Free energy landscapes of RNA/RNA complexes: With applications to snRNA complexes in spliceosomes

Journal of Molecular Biology

Volumn 357, Issue 1, 2006, Pages 292-312

  Cao, Song ^a   Chen, Shi Jie ^a  

^a University of Missouri   (United States)

Author keywords

Folding pathways; Free energy landscape; Major and minor spliceosomes; Misfolded state; RNA RNA complex

Indexed keywords

RIBOZYME; RNA; RNA HELICASE;

ARABIDOPSIS; ARTICLE; COMPLEX FORMATION; DROSOPHILA; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; RNA SPLICING; SPLICEOSOME;

ARABIDOPSIS;

EID: 33644779957     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.12.014     Document Type: Article

References (91)

1. S.M. Berget, C. Moore, and P.A. Sharp Spliced segments at 5′ terminus of adenovirus 2 late mRNA Proc. Natl Acad. Sci. USA 74 1977 3171 3175
2. L.T. Chow, R.E. Gelinas, T.R. Broker, and R.J. Roberts An amazing sequence arrangement at 5′ ends of adenovirus 2 messenger-RNA Cell 12 1977 1 8
3. C.L. Will, and R. Lührmann Protein functions in pre-mRNA splicing Curr. Opin. Cell Biol. 9 1997 320 328
4. J.P. Staley, and C. Guthrie Mechanical devices of the spliceosome: motors, clocks, springs, and things Cell 92 1998 315 326
5. C.A. Collins, and C. Guthrie The question remains: is the spliceosome a ribozyme? Nature Struct. Biol. 7 2000 850 854
6. M.S. Jurica, and M.J. Moore Pre-mRNA splicing: awash in a sea of proteins Mol. Cell. 12 2003 5 14
7. H.D. Madhani, R. Bordonné, and C. Guthrie Multiple roles for U6 snRNA in the splicing pathway Genes Dev. 4 1990 2264 2277
8. H.D. Madhani, and C. Guthrie A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome Cell 71 1992 803 817
9. D.S. McPheeters, and J. Abelson Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group-I introns Cell 71 1992 819 831
10. D.M. Fortner, R.G. Troy, and D.A. Brow A stem/loop in U6 RNA defines a conformational switch for pre-messenger RNA splicing Genes Dev. 8 1994 221 233
11. Ryan, D.E. & Abelson, J. (2002). The conserved central domain of yeast U6 snRNA: importance of U2-U6 helix I-a in spliceosome assembly, RNA, 8, 997-1010.
12. J.S. Sun, and J.L. Manley A novel U2-U6 snRNA structure is necessary for mammalian messenger-RNA splicing Genes Dev. 9 1995 843 854
13. J.S. Sun, and J.L. Manley The human U6 snRNA intramolecular helix: structural constraints and lack of sequence specificity RNA 3 1997 514 526
14. S. Valadkhan, and J.L. Manley A tertiary interaction detected in a human U2-U6 snRNA complex assembled in vitro resembles a genetically proven interaction in yeast RNA 6 2000 206 219
15. S. Valadkhan, and J.L. Manley Splicing-related catalysis by protein-free snRNAs Nature 413 2001 701 707
16. N.M. Fast, A.J. Roger, C.A. Richardson, and W.F. Doolittle U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome Nucl. Acids Res. 26 1998 3202 3207
17. A.P. Gultyaev, T. Franch, and K. Gerdes Coupled nucleotide covariations reveal dynamic RNA interaction patterns RNA 6 2000 1483 1491
18. A.K. Hilliker, and J.P. Staley Multiple functions for the invariant AGC triad of U6 snRNA RNA 10 2004 921 928
19. B.G.M. Luukkonen, and B. Séraphin A role for U2/U6 helix Ib in 5′ splice site selection RNA 4 1998 915 927
20. T. Wolff, R. Menssen, J. Hammel, and A. Bindereif Splicing function of mammalian U6 small nuclear-RNA: conserved positions in central domain and helix-I are essential during the 1st and 2nd step of pre-messenger RNA splicing Proc. Natl Acad. Sci. USA 91 1994 903 907
21. J.A. Wu, and J.L. Manley Multiple functional domains of human U2 small nuclear-RNA: strengthening conserved stem I can block splicing Mol. Cell. Biol. 12 1992 5464 5473
22. D.G. Sashital, G. Cornilescu, and S.E. Butcher U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction Nature Struct. Mol. Biol. 11 2004 1237 1242
23. M.J. Moore, and P.A. Sharp Evidence for 2 active-sites in the spliceosome provided by stereochemistry of pre-messenger RNA splicing Nature 365 1993 364 368
24. I.J. Jackson A reappraisal of non-consensus messenger-RNA splice sites Nucl. Acids Res. 19 1991 3795 3798
25. S.L. Hall, and R.A. Padgett Conserved sequences in a class of rare eukaryotic nuclear introns with nonconsensus splice sites J. Mol. Biol. 239 1994 357 365
26. W.Y. Tarn, and J.A. Steitz A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro Cell 84 1996 801 811
27. W.Y. Tarn, and J.A. Steitz Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns Science 273 1996 1824 1832
28. A.A. Patel, and J.A. Steitz Splicing double: insights from the second spliceosome Nature Rev. (Mol. Cell. Biol.) 4 2003 960 970
29. W.Y. Tarn, and J.A. Steitz Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge Trends Biochem. Sci. 22 1997 132 137
30. T.W. Nilsen RNA-RNA interactions in nuclear pre-mRNA splicing R.W. Simons M. Grunberg-Manago RNA Structure and Function 1998 Cold Spring Harbor Laboratory Press New York 279
31. Y.T. Yu, E.C. Scharl, M.S. Christine, and J.A. Steitz The growing world of small nuclear ribonucleoproteins R.F. Gesteland T.R. Cech J.F. Atkins The RNA World 2nd edit. 1999 Cold Spring Harbor Laboratory Press New York 487
32. C.B. Burge, T. Tuschl, and P.A. Sharp Splicing of precursors to mRNAs by the spliceosomes R.F. Gesteland T.R. Cech J.F. Atkins The RNA World 2nd edit. 1999 Cold Spring Harbor Laboratory Press New York 525
33. Q. Wu, and A.R. Krainer AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes Mol. Cell. Biol. 19 1999 3225 3236
34. G.C. Shukla, and R.A. Padgett Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants RNA 5 1999 525 538
35. R.A. Padgett, and G.C. Shukla A revised model for U4atac/U6atac snRNA base pairing RNA 8 2002 125 128
36. G.C. Shukla, A.J. Cole, R.C. Dietrich, and R.A. Padgett Domains of human U4atac snRNA required for U12-dependent splicing in vivo Nucl. Acids Res. 30 2002 4650 4657
37. G.C. Shukla, and R.A. Padgett A catalytically active group II intron domain 5 can function in the U12-dependent spliceosome Mol. Cell. 9 2002 145 150
38. J. SantaLucia Jr, and D. Hicks The thermodynamics of DNA structural motifs Annu. Rev. Biophys. Biomol. Struct. 33 2004 415 440
39. D.H. Mathews, M.E. Burkard, S.M. Freier, J.R. Wyatt, and D.H. Turner Predicting oligonucleotide affinity to nucleic acid targets RNA 5 1999 1458 1469
40. M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucl. Acids Res. 31 2003 3406 3415
41. R.A. Dimitrov, and M. Zuker Prediction of hybridization and melting for double-stranded nucleic acids Biophys. J. 87 2004 215 226
42. M. Rehmsmeier, P. Steffen, M. Höchsmann, and R. Giegerich Fast and effective prediction of microRNA/target duplexes RNA 10 2004 1507 1517
43. M. Andronescu, Z. Zhang, and A. Condon Secondary structure prediction of interacting RNA molecules J. Mol. Biol. 345 2005 987 1001
44. W.B. Zhang, and S.-J. Chen Predicting free energy landscapes for complexes of double-stranded chain molecules J. Chem. Phys. 114 2001 4253 4266
45. S. Cao, and S.-J. Chen Predicting RNA folding thermodynamics with a reduced chain representation model RNA 11 2005 1884 1897
46. C. Wersig, and A. Bindereif Conserved domains of human U4 snRNA required for snRNP and spliceosome assembly Nucl. Acids Res. 18 1990 6223 6229
47. M.J. Serra, and D.H. Turner Predicting thermodynamic properties of RNA Methods Enzymol. 259 1995 242 261
48. R. Kierzek, M.E. Burkard, and D.H. Turner Thermodynamics of single mismatches in RNA duplexes Biochemistry 38 1999 14214 14223
49. F. Michel, R. Umesono, and H. Ozeki Comparative and functional anatomy of group II catalytic introns - a review Gene 82 1989 5 30
50. P.B. Rupert, and A.R. Ferre-D'Amare Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410 2001 780 786
51. S.E. Butcher, and D.A. Brow Towards understanding the catalytic core structure of the spliceosome Biochem. Soc. Trans. 33 2005 447 449
52. A.E. Walter, and D.H. Turner Sequence dependence of stability for coaxial stacking of RNA helices with Watson-Crick base paired interfaces Biochemistry 33 1994 12715 12719
53. H.D. Madhani, and C. Guthrie Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome Genes Dev. 8 1994 1071 1086
54. D.E. Ryan, C.H. Kim, J.B. Murray, C.J. Adams, P.G. Stockley, and J. Abelson New tertiary constraints between the RNA components of active yeast spliceosomes: a photo-crosslinking RNA 10 2004 1251 1265
55. M.M. Konarska, and C.C. Query Insights into the mechanisms of splicing: more lessons from the ribosome Genes Dev. 19 2005 2255 2260
56. G. Donmez, K. Hartmuth, and R. Luhrmann Modified nucleotides at the 5′ end of human U2 snRNA are required for spliceosomal E-complex formation RNA 10 2004 1925 1933
57. J. Gu, J.R. Patton, S. Shimba, and R. Reddy Localization of modified nucleotides in Schizosaccharomyces pombe spliceosomal small nuclear RNAs: modified nucleotides are clustered in functionally important regions RNA 2 1996 909 918
58. J.R. Patton, M.R. Jacobson, and T. Pederson Pseudouridine formation in U2 small nuclear-RNA Proc. Natl Acad. Sci. USA 91 1994 3324 3328
59. M.J. Frilander, and J.A. Steitz Dynamic exchanges of RNA interactions leading to catalytic core formation in the U12-dependent spliceosome Mol. Cell. 7 2001 217 226
60. L.R. Otake, P. Scamborova, C. Hashimoto, and J.A. Steitz The divergent U12-type spliceosome is required for pre-mRNA splicing and is essential for development in Drosophila Mol. Cell. 9 2002 439 446
61. D.J. Field, and J.D. Friesen Functionally redundant interactions between U2 and U6 spliceosomal snRNAs Genes Dev. 10 1996 489 501
62. D.A. Brow, and C. Guthrie Spliceosomal RNA U6 is remarkably conserved from yeast to mammals Nature 334 1988 213 218
63. C. Guthrie, and B. Patterson Spliceosomal snRNAs Annu. Rev. Genet. 22 1988 387 419
64. S.L. Yean, and R.-J. Lin U4 small nuclear RNA dissociates from a yeast spliceosome and does not participate in the subsequent splicing reaction Mol. Cell. Biol. 11 1991 5571 5577
65. G.C. Shukla, and R.A. Padgett The intramolecular stem-loop structure of U6 snRNA can functionally replace the U6atac snRNA stem-loop RNA 7 2001 94 105
66. S.-J. Chen, and K.A. Dill RNA folding energy landscapes Proc. Natl Acad. Sci. USA 97 2000 646 651
67. E. Bornberg-Bauer, and H.S. Chan Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space Proc. Natl Acad. Sci. USA 96 1999 10689 10694
68. D.K. Treiber, M.S. Rook, P.P. Zarrinkar, and J.R. Williamson Kinetic intermediates trapped by native interactions in RNA folding Science 279 1998 1943 1946
69. J. Pan, D. Thirumalai, and S.A. Woodson Folding of RNA involves parallel pathways J. Mol. Biol. 273 1997 7 13
70. Tinoco, I., Jr, & Bustamante, C. (1999). How RNA folds J. Mol. Biol. 293, 271-281.
71. J. SantaLucia Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl Acad. Sci. USA 95 1998 1460 1465
72. P.G. Wolynes, J.N. Onuchic, and D. Thirumalai Navigating the folding routes Science 267 1995 1619 1620
73. K.A. Dill, and H.S. Chan From Levinthal to pathways to funnels Nature Struct. Biol. 4 1997 10 19
74. K.A. Dill Polymer principles and protein folding Protein Sci. 8 1999 1166 1180
75. J.S. McCaskill The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119
76. S.-J. Chen, and K.A. Dill Statistical thermodynamics of double-stranded polymer molecules J. Chem. Phys. 103 1995 5802 5813
77. S.-J. Chen, and K.A. Dill Theory for the conformational changes of double-stranded chain molecules J. Chem. Phys. 109 1998 4602 4616
78. I.L. Hofacker Vienna RNA secondary structure server Nucl. Acids Res. 31 2003 3429 3431
79. A.J. Enright, B. John, U. Gaul, T. Tuschl, C. Sander, and D.S. Marks MicroRNA targets in Drosophila Genome Biol. 5 2003 R1
80. B.P. Lewis, I.H. Snih, M.W. Jones-Rhoades, D.P. Bartel, and C.B. Burge Prediction of mammalian microRNA targets Cell 115 2003 787 798
81. N. Rajewsky, and N.D. Socci Computational identification of microRNA targets Dev. Biol. 267 2004 529 535
82. D. Vitiello, D.B. Pecchia, and J.M. Burke Intracellular ribozyme-catalyzed trans-cleavage of RNA monitored by fluorescence resonance energy transfer RNA 6 2000 628 637
83. Y. Kasai, H. Shizuku, Y. Takagi, M. Warashina, and K. Taira Measurements of weak interactions between truncated substrates and a hammerhead ribozyme by competitive kinetic analyses: implications for the design of new and efficient ribozymes with high sequence specificity Nucl. Acids Res. 30 2002 2383 2389
84. N.K. Vaish, A.R. Kore, and F. Eckstein Recent developments in the hammerhead ribozyme field Nucl. Acids Res. 26 1998 5237 5242
85. R. Hormes, M. Homann, I. Oelze, P. Marschall, M. Tabler, F. Eckstein, and G. Sczakiel The subcellular localization and length of hammerhead ribozymes determine efficacy in human cells Nucl. Acids Res. 25 1997 769 775
86. C. Schmidt, R. Welz, and S. Muller RNA double cleavage by a hairpin-derived twin ribozyme Nucl. Acids Res. 28 2000 886 894
87. A. Barroso-delJesus, and A. Berzal-Herranz Selection of targets and the most efficient hairpin ribozymes for inactivation of mRNAs using a self-cleaving RNA library EMBO Rep. 2 2001 1112 1118
88. K.J. Hampel, and J.M. Burke A conformational change in the "loop E-like" motif of the hairpin ribozyme is coincidental with domain docking and is essential for catalysis Biochemistry 40 2001 3723 3729
89. D. Lazarev, I. Puskarz, and R.R. Breaker Substrate specificity and reaction kinetics of an X-motif ribozyme RNA 9 2003 688 697
90. J. Tang, and R.R. Breaker Mechanism for allosteric inhibition of an ATP-sensitive ribozyme Nucl. Acids Res. 26 1998 4214 4221
91. S.S. Leung, and D.J. Koslowsky Interactions of mRNAs and gRNAs involved in trypanosome mitochondrial RNA editing: structure probing of an mRNA bound to its cognate gRNA RNA 7 2001 1803 1816