Kinetic regulation mechanism of pbuE riboswitch

Journal of Chemical Physics

Volumn 142, Issue 1, 2015, Pages

  Gong, Sha ^a   Wang, Yujie ^a   Zhang, Wenbing ^a  

^a WUHAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; GENE EXPRESSION; KINETICS; LIGANDS; NUCLEIC ACIDS; RNA;

BACILLUS SUBTILIS; CONFORMATION CHANGE; FOLDING BEHAVIOR; LIGAND CONCENTRATION; REGULATION MECHANISMS; SHAPE COMPLEMENTARITY; SPECIFIC INTERACTION; UNTRANSLATED REGIONS;

TRANSCRIPTION;

LIGAND; MESSENGER RNA; RIBOSWITCH;

BACILLUS SUBTILIS; CONFORMATION; GENETIC TRANSCRIPTION; GENETICS; KINETICS; METABOLISM; RIBOSWITCH; THERMODYNAMICS;

BACILLUS SUBTILIS; KINETICS; LIGANDS; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA, MESSENGER; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 84923783315     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4905214     Document Type: Article

References (67)

1. M. Mandal and R. R. Breaker, Nat. Rev. Mol. Cell Biol. 5, 451 (2004). 10.1038/nrm1403
2. W. C. Winkler and R. R. Breaker, ChemBioChem 4, 1024 (2003). 10.1002/cbic.200300685
3. A. G. Vitreschak, D. A. Rodionov, A. A. Mironov, and M. S. Gelfand, Trends Genet. 20, 44 (2004). 10.1016/j.tig.2003.11.008
4. A. Serganov and D. J. Patel, Curr. Opin. Struct. Biol. 22, 279 (2012). 10.1016/j.sbi.2012.04.005
5. A. Serganov and E. Nudler, Cell 152, 17 (2013). 10.1016/j.cell.2012.12.024
6. M. Mandal, B. Boese, J. E. Barrick, W. C. Winkler, and R. R. Breaker, Cell 113, 577 (2003). 10.1016/S0092-8674(03)00391-X
7. A. Villa, J. Wöhnert, and G. Stock, Nucleic Acids Res. 37, 4774 (2009). 10.1093/nar/gkp486
8. L. Huang, A. Serganov, and D. J. Patel, Mol. Cell 40, 774 (2010). 10.1016/j.molcel.2010.11.026
9. M. Mandal, M. Lee, J. E. Barrick, Z. Weinberg, G. M. Emilsson, W. L. Ruzzo, and R. R. Breaker, Science 306, 275 (2004). 10.1126/science.1100829
10. W. C. Winkler, A. Nahvi, N. Sudarsan, J. E. Barrick, and R. R. Breaker, Nat. Struct. Biol. 10, 701 (2003). 10.1038/nsb967
11. W. Huang, J. Kim, S. Jha, and F. Aboul-ela, Nucleic Acids Res. 37, 6528 (2009). 10.1093/nar/gkp664
12. S. Li and R. R. Breaker, Nucleic Acids Res. 41, 3022 (2013). 10.1093/nar/gkt057
13. J. A. Liberman and J. E. Wedekind, Wiley Interdiscip. Rev.: RNA 3, 369 (2012). 10.1002/wrna.114
14. W. C. Winkler, S. Cohen-Chalamish, and R. R. Breaker, Proc. Natl. Acad. Sci. U. S. A. 99, 15908 (2002). 10.1073/pnas.212628899
15. R. Rieder, K. Lang, D. Graber, and R. Micura, ChemBioChem 8, 896 (2007). 10.1002/cbic.200700057
16. S. D. Gilbert, R. K. Montange, C. D. Stoddard, and R. T. Batey, Cold Spring Harbor Symp. Quant. Biol. 71, 259 (2006). 10.1101/sqb.2006.71.015
17. F. J. Grundy and T. M. Henkin, Mol. Microbiol. 30, 737 (1998). 10.1046/j.1365-2958.1998.01105.x
18. R. T. Batey, S. D. Gilbert, and R. K. Montange, Nature 432, 411 (2004). 10.1038/nature03037
19. J.-C. Lin and D. Thirumalai, J. Am. Chem. Soc. 135, 16641 (2013). 10.1021/ja408595e
20. A. Reining, S. Nozinovic, K. Schlepckow, F. Buhr, B. Fürtig, and H. Schwalbe, Nature 499, 355 (2013). 10.1038/nature12378
21. M. T. Cheah, A. Wachter, N. Sudarsan, and R. R. Breaker, Nature 447, 497 (2007). 10.1038/nature05769
22. K. Neupane, H. Yu, D. A. N. Foster, F. Wang, and M. T. Woodside, Nucleic Acids Res. 39, 7677 (2011). 10.1093/nar/gkr305
23. U. D. Priyakumar and A. D. MacKerell, Jr., J. Mol. Biol. 396, 1422 (2010). 10.1016/j.jmb.2009.12.024
24. Z. Gong, Y. Zhao, C. Chen, and Y. Xiao, J. Biomol. Struct. Dyn. 29, 403 (2011). 10.1080/07391102.2011.10507394
25. J.-F. Lemay and D. A. Lafontaine, RNA 13, 339 (2007). 10.1261/rna.142007
26. J.-F. Lemay, G. Desnoyers, S. Blouin, B. Heppell, L. Bastet, P. St-Pierre, E. Massé, and D. A. Lafontaine, PLoS Genet. 7, e1001278 (2011). 10.1371/journal.pgen.1001278
27. J. Noeske, C. Richter, M. A. Grundl, H. R. Nasiri, H. Schwalbe, and J. Wöhnert, Proc. Natl. Acad. Sci. U. S. A. 102, 1372 (2005). 10.1073/pnas.0406347102
28. M. Mandal and R. R. Breaker, Nat. Struct. Mol. Biol. 11, 29 (2004). 10.1038/nsmb710
29. S. D. Gilbert, C. D. Stoddard, S. J. Wise, and R. T. Batey, J. Mol. Biol. 359, 754 (2006). 10.1016/j.jmb.2006.04.003
30. J.-C. Lin and D. Thirumalai, J. Am. Chem. Soc. 130, 14080 (2008). 10.1021/ja8063638
31. J.-C. Lin, C. Hyeon, and D. Thirumalai, Phys. Chem. Chem. Phys. 16, 6376 (2014). 10.1039/c3cp53932f
32. J. K. Wickiser, M. T. Cheah, R. R. Breaker, and D. M. Crothers, Biochemistry 44, 13404 (2005). 10.1021/bi051008u
33. C. D. Stoddard, S. D. Gilbert, and R. T. Batey, RNA 14, 675 (2008). 10.1261/rna.736908
34. O. Allnér, L. Nilsson, and A. Villa, RNA 19, 916 (2013). 10.1261/rna.037549.112
35. J.-F. Lemay, J. C. Penedo, R. Tremblay, D. M. J. Lilley, and D. A. Lafontaine, Chem. Biol. 13, 857 (2006). 10.1016/j.chembiol.2006.06.010
36. J. Noeske, J. Buck, B. Fürtig, H. R. Nasiri, H. Schwalbe, and J. Wöhnert, Nucleic Acids Res. 35, 572 (2007). 10.1093/nar/gkl1094
37. O. M. Ottink, S. M. Rampersad, M. Tessari, G. J. R. Zaman, H. A. Heus, and S. S. Wijmenga, RNA 13, 2202 (2007). 10.1261/rna.635307
38. G. Quarta, K. Sin, and T. Schlick, PLoS Comput. Biol. 8, e1002368 (2012). 10.1371/journal.pcbi.1002368
39. T. N. Wong, T. R. Sosnick, and T. Pan, Proc. Natl. Acad. Sci. U. S. A. 104, 17995 (2007). 10.1073/pnas.0705038104
40. F. R. Kramer and D. R. Mills, Nucleic Acids Res. 9, 5109 (1981). 10.1093/nar/9.19.5109
41. P. Zhao, W. Zhang, and S.-J. Chen, J. Chem. Phys. 135, 245101 (2011). 10.1063/1.3671644
42. J. K. Wickiser, W. C. Winkler, R. R. Breaker, and D. M. Crothers, Mol. Cell 18, 49 (2005). 10.1016/j.molcel.2005.02.032
43. K. L. Frieda and S. M. Block, Science 338, 397 (2012). 10.1126/science.1225722
44. P. Zhao, W. B. Zhang, and S. J. Chen, Biophys. J. 98, 1617 (2010). 10.1016/j.bpj.2009.12.4319
45. W. Zhang and S.-J. Chen, Biophys. J. 90, 765 (2006). 10.1529/biophysj.105.062935
46. J. Chen, S. Gong, Y. Wang, and W. Zhang, J. Chem. Phys. 140, 025102 (2014). 10.1063/1.4861037
47. J. Chen and W. Zhang, J. Chem. Phys. 137, 225102 (2012). 10.1063/1.4769821
48. W. J. Greenleaf, K. L. Frieda, D. A. N. Foster, M. T. Woodside, and S. M. Block, Science 319, 630 (2008). 10.1126/science.1151298
49. N. Komissarova, J. Becker, S. Solter, M. Kireeva, and M. Kashlev, Mol. Cell 10, 1151 (2002). 10.1016/S1097-2765(02)00738-4
50. I. Gusarov and E. Nudler, Mol. Cell 3, 495 (1999). 10.1016/S1097-2765(00)80477-3
51. L. Lubkowska, A. S. Maharjan, and N. Komissarova, J. Biol. Chem. 286, 31576 (2011). 10.1074/jbc.M111.249359
52. T. Xia, J. Santalucia, Jr., M. E. Burkard, R. Kierzek, S. J. Schroeder, X. Jiao, C. Cox, and D. H. Turner, Biochemistry 37, 14719 (1998). 10.1021/bi9809425
53. D. H. Mathews, J. Sabina, M. Zuker, and D. H. Turner, J. Mol. Biol. 288, 911 (1999). 10.1006/jmbi.1999.2700
54. I. Artsimovitch, V. Svetlov, L. Anthony, R. R. Burgess, and R. Landick, J. Bacteriol. 182, 6027 (2000). 10.1128/JB.182.21.6027-6035.2000
55. R. A. Mooney, I. Artsimovitch, and R. Landick, J. Bacteriol. 180, 3265 (1998).
56. L. E. Johansen, P. Nygaard, C. Lassen, Y. AgersΦ, and H. H. Saxild, J. Bacteriol. 185, 5200 (2003). 10.1128/JB.185.17.5200-5209.2003
57. U. Vogel and K. F. Jensen, J. Biol. Chem. 272, 12265 (1997). 10.1074/jbc.272.19.12265
58. S. F. Tolić-Nørrelykke, A. M. Engh, R. Landick, and J. Gelles, J. Biol. Chem. 279, 3292 (2004). 10.1074/jbc.m310290200
59. A. Haller, M. F. Soulière, and R. Micura, Acc. Chem. Res. 44, 1339 (2011). 10.1021/ar200035g
60. I. Artsimovitch and R. Landick, Proc. Natl. Acad. Sci. U. S. A. 97, 7090 (2000). 10.1073/pnas.97.13.7090
61. N. Komissarova and M. Kashlev, Proc. Natl. Acad. Sci. U. S. A. 95, 14699 (1998). 10.1073/pnas.95.25.14699
62. J. A. Monforte, J. D. Kahn, and J. E. Hearst, Biochemistry 29, 7882 (1990). 10.1021/bi00486a015
63. D. E. Draper, RNA 10, 335 (2004). 10.1261/rna.5205404
64. D. E. Draper, D. Grilley, and A. M. Soto, Annu. Rev. Biophys. Biomol. Struct. 34, 221 (2005). 10.1146/annurev.biophys.34.040204.144511
65. D. Grilley, A. M. Soto, and D. E. Draper, Proc. Natl. Acad. Sci. U. S. A. 103, 14003 (2006). 10.1073/pnas.0606409103
66. Z. J. Tan and S. J. Chen, Biophys. J. 99, 1565 (2010). 10.1016/j.bpj.2010.06.029
67. Z. J. Tan and S. J. Chen, Biophys. J. 101, 176 (2011). 10.1016/j.bpj.2011.05.050