A time-resolved investigation of ribosomal subunit association

Journal of Molecular Biology

Volumn 346, Issue 5, 2005, Pages 1243-1258

  Hennelly, Scott P ^a,b   Antoun, Ayman ^c   Ehrenberg, Måns ^c   Gualerzi, Claudio O ^b   Knight, William ^a   Lodmell, J Stephen ^a   Hill, Walter E ^a  

^a UNIVERSITY OF MONTANA   (United States)

^b UNIVERSITY OF CAMERINO   (Italy)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Dynamics; Ribosome; RNA; Structure; Subunit association

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

ARTICLE; BINDING SITE; CHEMICAL MODIFICATION; CONFORMATION; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RNA STRUCTURE;

EID: 13844280352     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.12.054     Document Type: Article

References (54)

1. W. Herr, N.M. Chapman, and H.F. Noller Mechanism of ribosomal subunit association: discrimination of specific sites in 16 S RNA essential for association activity J. Mol. Biol. 130 1979 433 449
2. N.M. Chapman, and H.F. Noller Protection of specific sites in 16 S RNA from chemical modification by association of 30 S and 50 S ribosomes J. Mol. Biol. 109 1977 131 149
3. C. Merryman, D. Moazed, G. Daubresse, and H.F. Noller Nucleotides in 23 S rRNA protected by the association of 30 S and 50 S ribosomal subunits J. Mol. Biol. 285 1999 107 113
4. C. Merryman, D. Moazed, J. McWhirter, and H.F. Noller Nucleotides in 16 S rRNA protected by the association of 30 S and 50 S ribosomal subunits J. Mol. Biol. 285 1999 97 105
5. P. Mitchell, M. Osswald, and R. Brimacombe Identification of intermolecular RNA cross-links at the subunit interface of the Escherichia coli ribosome Biochemistry 31 1992 3004 3011
6. J. Frank, A. Verschoor, Y. Li, J. Zhu, R.K. Lata, and M. Radermacher A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome Biochem. Cell. Biol. 73 1995 757 765
7. J. Frank, J. Zhu, P. Penczek, Y. Li, S. Srivastava, and A. Verschoor A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome Nature 376 1995 441 444
8. H. Stark, E.V. Orlova, J. Rinke-Appel, N. Junke, F. Mueller, and M. Rodnina Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy Cell 88 1997 19 28
9. M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, T.N. Earnest, J.H. Cate, and H.F. Noller Crystal structure of the ribosome at 5.5 Å resolution Science 292 2001 883 896
10. J.H. Cate, M.M. Yusupov, G.Z. Yusupova, T.N. Earnest, and H.F. Noller X-ray crystal structures of 70 S ribosome functional complexes Science 285 1999 2095 2104
11. H. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, and S.M. Stagg Study of the structural dynamics of the E. coli 70 S ribosome using real-space refinement Cell 113 2003 789 801
12. I.S. Gabashvili, R.K. Agrawal, C.M. Spahn, R.A. Grassucci, D.I. Svergun, J. Frank, and P. Penczek Solution structure of the E. coli 70 S ribosome at 11.5 Å resolution Cell 100 2000 537 549
13. C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, and J. Frank Structure of the 80 S ribosome from Saccharomyces cerevisiae-tRNA- ribosome and subunit-subunit interactions Cell 107 2001 373 386
14. U. Maivali, and J. Remme Definition of bases in 23 S rRNA essential for ribosomal subunit association RNA 10 2004 600 604
15. 2+ in ribosomal subunit association: kinetics and equilibrium in the presence of other divalent metal ions J. Mol. Biol. 116 1977 577 591
16. 2+ J. Mol. Biol. 93 1975 499 515
17. B. Hapke, and H. Noll Structural dynamics of bacterial ribosomes. IV. Classification of ribosomes by subunit interaction J. Mol. Biol. 105 1976 97 109
18. G. Blaha, N. Burkhardt, and K.H. Nierhaus Formation of 70 S ribosomes: large activation energy is required for the adaptation of exclusively the small ribosomal subunit Biophys. Chem. 96 2002 153 161
19. A. Antoun, M.Y. Pavlov, T. Tenson, and M. Ehrenberg Ribosome formation from subunits studied by stopped-flow and Rayleigh light scattering Biol. Proced. Online 2004 35 54
20. I.S. Gabashvili, M. Whirl-Carrillo, M. Bada, D.R. Banatao, and R.B. Altman Ribosomal dynamics inferred from variations in experimental measurements RNA 9 2003 1301 1307
21. J.S. Lodmell, and S.P. Hennelly Conformational dynamics within the ribosome L. Brakier-Gingras J. Lapointe Translational Mechanisms 2002 Landes Bioscience Austin, TX 264 279
22. M.H. de Smit, and J. van Duin Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA J. Mol. Biol. 331 2003 737 743
23. P.B. Moore, and T.A. Steitz The structural basis of large ribosomal subunit function Annu. Rev. Biochem. 72 2003 813 850
24. K.S. Wilson, and H.F. Noller Molecular movement inside the translational engine Cell 92 1998 337 349
25. M. Valle, A. Zavialov, J. Sengupta, U. Rawat, M. Ehrenberg, and J. Frank Locking and unlocking of ribosomal motions Cell 114 2003 123 134
26. N. Polacek, S. Patzke, K.H. Nierhaus, and A. Barta Periodic conformational changes in rRNA: monitoring the dynamics of translating ribosomes Mol. Cell 6 2000 159 171
27. H. Stark, M.V. Rodnina, H.J. Wieden, M. van Heel, and W. Wintermeyer Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation Cell 100 2000 301 309
28. A. Savelsbergh, V.I. Katunin, D. Mohr, F. Peske, M.V. Rodnina, and W. Wintermeyer An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation Mol. Cell 11 2003 1517 1523
29. M. Ehrenberg, N. Bilgin, and C. Kurland Design and use of a fast and accurate in vitro translation system Ribosomes and Protein Synthesis. A Practical Approach 1990 Oxford University Press Oxford 101 128
30. W. Herr, and H.F. Noller Protection of specific sites in 23 S and 5 S RNA from chemical modification by association of 30 S and 50 S ribosomes J. Mol. Biol. 130 1979 421 432
31. J.S. Lodmell, and A.E. Dahlberg A conformational switch in Escherichia coli 16 S ribosomal RNA during decoding of messenger RNA Science 277 1997 1262 1267
32. D. Rodriguez-Correa, and A.E. Dahlberg Genetic evidence against the 16 S ribosomal RNA helix 27 conformational switch model RNA 10 2004 28 33
33. F. Belanger, M. Leger, A.A. Saraiya, P.R. Cunningham, and L. Brakier-Gingras Functional studies of the 900 tetraloop capping helix 27 of 16 S ribosomal RNA J. Mol. Biol. 320 2002 979 989
34. F. Belanger, M.G. Gagnon, S.V. Steinberg, P.R. Cunningham, and L. Brakier-Gingras Study of the functional interaction of the 900 Tetraloop of 16 S ribosomal RNA with helix 24 within the bacterial ribosome J. Mol. Biol. 338 2004 683 693
35. F. Tama, M. Valle, J. Frank, and C.L. Brooks 3rd Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc. Natl Acad. Sci. USA 100 2003 9319 9323
36. I.V. Velichutina, J. Dresios, J.Y. Hong, C. Li, A. Mankin, D. Synetos, and S.W. Liebman Mutations in helix 27 of the yeast Saccharomyces cerevisiae 18 S rRNA affect the function of the decoding center of the ribosome RNA 6 2000 1174 1184
37. I.S. Gabashvili, R.K. Agrawal, R. Grassucci, C.L. Squires, A.E. Dahlberg, and J. Frank Major rearrangements in the 70 S ribosomal 3D structure caused by a conformational switch in 16 S ribosomal RNA EMBO J. 18 1999 6501 6507
38. A.P. Carter, W.M. Clemons, D.E. Brodersen, R.J. Morgan-Warren, B.T. Wimberly, and V. Ramakrishnan Functional insights from the structure of the 30 S ribosomal subunit and its interactions with antibiotics Nature 407 2000 340 348
39. F. Schluenzen, A. Tocilj, R. Zarivach, J. Harms, M. Gluehmann, and D. Janell Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution Cell 102 2000 615 623
40. S.K. Vassilenko, P. Carbon, J.P. Ebel, and C. Ehresmann Topography of 16 S RNA in 30 S subunits and 70 S ribosomes accessibility to cobra venom ribonuclease J. Mol. Biol. 152 1981 699 721
41. D. Moazed, and H.F. Noller Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA J. Mol. Biol. 211 1990 135 145
42. D. Moazed, and H.F. Noller Transfer RNA shields specific nucleotides in 16 S ribosomal RNA from attack by chemical probes Cell 47 1986 985 994
43. N. Ban, P. Nissen, J. Hansen, P.B. Moore, and T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution Science 289 2000 905 920
44. J.M. Ogle, F.V. Murphy, M.J. Tarry, and V. Ramakrishnan Selection of tRNA by the ribosome requires a transition from an open to a closed form Cell 111 2002 721 732
45. K.D. Dahlquist, and J.D. Puglisi Interaction of translation initiation factor IF1 with the E. coli ribosomal A site J. Mol. Biol. 299 2000 1 15
46. B.T. Wimberly, D.E. Brodersen, W.M. Clemons Jr, R.J. Morgan-Warren, A.P. Carter, and C. Vonrhein Structure of the 30 S ribosomal subunit Nature 407 2000 327 339
47. D. Moazed, and H.F. Noller Interaction of antibiotics with functional sites in 16 S ribosomal RNA Nature 327 1987 389 394
48. L. Brakier-Gingras, R. Pinard, and F. Dragon Pleiotropic effects of mutations at positions 13 and 914 in Escherichia coli 16 S ribosomal RNA Biochem. Cell. Biol. 73 1995 907 913
49. R. Pinard, M. Cote, C. Payant, and L. Brakier-Gingras Positions 13 and 914 in Escherichia coli 16 S ribosomal RNA are involved in the control of translational accuracy Nucl. Acids Res. 22 1994 619 624
50. A.P. Carter, W.M. Clemons Jr, D.E. Brodersen, R.J. Morgan-Warren, T. Hartsch, B.T. Wimberly, and V. Ramakrishnan Crystal structure of an initiation factor bound to the 30 S ribosomal subunit Science 291 2001 498 501
51. M. Grunberg-Manago, P. Dessen, D. Pantaloni, T. Godefroy-Colburn, A.D. Wolfe, and J. Dondon Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes J. Mol. Biol. 94 1975 461 478
52. R.A. Calogero, C.L. Pon, M.A. Canonaco, and C.O. Gualerzi Selection of the mRNA translation initiation region by Escherichia coli ribosomes Proc. Natl Acad. Sci. USA 85 1988 6427 6431
53. A. Antoun, M.Y. Pavlov, K. Andersson, T. Tenson, and M. Ehrenberg The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis EMBO J. 22 2003 5593 5601
54. J. Harms, F. Schluenzen, R. Zarivach, A. Bashan, S. Gat, and I. Agmon High resolution structure of the large ribosomal subunit from a mesophilic eubacterium Cell 107 2001 679 688