A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence-structure relationships

RNA

Volumn 13, Issue 9, 2007, Pages 1537-1545

  Lisi, Véronique ^a   Major, François ^a  

^a INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

Author keywords

Comparative analysis; Motif; RNA; Structure; Three dimensional modeling; Triloop

Indexed keywords

LIGAND; NUCLEOTIDE; PAROMOMYCIN; RNA;

ARTICLE; CRYSTAL STRUCTURE; LIGAND BINDING; PRIORITY JOURNAL; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; THREE DIMENSIONAL IMAGING; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; CRYSTALLOGRAPHY, X-RAY; HALOARCULA MARISMORTUI; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, ARCHAEAL; RNA, RIBOSOMAL, 23S; SEQUENCE ANALYSIS, RNA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 34548342932     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.597507     Document Type: Article

References (42)

1. Antao, V.P., Lai, S.Y., and Tinoco Jr., I. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19: 5901-5905.
2. 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 Å resolution. Science 289: 905-920.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. 2000. The protein data bank. Nucleic Acids Res. 28: 235-242.
4. Brodersen, D.E., Clemons, J.W.M., Carter, A.P., Wimberly, B.T., and Ramakrishnan, V. 2002. Crystal structure of the 30 s ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16 s RNA. J. Mol. Biol. 316: 725.
5. Cheong, C., Varani, G., and Tinoco Jr., I. 1990. Solution structure of an unusually stable RNA hairpin, 5′-GGAC(UUCG)GUCC. Nature 346: 680-682.
6. Gabb, H.A., Sanghani, S.R., Robert, C.H., and Prevost, C. 1996. Finding and visualizing nucleic acid base stacking. J. Mol. Graph. 14: 6-11, 23-24.
7. Gendron, P., Lemieux, S., and Major, F. 2001. Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol. 308: 919.
8. Genesereth, M.R. and Nilsson, N.J. 1987. Logical foundations of artificial intelligence. Morgan Kaufmann Publishers, Los Altos, CA.
9. Giedroc, D.P., Theimer, C.A., and Nixon, P.L. 2000. Structure, stability, and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J. Mol. Biol. 298: 167-185.
10. Gutell, R.R., Cannone, J.J., Konings, D., and Gautheret, D. 2000. Predicting U-turns in ribosomal RNA with comparative sequence analysis. J. Mol. Biol. 300: 791-803.
11. Haasnoot, P.C.J., Bol, J.F., and Olsthoorn, R.C.L. 2003. A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions. Proc. Natl. Acad. Sci. 100: 12596-12600.
12. Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. 2001. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107: 679.
13. Heus, H.A. and Pardi, A. 1991. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253: 191-194.
14. Hoffmann, B., Mitchell, G.T., Gendron, P., Major, F., Andersen, A.A., Collins, R.A., and Legault, P. 2003. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc. Natl. Acad. Sci. 100: 7003-7008.
15. Huang, H., Alexandrov, A., Chen, X.Y., Barnes, T.W., Zhang, H., Dutta, K., and Pascal, S.M. 2001. Structure of an RNA hairpin from HRV-14. Biochemistry 40: 8055-8064.
16. Huang, H.-C., Nagaswamy, U.M.A., and Fox, G.E. 2005. The application of cluster analysis in the intercomparison of loop structures in RNA. RNA 11: 412-423.
17. Jossinet, F. and Westhof, E. 2005. Sequence to structure (S2S): Display, manipulate, and interconnect RNA data from sequence to structure. Bioinformatics 21: 3320-3321.
18. Jucker, F.M. and Pardi, A. 1995. GNRA tetraloops make a U-turn. RNA 1: 219-222.
19. Jucker, F.M., Heus, H.A., Yip, P.F., Moors, E.H.M., and Pardi, A. 1996. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264: 968-980.
20. Klein, D.J., Schmeing, T.M., Moore, P.B., and Steitz, T.A. 2001. The kink-turn: A new RNA secondary structure motif. EMBO J. 20: 4212-4221.
21. Kondo, J., Urzhumtsev, A., and Westhof, E. 2006. Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site. Nucleic Acids Res. 34: 676-685.
22. Lee, J.C., Cannone, J.J., and Gutell, R.R. 2003. The lone-pair triloop: A new motif in RNA structure. J. Mol. Biol. 325: 65.
23. Lemieux, S. and Major, F. 2002. RNA canonical and noncanonical base-pairing types: A recognition method and complete repertoire. Nucleic Acids Res. 30: 4250-4263.
24. Lemieux, S. and Major, F. 2006. Automated extraction and classification of RNA tertiary structure cyclic motifs. Nucleic Acids Res. 34: 2340-2346.
25. Leontis, N.B. and Westhof, E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
26. Leontis, N.B., Altman, R.B., Berman, H.M., Brenner, S.E., Brown, J.W., Engelke, D.R., Harvey, S.C., Holbrook, S.R., Jossinet, F., Lewis, S.E., et al. 2006. The RNA Ontology Consortium: An open invitation to the RNA community. RNA 12: 533-541.
27. Lescoute, A., Leontis, N.B., Massire, C., and Westhof, E. 2005. Recurrent structural RNA motifs, isostericity matrices, and sequence alignments. Nucleic Acids Res. 33: 2395-2409.
28. Major, F. and Thibault, P. 2007. RNA tertiary structure prediction. In Bioinformatics: From genomes to therapies (ed. T. Lengauer). pp. 491-539. Wiley-VCH, Weinheim, Germany.
29. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, E., and Cedergren, R. 1991. The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 253: 1255-1260.
30. Massire, C. and Westhof, E. 1998. MANIP: An interactive tool for modeling RNA. J. Mol. Graph. Model. 16: 197-205, 255-257.
31. McCallum, S.A. and Pardi, A. 2003. Refined solution structure of the iron-responsive element RNA using residual dipolar couplings. J. Mol. Biol. 326: 1037-1050.
32. Nagaswamy, U. and Fox, G.E. 2002. Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA 8: 1112-1119.
33. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B., and Steitz, T.A. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. 98: 4899-4903.
34. Olivier, C., Poirier, G., Gendron, P., Boisgontier, A., Major, F., and Chartrand, P. 2005. Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol. Cell. Biol. 25: 4752-4766.
35. Olsthoorn, R.C.L. and Bol, J.F. 2002. Role of an essential triloop hairpin and flanking structures in the 3′-untranslated region of alfalfa mosaic virus RNA in in vitro transcription. J. Virol. 76: 8747-8756.
36. Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., et al. 2000. Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell 102: 615-623.
37. Shankar, N., Kennedy, S.D., Chen, G., Krugh, T.R., and Turner, D.H. 2006. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry 45: 11776-11789.
38. Szewczak, A.A. and Moore, P.B. 1995. The sarcin/ricin loop, a modular RNA. J. Mol. Biol. 247: 81-98.
39. Varani, G., Wimberly, B., and Tinoco Jr., I. 1989. Conformation and dynamics of an RNA internal loop. Biochemistry 28: 7760-7772.
40. Wimberly, B., Varani, G., and Tinoco Jr., I. 1993. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry 32: 1078-1087.
41. Wimberly, B.T., Brodersen, D.E., Clemons, W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T., and Ramakrishnan, V. 2000. Structure of the 30S ribosomal subunit. Nature 407: 327.
42. Woese, C.R., Winker, S., and Gutell, R.R. 1990. Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops." Proc. Natl. Acad. Sci. 87: 8467-8471.