jul 5;167(3):595–605. doi: 10.1016/s0022-2836(83)80100-4. [DOI] [PubMed] [Google Scholar]
  37. Xu M. Q., Kathe S. D., Goodrich-Blair H., Nierzwicki-Bauer S. A., Shub D. A. Bacterial origin of a chloroplast intron: conserved self-splicing group I introns in cyanobacteria. Science. 1990 Dec 14;250(4987):1566–1570. doi: 10.1126/science.2125747. [DOI] [PubMed] [Google Scholar]
  38. Zaug A. J., Been M. D., Cech T. R. The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature. 1986 Dec 4;324(6096):429–433. doi: 10.1038/324429a0. [DOI] [PubMed] [Google Scholar]
  39. Zaug A. J., Dávila-Aponte J. A., Cech T. R. Catalysis of RNA cleavage by a ribozyme derived from the group I intron of Anabaena pre-tRNA(Leu). Biochemistry. 1994 Dec 13;33(49):14935–14947. doi: 10.1021/bi00253a033. [DOI] [PubMed] [Google Scholar]
  40. Zaug A. J., McEvoy M. M., Cech T. R. Self-splicing of the group I intron from Anabaena pre-tRNA: requirement for base-pairing of the exons in the anticodon stem. Biochemistry. 1993 Aug 10;32(31):7946–7953. doi: 10.1021/bi00082a016. [DOI] [PubMed] [Google Scholar]

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