The interaction networks of structured RNAs

Nucleic Acids Research

Volumn 34, Issue 22, 2006, Pages 6587-6604

  Lescoute, A ^a   Westhof, E ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE; HAMMERHEAD RIBOZYME; PEGINTERFERON ALPHA2B; PURINE; PYRIMIDINE; RIBONUCLEASE; RIBONUCLEASE A; RNA 16S; RNA 23S;

ARTICLE; BASE PAIRING; GENE MAPPING; GENE SEQUENCE; HEPATITIS DELTA VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN INTERACTION; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS;

BASE PAIRING; BASE SEQUENCE; INTRONS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RIBONUCLEASE P; RNA; RNA, CATALYTIC; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 23S;

EID: 33845909256     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl963     Document Type: Article

References (98)

1. Leontis,N.B. and Westhof,E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
2. Leontis,N.B., Lescoute,A. and Westhof,E. (2006) The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol., 16, 279-287.
3. Yang,H., Jossinet,F., Leontis,N., Chen,L., Westbrook,J., Berman,H. and Westhof,E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460.
4. Gendron,P., Lemieux,S. and Major,F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
5. Lemieux,S. and Major,F. (2002) RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Res., 30, 4250-4263.
6. Jossinet,F. and Westhof,E. (2005) Sequence to Structure (S2S): Display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics, 21, 3320-3321.
7. Michel,F. and Westhof,E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
8. Lehnert,V., Jaeger,L., Michel,F. and Westhof,E. (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol., 3, 993-1009.
9. Adams,P.L., Stahley,M.R., Gill,M.L., Kosek,A.B., Wang,J. and Strobel,S.A. (2004) Crystal structure of a group I intron splicing intermediate. RNA, 10, 1867-1887.
10. Golden,B.L., Kim,H. and Chase,E. (2005) Crystal structure of a phage Twort group I ribozyme-product complex. Nature Struct. Mol. Biol., 12, 82-89.
11. Guo,F., Gooding,A.R. and Cech,T.R. (2004) Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site. Mol. Cell, 16, 351-362.
12. Woodson,S.A. (2005) Structure and assembly of group I introns. Curr. Opin. Struct. Biol., 15, 324-330.
13. Vicens,Q. and Cech,T.R. (2006) Atomic level architecture of group I introns revealed. Trends Biochem. Sci., 31, 41-51.
14. Costa,M. and Michel,F. (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J., 14, 1276-1285.
15. Costa,M. and Michel,F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution. EMBO J., 16, 3289-3302.
16. Costa,M., Michel,F. and Westhof,E. (2000) A three-dimensional perspective on exon binding by a group II self-splicing intron. EMBO J., 19, 5007-5018.
17. Khvorova,A., Lescoute,A., Westhof,E. and Jayasena,S.D. (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nature Struct. Biol., 10, 708-712.
18. Penedo,J.C., Wilson,T.J., Jayasena,S.D., Khvorova,A. and Lilley,D.M. (2004) Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA, 10, 880-888.
19. Canny,M.D., Jucker,F.M., Kellogg,E., Khvorova,A., Jayasena,S.D. and Pardi,A. (2004) Fast cleavage kinetics of a natural hammerhead ribozyme. J. Am. Chem. Soc., 126, 10848-10849.
20. Michel,F., Jacquier,A. and Dujon,B. (1982) Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure. Biochimie, 64, 867-881.
21. Burke,J.M., Belfort,M., Cech,T.R., Davies,R.W., Schweyen,R.J., Shub,D.A., Szostak,J.W. and Tabak,H.F. (1987) Structural conventions for group I introns. Nucleic Acids Res., 15, 7217-7221.
22. Cech,T.R., Damberger,S.H. and Gutell,R.R. (1994) Representation of the secondary and tertiary structure of group I introns. Nature Struct. Biol., 1, 273-280.
23. Michel,F., Ellington,A.D., Couture,S. and Szostak,J.W. (1990) Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature, 347, 578-580.
24. Strobel,S.A., Adams,P.L., Stahley,M.R. and Wang,J. (2004) RNA kink turns to the left and to the right. RNA, 10, 1852-1854.
25. James,B.D., Olsen,G.J., Liu,J. and Pace,N.R. (1988) The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell, 52, 19-26.
26. Brown,J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res., 27, 314.
27. Harris,M.E., Kazantchev,A.V., Chen,J.L. and Pace,N.R. (1997) Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking. RNA, 3, 561-574.
28. Massire,C., Jaeger,L. and Westhof,E. (1998) Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol., 279, 773-793.
29. Krasilnikov,A.S., Xiao,Y., Pan,T. and Mondragon,A. (2004) Basis for structural diversity in homologous RNAs. Science, 306, 104-107.
30. Krasilnikov,A.S., Yang,X., Pan,T. and Mondragon,A. (2003) Crystal structure of the specificity domain of ribonuclease P. Nature, 421, 760-764.
31. Kazantsev,A.V., Krivenko,A.A., Harrington,D.J., Holbrook,S.R., Adams,P.D. and Pace,N.R. (2005) Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl Acad. Sci. USA, 102, 13392-13397.
32. Torres-Larios,A., Swinger,K.K., Krasilnikov,A.S., Pan,T. and Mondragon,A. (2005) Crystal structure of the RNA component of bacterial ribonuclease P. Nature, 437, 584-587.
33. Krasilnikov,A.S. and Mondragon,A. (2003) On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA, 9, 640-643.
34. Hermann,T. and Patel,D.J. (2000) RNA bulges as architectural and recognition motifs. Structure, 8, R47-R54.
35. Wimberly,B.T., Brodersen,D.E., Clemons,W.M., 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.
36. Schuwirth,B.S., Borovinskaya,M.A., Hau,C.W., Zhang,W., Vila-Sanjurjo,A., Holton,J.M. and Cate,J.H. (2005) Structures of the bacterial ribosome at 3.5 s resolution. Science, 310, 827-834.
37. Serganov,A., Keiper,S., Malinina,L., Tereshko,V., Skripkin,E., Hobartner,C., Polonskaia,A., Phan,A.T., Wombacher,R., Micura,R. et al. (2005) Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nature Struct. Mol. Biol., 12, 218-224.
38. Keiper,S., Bebenroth,D., Seelig,B., Westhof,E. and Jaschke,A. (2004) Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem. Biol., 11, 1217-1227.
39. Perrotta,A.T. and Been,M.D. (1991) A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature, 350, 434-436.
40. Ferre-D'Amare,A.R., Zhou,K. and Doudna,J.A. (1998) Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574.
41. Wadkins,T.S., Perrotta,A.T., Ferre-D'Amare,A.R., Doudna,J.A. and Been,M.D. (1999) A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes. RNA, 5, 720-727.
42. Tanner,N.K., Thill,G., Petit-Kostas,E., Crain-Denoyelle,A.M. and Westhof,E. (1994) A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses. Curr. Biol., 4, 488-498.
43. Ennifar,E., Nikulin,A., Tishchenko,S., Serganov,A., Nevskaya,N., Garber,M., Ehresmann,B., Ehresmann,C., Nikonov,S. and Dumas,P. (2000) The crystal structure of UUCG tetraloop. J. Mol. Biol., 304, 35-42.
44. Rupert,P.B. and Ferre-D'Amare,A.R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature, 410, 780-786.
45. Chowrira,B.M., Berzal-Herranz,A., Keller,C.F. and Burke,J.M. (1993) Four ribose 2′-hydroxyl groups essential for catalytic function of the hairpin ribozyme. J. Biol. Chem., 268, 19458-19462.
46. Earnshaw,D.J., Masquida,B., Müller,S., Sigurdsson,S.T., Eckstein,F., Westhof,E. and Gait,M.J. (1997) Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J. Mol. Biol., 274, 197-212.
47. Butcher,S.E., Allain,F.H.-T. and Feigon,J. (1999) Solution structure of the loop B from the hairpin ribozyme. Nature Struct. Biol., 6, 212-216.
48. Scott,W.G., Finch,J.T. and Klug,A. (1995) The crystal structure of an all-RNA hammerhead ribozyme. Nucleic Acids Symp. Ser., 34, 214-216.
49. Martick,M. and Scott,W.G. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell, 126, 309-320.
50. Serganov,A., Yuan,Y.R., Pikovskaya,O., Polonskaia,A., Malinina,L., Phan,A.T., Hobartner,C., Micura,R., Breaker,R.R. and Patel,D.J. (2004) Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol., 11, 1729-1741.
51. Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
52. Montange,R.K. and Batey,R.T. (2006) Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature, 441, 1172-1175.
53. Thore,S., Leibundgut,M. and Ban,N. (2006) Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science, 312, 1208-1211.
54. Serganov,A., Polonskaia,A., Phan,A.T., Breaker,R.R. and Patel,D.J. (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature, 441, 1167-1171.
55. Lescoute,A. and Westhof,E. (2005) Riboswitch structures: Purine ligands replace tertiary contacts. Chem. Biol., 12, 10-13.
56. Lescoute,A. and Westhof,E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
57. 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, 4214-4221.
58. 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.
59. 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. USA, 98, 4899-4903.
60. Lescoute,A. and Westhof,E. (2006) The A-minor motifs in the decoding recognition process. Biochimie, 88, 993-999.
61. Barta,A., Steiner,G., Brosius,J., Noller,H.F. and Kuechler,E. (1984) Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc. Natl Acad. Sci. USA, 81, 3607-3611.
62. 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.
63. Lata,K.R., Agrawal,R.K., Penczek,P., Grassucci,R., Zhu,J. and Frank,J. (1996) Three-dimensional reconstruction of the Escherichia coli 30S ribosomal subunit in ice. J. Mol. Biol., 262, 43-52.
64. Clemons,W.M., Jr, May,J.L., Wimberly,B.T., McCutcheon,J.P., Capel,M.S. and Ramakrishnan,V. (1999) Structure of a bacterial 30S ribosomal subunit at 5.5 s resolution. Nature, 400, 833-840.
65. Mizushima,S. and Nomura,M. (1970) Assembly mapping of 30S ribosomal proteins from E.coli. Nature, 226, 1214.
66. Nomura,M. and Erdmann,V.A. (1970) Reconstitution of 50S ribosomal subunits from dissociated molecular components. Nature, 228, 744-748.
67. Grondek,J.F. and Culver,G.M. (2004) Assembly of the 30S ribosomal subunit: Positioning ribosomal protein S13 in the S7 assembly branch. RNA, 10, 1861-1866.
68. Serdyuk,I., Baranov,V., Tsalkova,T., Gulyamova,D., Pavlov,M., Spirin,A. and May,R. (1992) Structural dynamics of translating ribosomes. Biochimie, 74, 299-306.
69. Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5 A resolution. Science, 292, 883-896.
70. Frank,J., Verschoor,A., Li,Y., Zhu,J., Lata,R.K., Radermacher,M., Penczek,P., Grassucci,R., Agrawal,R.K. and Srivastava,S. (1995) A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Biochem. Cell Biol., 73, 757-765.
71. Cate,J.H., Yusupov,M.M., Yusupova,G.Z., Earnest,T.N. and Noller,H.F. (1999) X-ray crystal structures of 70S ribosome functional complexes. Science, 285, 2095-2104.
72. Vicens,Q. and Westhof,E. (2001) Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure, 9, 647-658.
73. Francois,B., Russell,R.J., Murray,J.B., Aboul-ela,F., Masquida,B., Vicens,Q. and Westhof,E. (2005) Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: Role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic Acids Res., 33, 5677-5690.
74. Noller,H.F. (2005) RNA structure: Reading the ribosome. Science, 309, 1508-1514.
75. Leontis,N.B. and Westhof,E. (1998) A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J. Mol. Biol., 283, 571-583.
76. Moore,P.B. (1999) Structural motifs in RNA. Annu. Rev. Biochem., 68, 287-300.
77. 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.
78. Westhof,E. and Fritsch,V. (2000) RNA folding: Beyond Watson-Crick pairs. Structure, 8, R55-R65.
79. Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie, 84, 961-973.
80. Leontis,N.B. and Westhof,E. (2003) Analysis of RNA motifs. Curr. Opin. Struct. Biol., 13, 300-308.
81. Lee,J.C., Cannone,J.J. and Gutell,R.R. (2003) The lonepair triloop: A new motif in RNA structure. J. Mol. Biol., 325, 65-83.
82. Lee,J.C., Gutell,R.R. and Russell,R. (2006) The UAA/GAN internal loop motif: A new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions. J. Mol. Biol., 360, 978-988.
83. Strogatz,S.H. (2001) Exploring complex networks. Nature, 410, 268-276.
84. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional organization. Nature Rev. Genet., 5, 101-113.
85. Watts,D.J. and Strogatz,S.H. (1998) Collective dynamics of 'small-world' networks. Nature, 393, 440-442.
86. Barabasi,A.L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
87. Ravasz,E., Somera,A.L., Mongru,D.A., Oltvai,Z.N. and Barabasi,A.L. (2002) Hierarchical organization of modularity in metabolic networks. Science, 297, 1551-1555.
88. Greene,L.H. and Higman,V.A. (2003) Uncovering network systems within protein structures. J. Mol. Biol., 334, 781-791.
89. Amitai,G., Shemesh,A., Sitbon,E., Shklar,M., Netanely,D., Venger,I. and Pietrokovski,S. (2004) Network analysis of protein structures identifies functional residues. J. Mol. Biol., 344, 1135-1146.
90. del Sol,A., Fujihashi,H., Amoros,D. and Nussinov,R. (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol., 2, 2006. 0019.
91. Klein,D.J., Moore,P.B. and Steitz,T.A. (2004) The contribution of metal ions to the structural stability of the large ribosomal subunit. RNA, 10, 1366-1379.
92. Hansen,J.L., Schmeing,T.M., Moore,P.B. and Steitz,T.A. (2002) Structural insights into peptide bond formation. Proc. Natl Acad. Sci. USA, 99, 11670-11675.
93. 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.
94. Nissen,P., Hansen,J., Ban,N., Moore,P.B. and Steitz,T.A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science, 289, 920-930.
95. Mengel-Jorgensen,J., Jensen,S.S., Rasmussen,A., Poehlsgaard,J., Iversen,J.J. and Kirpekar,F. (2006) Modifications in Thermus thermophilus 23S ribosomal RNA are centered in regions of RNA-RNA contact. J. Biol. Chem., 281, 22108-22117.
96. Kowalak,J.A., Bruenger,E. and McCloskey,J.A. (1995) Posttranscriptional modification of the central loop of domain V in Escherichia coli 23S ribosomal RNA. J. Biol. Chem., 270, 17758-17764.
97. Brodersen,D.E., Clemons,W.M., Jr, Carter,A.P., Wimberly,B.T. and Ramakrishnan,V. (2002) Crystal structure of the 30S ribosomal subunit from Thermus thermophilus: Structure of the proteins and their interactions with 16S RNA. J. Mol. Biol., 316, 725-768.
98. McCloskey,J.A. and Rozenski,J. (2005) The small subunit rRNA modification database. Nucleic Acids Res., 33, D135-D138.