Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 (original) (raw)

Abstract

The Bacillus stearothermophilus ribosomal protein S15 binds to a phylogenetically conserved three-way junction formed by the intersection of helices 20, 21, and 22 of eubacterial 16S ribosomal RNA, inducing a large conformational change in the RNA. Like many RNA structures, this three-way junction can also be folded by the addition of polyvalent cations such as magnesium, as demonstrated by comparing the mobilities of the wild-type and mutant junctions in the absence and presence of polyvalent cations in nondenaturing polyacrylamide gels. Using a modification interference assay, critical nucleotides for folding have been identified as the phylogenetically conserved nucleotides in the three-way junction. NMR spectroscopy of the junction reveals that the conformations induced by the addition of magnesium or S15 are extremely similar. Thus, the folding of the junction is determined entirely by RNA elements within the phylogenetically conserved junction core, and the role of Mg2+ and S15 is to stabilize this intrinsically unstable structure. The organization of the junction by Mg2+ significantly enhances the bimolecular association rate (k(on)) of S15 binding, suggesting that S15 binds specifically to the folded form of the three-way junction via a tertiary structure capture mechanism.

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Selected References

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  1. Bassi G. S., Murchie A. I., Lilley D. M. The ion-induced folding of the hammerhead ribozyme: core sequence changes that perturb folding into the active conformation. RNA. 1996 Aug;2(8):756–768. [PMC free article] [PubMed] [Google Scholar]
  2. Bassi G. S., Møllegaard N. E., Murchie A. I., von Kitzing E., Lilley D. M. Ionic interactions and the global conformations of the hammerhead ribozyme. Nat Struct Biol. 1995 Jan;2(1):45–55. doi: 10.1038/nsb0195-45. [DOI] [PubMed] [Google Scholar]
  3. Batey R. T., Williamson J. R. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: I. Defining the minimal RNA site. J Mol Biol. 1996 Aug 30;261(4):536–549. doi: 10.1006/jmbi.1996.0481. [DOI] [PubMed] [Google Scholar]
  4. Batey R. T., Williamson J. R. Interaction of the Bacillus stearothermophilus ribosomal protein S15 with 16 S rRNA: II. Specificity determinants of RNA-protein recognition. J Mol Biol. 1996 Aug 30;261(4):550–567. doi: 10.1006/jmbi.1996.0482. [DOI] [PubMed] [Google Scholar]
  5. Brunel C., Romby P., Westhof E., Ehresmann C., Ehresmann B. Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling. J Mol Biol. 1991 Sep 5;221(1):293–308. doi: 10.1016/0022-2836(91)80220-o. [DOI] [PubMed] [Google Scholar]
  6. Cate J. H., Doudna J. A. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 1996 Oct 15;4(10):1221–1229. doi: 10.1016/s0969-2126(96)00129-3. [DOI] [PubMed] [Google Scholar]
  7. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. doi: 10.1126/science.273.5282.1678. [DOI] [PubMed] [Google Scholar]
  8. Cate J. H., Hanna R. L., Doudna J. A. A magnesium ion core at the heart of a ribozyme domain. Nat Struct Biol. 1997 Jul;4(7):553–558. doi: 10.1038/nsb0797-553. [DOI] [PubMed] [Google Scholar]
  9. Chastain M., Tinoco I., Jr Structural elements in RNA. Prog Nucleic Acid Res Mol Biol. 1991;41:131–177. doi: 10.1016/S0079-6603(08)60008-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dahm S. C., Uhlenbeck O. C. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry. 1991 Oct 1;30(39):9464–9469. doi: 10.1021/bi00103a011. [DOI] [PubMed] [Google Scholar]
  11. Delaglio F., Grzesiek S., Vuister G. W., Zhu G., Pfeifer J., Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995 Nov;6(3):277–293. doi: 10.1007/BF00197809. [DOI] [PubMed] [Google Scholar]
  12. Gutell R. R. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 1994 Sep;22(17):3502–3507. doi: 10.1093/nar/22.17.3502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Held W. A., Ballou B., Mizushima S., Nomura M. Assembly mapping of 30 S ribosomal proteins from Escherichia coli. Further studies. J Biol Chem. 1974 May 25;249(10):3103–3111. [PubMed] [Google Scholar]
  14. Jack A., Ladner J. E., Klug A. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution. J Mol Biol. 1976 Dec 25;108(4):619–649. doi: 10.1016/s0022-2836(76)80109-x. [DOI] [PubMed] [Google Scholar]
  15. Kieft J. S., Tinoco I., Jr Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure. 1997 May 15;5(5):713–721. doi: 10.1016/s0969-2126(97)00225-6. [DOI] [PubMed] [Google Scholar]
  16. Kooi E. A., Rutgers C. A., Mulder A., Van't Riet J., Venema J., Raué H. A. The phylogenetically conserved doublet tertiary interaction in domain III of the large subunit rRNA is crucial for ribosomal protein binding. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):213–216. doi: 10.1073/pnas.90.1.213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Laing L. G., Gluick T. C., Draper D. E. Stabilization of RNA structure by Mg ions. Specific and non-specific effects. J Mol Biol. 1994 Apr 15;237(5):577–587. doi: 10.1006/jmbi.1994.1256. [DOI] [PubMed] [Google Scholar]
  18. Long D. M., Uhlenbeck O. C. Self-cleaving catalytic RNA. FASEB J. 1993 Jan;7(1):25–30. doi: 10.1096/fasebj.7.1.8422971. [DOI] [PubMed] [Google Scholar]
  19. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mohr G., Caprara M. G., Guo Q., Lambowitz A. M. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature. 1994 Jul 14;370(6485):147–150. doi: 10.1038/370147a0. [DOI] [PubMed] [Google Scholar]
  21. Mohr G., Zhang A., Gianelos J. A., Belfort M., Lambowitz A. M. The neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell. 1992 May 1;69(3):483–494. doi: 10.1016/0092-8674(92)90449-m. [DOI] [PubMed] [Google Scholar]
  22. Orr J. W., Hagerman P. J., Williamson J. R. Protein and Mg(2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA. J Mol Biol. 1998 Jan 23;275(3):453–464. doi: 10.1006/jmbi.1997.1489. [DOI] [PubMed] [Google Scholar]
  23. Philippe C., Eyermann F., Bénard L., Portier C., Ehresmann B., Ehresmann C. Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4394–4398. doi: 10.1073/pnas.90.10.4394. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 1994 Nov 3;372(6501):68–74. doi: 10.1038/372068a0. [DOI] [PubMed] [Google Scholar]
  25. Portier C., Dondon L., Grunberg-Manago M. Translational autocontrol of the Escherichia coli ribosomal protein S15. J Mol Biol. 1990 Jan 20;211(2):407–414. doi: 10.1016/0022-2836(90)90361-O. [DOI] [PubMed] [Google Scholar]
  26. Portier C., Philippe C., Dondon L., Grunberg-Manago M., Ebel J. P., Ehresmann B., Ehresmann C. Translational control of ribosomal protein S15. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):328–336. doi: 10.1016/0167-4781(90)90190-d. [DOI] [PubMed] [Google Scholar]
  27. Powers T., Noller H. F. Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA. 1995 Apr;1(2):194–209. [PMC free article] [PubMed] [Google Scholar]
  28. Ryan P. C., Draper D. E. Thermodynamics of protein-RNA recognition in a highly conserved region of the large-subunit ribosomal RNA. Biochemistry. 1989 Dec 26;28(26):9949–9956. doi: 10.1021/bi00452a012. [DOI] [PubMed] [Google Scholar]
  29. Ryan P. C., Lu M., Draper D. E. Recognition of the highly conserved GTPase center of 23 S ribosomal RNA by ribosomal protein L11 and the antibiotic thiostrepton. J Mol Biol. 1991 Oct 20;221(4):1257–1268. doi: 10.1016/0022-2836(91)90932-v. [DOI] [PubMed] [Google Scholar]
  30. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. doi: 10.1016/s0092-8674(05)80004-2. [DOI] [PubMed] [Google Scholar]
  31. Serganov A. A., Masquida B., Westhof E., Cachia C., Portier C., Garber M., Ehresmann B., Ehresmann C. The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli S15, minimum site and structure. RNA. 1996 Nov;2(11):1124–1138. [PMC free article] [PubMed] [Google Scholar]
  32. Serganov A., Rak A., Garber M., Reinbolt J., Ehresmann B., Ehresmann C., Grunberg-Manago M., Portier C. Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein. Eur J Biochem. 1997 Jun 1;246(2):291–300. doi: 10.1111/j.1432-1033.1997.00291.x. [DOI] [PubMed] [Google Scholar]
  33. Uhlenbeck O. C. A small catalytic oligoribonucleotide. Nature. 1987 Aug 13;328(6131):596–600. doi: 10.1038/328596a0. [DOI] [PubMed] [Google Scholar]
  34. Weeks K. M., Cech T. R. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science. 1996 Jan 19;271(5247):345–348. doi: 10.1126/science.271.5247.345. [DOI] [PubMed] [Google Scholar]
  35. Weeks K. M., Cech T. R. Protein facilitation of group I intron splicing by assembly of the catalytic core and the 5' splice site domain. Cell. 1995 Jul 28;82(2):221–230. doi: 10.1016/0092-8674(95)90309-7. [DOI] [PubMed] [Google Scholar]
  36. Westhof E., Romby P., Romaniuk P. J., Ebel J. P., Ehresmann C., Ehresmann B. Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs. J Mol Biol. 1989 May 20;207(2):417–431. doi: 10.1016/0022-2836(89)90264-7. [DOI] [PubMed] [Google Scholar]
  37. Wyatt J. R., Chastain M., Puglisi J. D. Synthesis and purification of large amounts of RNA oligonucleotides. Biotechniques. 1991 Dec;11(6):764–769. [PubMed] [Google Scholar]
  38. Zarrinkar P. P., Williamson J. R. The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding. Nat Struct Biol. 1996 May;3(5):432–438. doi: 10.1038/nsb0596-432. [DOI] [PubMed] [Google Scholar]