Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding

Nucleic Acids Research

Volumn 34, Issue 7, 2006, Pages 2015-2026

  Schoemaker, Ruud J W ^a   Gultyaev, Alexander P ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL RNA; C BOX TRANSFER RNA; CHAPERONE; D BOX TRANSFER RNA; RIBOSOME RNA; TRANSFER RNA; UNCLASSIFIED DRUG; COMPLEMENTARY RNA; GUIDE RNA; RNA 16S; SMALL NUCLEOLAR RNA;

ARCHAEOGLOBUS FULGIDUS; ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; GENETIC ALGORITHM; NONHUMAN; NUCLEIC ACID PROBE; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PYROCOCCUS ABYSSI; RNA ANALYSIS; RNA BINDING; RNA STRUCTURE; RNA TRANSCRIPTION; BINDING SITE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MOLECULAR GENETICS; TEMPERATURE;

ARCHAEA; ARCHAEOGLOBUS FULGIDUS; EUKARYOTA; PYROCOCCUS ABYSSI;

ARCHAEOGLOBUS FULGIDUS; BASE SEQUENCE; BINDING SITES; COMPUTER SIMULATION; MOLECULAR CHAPERONES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PYROCOCCUS ABYSSI; RNA, ANTISENSE; RNA, ARCHAEAL; RNA, GUIDE; RNA, RIBOSOMAL, 16S; RNA, SMALL NUCLEOLAR; TEMPERATURE;

EID: 33645801760     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl154     Document Type: Article

References (66)

1. Woodson,S.A. (2000) Recent insights on RNA folding mechanisms from catalytic RNA. Cell Mol. Life Sci., 57, 796-808.
2. Thirumalai,D. and Woodson,S.A. (1996) Kinetics of folding of proteins and RNA. Acc. Chem. Res., 29, 433-439.
3. Pan,T., Thirumalai,D. and Woodson,S.A. (1997) Folding of RNA involves parallel pathways. J. Mol. Biol., 273, 7-13.
4. Fang,X.W., Pan,T. and Sosnick,T.R. (1999) Mg2+-dependent folding of a large ribozyme without kinetic traps. Nature Struct. Biol., 6, 1091-1095.
5. Su,L.J., Brenowitz,M. and Pyle,A.M. (2003) An alternative route for the folding of large RNAs: Apparent two-state folding by a group II intron ribozyme. J. Mol. Biol., 334, 639-652.
6. Gultyaev,A.P., van Batenburg,F.H. and Pleij,C.W.A. (1995) The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250, 37-51.
7. Higgs,P.G. (1995) Thermodynamic properties of transfer-RNA - a computational study. J. Chem. Soc. Faraday Trans., 91, 2531-2540.
8. Huynen,M., Gutell,R. and Konings,D. (1997) Assessing the reliability of RNA folding using statistical mechanics. J. Mol. Biol., 267, 1104-1112.
9. Schultes,E.A., Hraber,P.T. and LaBean,T.H. (1999) Estimating the contributions of selection and self-organization in RNA secondary structure. J. Mol. Evol., 49, 76-83.
10. Gultyaev,A.P., van Batenburg,F.H. and Pleij,C.W.A. (2002) Selective pressures on RNA hairpins in vivo and in vitro. J. Mol. Evol., 54, 1-8.
11. Kramer,F.R. and Mills,D.R. (1981) Secondary structure formation during RNA synthesis. Nucleic Acids Res., 9, 5109-5124.
12. Lewicki,B.T., Margus,T., Remme,J. and Nierhaus,K.H. (1993) Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase. J. Mol. Biol., 231, 581-593.
13. Heilman-Miller,S.L. and Woodson,S.A. (2003) Effect of transcription on folding of the Tetrahymena ribozyme. RNA, 9, 722-733.
14. Meyer,I.M. and Miklos,I. (2004) Co-transcriptional folding is encoded within RNA genes. BMC Mol. Biol., 5, 10.
15. Ma,C.K., Kolesnikow,T., Rayner,J.C., Simons,E.L., Yim,H. and Simons,R.W. (1994) Control of translation by mRNA secondary structure: The importance of the kinetics of structure formation. Mol. Microbiol., 14, 1033-1047.
16. Gultyaev,A.P., Franch,T. and Gerdes,K. (1997) Programmed cell death by hok/sok of plasmid R1: Coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs. J. Mol. Biol., 273, 26-37.
17. Poot,R.A., Tsareva,N.V., Boni,I.B. and van Duin,J. (1997) RNA folding kinetics regulate translation of phage MS2 maturation gene. Proc. Natl Acad. Sci. USA, 94, 10110-10115.
18. Morgan,S.R. and Higgs,P.G. (1996) Evidence for kinetic effects in the folding of large RNA molecules. J. Chem. Phys., 105, 7152-7157.
19. Herschlag,D. (1995) RNA chaperones and the RNA folding problem. J. Biol. Chem., 270, 20871-20874.
20. Schroeder,R., Barta,A. and Semrad,K. (2004) Strategies for RNA folding and assembly. Nature Rev. Mol. Cell Biol., 5, 908-919.
21. Bachellerie,J.P., Michot,B., Nicoloso,M., Balakin,A., Ni,J. and Fournier,M.J. (1995) Antisense snoRNAs: A family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem. Sci., 20, 261-264.
22. Steitz,J.A. and Tycowski,K.T. (1995) Small RNA chaperones for ribosome biogenesis. Science, 270, 1626-1627.
23. Gerbi,S.A. (1995) Small nucleolar RNA. Biochem. Cell Biol., 73, 845-858.
24. Hughes,J.M.X. (1996) Functional-base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J. Mol. Biol., 259, 645-654.
25. Liang,W.Q. and Fournier,M.J. (1995) U14 base-pairs with 18S rRNA: A novel snoRNA interaction required for rRNA processing. Genes Dev., 9, 2433-2443.
26. Peculis,B.A. (2001) snoRNA nuclear import and potential for cotranscriptional function in pre-rRNA processing. RNA, 7, 207-219.
27. Bachellerie,J.P. and Cavaille,J. (1997) Guiding ribose methylation of rRNA. Trends Biochem. Sci., 22, 257-261.
28. Dennis,P.P., Omer,A. and Lowe,T. (2001) A guided tour: Small RNA function in Archaea. Mol. Microbiol., 40, 509-519.
29. Gaspin,C., Cavaille,J., Erauso,G. and Bachellerie,J.P. (2000) Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: Lessons from the Pyrococcus genomes. J. Mol. Biol., 297, 895-906.
30. Barneche,F., Gaspin,C., Guyot,R. and Echeverria,M. (2001) Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: Extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2′-O-methylation sites. J. Mol. Biol., 311, 57-73.
31. Ziesche,S.M., Omer,A.M. and Dennis,P.P. (2004) RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea. Mol. Microbiol., 54, 980-993.
32. Tran,E.J., Zhang,X. and Maxwell,E.S. (2003) Efficient RNA 2′-O-methylation requires juxtaposed and symmetrically assembled archaeal box C/D and C′/D′ RNPs. EMBO J., 22, 3930-3940.
33. Omer,A.D., Lowe,T.M., Russell,A.G., Ebhardt,H., Eddy,S.R. and Dennis,P.P. (2000) Homologs of small nucleolar RNAs in Archaea. Science, 288, 517-522.
34. Dragon,F., Gallagher,J.E.G., Compagnone-Post,P.A., Mitchell,B.M., Porwancher,K.A., Wehner,K.A., Wormsley,S., Settlage,R.E., Shabanowitz,J., Oshelm,Y. et al. (2002) A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature, 417, 967-970.
35. Maden,B.E. (1990) The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol., 39, 241-303.
36. Venema,J. and Tollervey,D. (1999) Ribosome synthesis in Saccharomyces cerevisiae. Annu. Rev. Genet., 33, 261-311.
37. Speckman,W.A., Li,Z.-H., Lowe,T.M., Eddy,S.R., Terns,R.M. and Terns,M.P. (2002) Archaeal guide RNAs function in rRNA modification in the eukaryotic nucleus. Curr. Biol., 12, 199-203.
38. Gultyaev,A.P., van Batenburg,F.H. and Pleij,C.W.A. (1995) The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics. Nucleic Acids Res., 23, 3718-3725.
39. Gultyaev,A.P., van Batenburg,F.H. and Pleij,C.W.A. (1998) Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm. J. Mol. Biol., 276, 43-55.
40. Abrahams,J.P., van den Berg,M., van Batenburg,E. and Pleij,C.W.A. (1990) Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res., 18, 3035-3044.
41. Walter,A.E., Turner,D.H., Kim,J., Lyttle,M.H., Muller,P., Mathews,D.H. and Zuker,M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA, 91, 9218-9222.
42. Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
43. Wuyts,J., Perriere,G. and Van de Peer,Y. (2004) The European ribosomal RNA database. Nucleic Acids Res., 32, D101-D103.
44. Samarsky,D.A. and Fournier,M.J. (1999) A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae. Nucleic Acids Res., 27, 161-164.
45. Dunbar,D.A. and Baserga,S.J. (1998) The U14 snoRNA is required for 2′-O-methylation of the pre-18S rRNA in Xenopus oocytes. RNA, 4, 195-204.
46. Konings,D.A. and Gutell,R.R. (1995) A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA, 1, 559-574.
47. Pardon,B. and Wagner,R. (1995) The Escherichia coli ribosomal RNA leader nut region interacts specifically with mature 16S RNA. Nucleic Acids Res., 23, 932-941.
48. Besancon,W. and Wagner,R. (1999) Characterization of transient RNA-RNA interactions important for the facilitated structure formation of bacterial ribosomal 16S RNA. Nucleic Acids Res., 27, 4353-4362.
49. Cote,C.A., Greer,C.L. and Peculis,B.A. (2002) Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA, 8, 786-797.
50. Liiv,A. and Remme,J. (2004) Importance of transient structures during post-transcriptional refolding of the pre-23S rRNA and ribosomal large subunit assembly. J. Mol. Biol., 342, 725-741.
51. Pan,T., Artsimovitch,I., Fang,X.W., Landick,R. and Sosnick,T.R. (1999) Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc. Natl Acad. Sci. USA, 96, 9545-9550.
52. Isambert,H. and Siggia,E.D. (2000) Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
53. Diegelman-Parente,A. and Bevilacqua,P.C. (2002) A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. J. Mol. Biol., 324, 1-16.
54. Solem,A., Chatterjee,P. and Caprara,M.G. (2002) A novel mechanism for protein-assisted group I intron splicing. RNA, 8, 412-425.
55. Favaretto,P., Bhutkar,A. and Smith,T.F. (2005) Constraining ribosomal RNA conformational space. Nucleic Acids Res., 33, 5106-5111.
56. Dubins,D.N., Lee,A., Macgregor,R.B.Jr and Chalikian,T.V. (2001) On the stability of double stranded nucleic acids. J. Am. Chem. Soc., 123, 9254-9259.
57. Webb,A.E. and Weeks,K.M. (2001) A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex. Nature Struct. Biol., 8, 135-140.
58. Grossberger,R., Mayer,O., Waldsich,C., Semrad,K., Urschitz,S. and Schroeder,R. (2005) Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA. Nucleic Acids Res., 33, 2280-2289.
59. Waldsich,C., Grossberger,R. and Schroeder,R. (2002) RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo. Genes Dev., 16, 2300-2312.
60. Mohr,G., Caprara,M.G., Guo,Q. and Lambowitz,A.M. (1994) A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature, 370, 147-150.
61. Wimberly,B.T., Brodersen,D.E., Clemons,W.M.C.Jr, Morgan-Warren,R.J., Carter,A.P., Vonrhein,C., Hartsch,T. and Ramakrishnan,V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
62. Vitali,P., Royo,H., Seitz,H., Bachellerie,J.-P., Huttenhofer,A. and Cavaille,J. (2003) Identification of 13 novel human modification guide RNAs. Nucleic Acids Res., 31, 6543-6551.
63. Xayaphoummine,A., Bucher,T., Thalmann,F. and Isambert,H. (2003) Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl Acad. Sci. USA, 100, 15310-15315.
64. Xayaphoummine,A., Bucher,T. and Isambert,H. (2005) Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res., 33, W605-W610.
65. Wolfinger,M.T., Svrcek-Seiler,W.A., Flamm,C., Hofacker,I.L. and Stadler,P.F. (2004) Efficient computation of RNA folding dynamics. J. Phys. A Math. Gen., 37, 4731-4741.
66. Hackermuller,J., Meisner,N.C., Auer,M., Jaritz,M. and Stadler,P.F. (2005) The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: A quantitative model. Gene, 345, 3-12.