Analysis of conformational changes in 16 S rRNA during the course of 30 S subunit assembly

Journal of Molecular Biology

Volumn 354, Issue 2, 2005, Pages 340-357

  Holmes, Kristi L ^a   Culver, Gloria M ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

16 S rRNA; 30 S subunit; Conformational change; Ribosomal protein; Ribosome

Indexed keywords

RIBOSOME PROTEIN; RIBOSOME RNA;

ARTICLE; BASE PAIRING; CONFORMATION; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN ASSEMBLY; RIBOSOME SUBUNIT;

ESCHERICHIA COLI;

EID: 27644536231     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.09.056     Document Type: Article

References (50)

1. P. Traub, and M. Nomura Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30 S ribosomal particles from RNA and proteins Proc. Natl Acad. Sci. USA 59 1968 777 784
2. S. Mizushima, and M. Nomura Assembly mapping of 30 S ribosomal proteins in E. coli Nature 226 1970 1214 1218
3. W.A. Held, S. Mizushima, and M. Nomura Reconstitution of Escherichia coli 30 S ribosomal subunits from purified molecular components J. Biol. Chem. 248 1973 5720 5730
4. G.M. Culver, and H.F. Noller Efficient reconstitution of functional Escherichia coli 30 S ribosomal subunits from a complete set of recombinant small subunit ribosomal proteins RNA 5 1999 832 843
5. G.M. Culver, and H.F. Noller In vitro reconstitution of 30 S ribosomal subunits using complete set of recombinant proteins Methods Enzymol. 318 2000 446 460
6. M. Nomura, S. Mizushima, M. Ozaki, P. Traub, and C.V. Lowry Structure and function of ribosomes and their molecular components Cold Spring Harbor Symp. Quant. Biol. 34 1969 49 61
7. G.M. Culver Assembly of the 30 S subunit Biopolymers 68 2003 234 249
8. C. Guthrie, H. Nashimoto, and M. Nomura Structure and function of E. coli ribosomes. VIII. Cold-sensitive mutants defective in ribosome assembly Proc. Natl Acad. Sci. USA 63 1969 384 391
9. H. Nashimoto, W. Held, E. Kaltschmidt, and M. Nomura Structure and function of bacterial ribosomes. XII. Accumulation of 21 S particles by some cold-sensitive mutants of E. coli J. Mol. Biol. 62 1971 121 138
10. K.H. Nierhaus, K. Bordasch, and H.E. Homann Ribosomal proteins. XLIII. In vivo assembly of Escherichia coli ribosomal proteins J. Mol. Biol. 74 1973 587 597
11. L. Lindahl Intermediates and time kinetics of the in vivo assembly of Escherichia coli ribosomes J. Mol. Biol. 92 1975 15 37
12. J.H. Alix, and M.F. Guerin Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli Proc. Natl Acad. Sci. USA 90 1993 9725 9729
13. P. Traub, and M. Nomura Structure and function of E. coli ribosomes. VI. Mechanism of assembly of 30 S ribosomes studied in vitro J. Mol. Biol. 40 1969 391 413
14. W.A. Held, and M. Nomura Rate determining step in the reconstitution of Escherichia coli 30 S ribosomal subunits Biochemistry 12 1973 3273 3281
15. M.F. Tam, and W.E. Hill Physical characteristics of the reconstitution intermediates (RI30 and RI30*) from the 30 S ribosomal subunit of Escherichia coli Biochemistry 20 1981 6480 6484
16. K.L. Holmes, and G.M. Culver Mapping structural differences between 30 S ribosomal subunit assembly intermediates Nature Struct. Mol. Biol. 11 2004 179 186
17. T. Powers, and H.F. Noller Hydroxyl radical footprinting of ribosomal proteins on 16 S rRNA RNA 1 1995 194 209
18. T. Powers, and H.F. Noller A temperature-dependent conformational rearrangement in the ribosomal protein S4.16 S rRNA complex J. Biol. Chem. 270 1995 1238 1242
19. T. Powers, G. Daubresse, and H.F. Noller Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits J. Mol. Biol. 232 1993 362 374
20. B.T. Wimberly, D.E. Brodersen, W.M.J. Clemons, R.J. Morgan-Warren, A.P. Carter, and C. Vonrhein Structure of the 30 S ribosomal subunit Nature 407 2000 327 339
21. D.E. Brodersen, W.M.J. Clemons, A.P. Carter, B.T. Wimberly, and V. Ramakrishnan 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 2002 725 768
22. D. Moazed, S. Stern, and H.F. Noller Rapid chemical probing of conformations in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension J. Mol. Biol. 187 1986 399 416
23. J.J. Cannone, S. Subramanian, M.N. Schnare, J.R. Collett, L.M. D'Souza, and Y. Du The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs BMC Bioinformatics 3 2002 2
24. T. Powers, L. Changchien, G. Craven, and H. Noller Probing the assembly of the 3′ major domain of 16 S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19 J. Mol. Biol. 200 1988 309 319
25. S. Stern, L.-M. Changchien, G.R. Craven, and H.F. Noller Interaction of proteins S16, S17 and S20 with 16 S ribosomal RNA J. Mol. Biol. 200 1988 291 299
26. P. Svensson, L.M. Changchien, G.R. Craven, and H.F. Noller Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA J. Mol. Biol. 200 1988 301 308
27. T. Powers, S. Stern, L.M. Changchien, and H.F. Noller Probing the assembly of the 3′ major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14 J. Mol. Biol. 201 1988 697 716
28. S. Stern, T. Powers, L.M. Changchien, and H.F. Noller Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA J. Mol. Biol. 201 1988 683 695
29. V. Ramakrishnan, and S.W. White The structure of ribosomal protein S5 reveals sites of interaction with 16 S rRNA Nature 358 1992 768 771
30. 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
31. 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
32. C. Merryman, D. Moazed, J. McWhirter, and H.F. Noller Nucleotides in 16 S rRNA protected by the association of 30 S and 50S ribosomal subunits J. Mol. Biol. 285 1999 97 105
33. 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
34. J.A. Maki, D.J. Schnobrich, and G.M. Culver The DnaK chaperone system facilitates 30 S ribosomal subunit assembly Mol. Cell 10 2002 129 138
35. M.I. Recht, and J.R. Williamson RNA tertiary structure and cooperative assembly of a large ribonucleoprotein complex J. Mol. Biol. 344 2004 395 407
36. T. Adilakshmi, P. Ramaswamy, and S.A. Woodson Protein-independent folding pathway of the 16 S rRNA 5′ domain J. Mol. Biol. 351 2005 508 519
37. W.A. Held, and M. Nomura Escherichia coli 30 S ribosomal proteins uniquely required for assembly J. Biol. Chem. 250 1975 3179 3184
38. V. Ramakrishnan, V. Graziano, and M.S. Capel A role for proteins S3 and S14 in the 30 S ribosomal subunit J. Biol. Chem. 261 1986 15049 15052
39. V. Nowotny, and K.H. Nierhaus Assembly of the 30 S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7 Biochemistry 27 1988 7051 7055
40. H.F. Noller RNA structure: reading the ribosome Science 309 2005 1508 1514
41. H.F. Noller, and A. Baucom Structure of the 70 S ribosome: implications for movement Biochem. Soc. Trans. 30 2002 1159 1161
42. T. Powers, and H.F. Noller A functional pseudoknot in 16 S ribosomal RNA EMBO J. 10 1991 2203 2214
43. F. Belanger, G. Theberge-Julien, P.R. Cunningham, and L. Brakier-Gingras A functional relationship between helix 1 and the 900 tetraloop of 16 S ribosomal RNA within the bacterial ribosome RNA 11 2005 906 913
44. R.R. Samaha, B. O'Brien, T.W. O'Brien, and H.F. Noller Independent in vitro assembly of a ribonucleoprotein particle containing the 3′ domain of 16 S rRNA Proc. Natl Acad. Sci. USA 91 1994 7884 7888
45. S.C. Agalarov, E.N. Zheleznyakova, O.M. Selivanova, L.A. Zheleznaya, N.I. Matvienko, V.D. Vasiliev, and A.S. Spirin In vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30 S ribosomal subunit Proc. Natl Acad. Sci. USA 95 1998 999 1003
46. S.C. Agalarov, O.M. Selivanova, E.N. Zheleznyakova, L.A. Zheleznaya, N.I. Matvienko, and A.S. Spirin Independent in vitro assembly of all three major morphological parts of the 30 S ribosomal subunit of Thermus thermophilus Eur. J. Biochem. 266 1999 533 537
47. L. Lancaster, G.M. Culver, G.Z. Yusopova, J.H. Cate, M.M. Yusopov, and H.F. Noller The location of protein S8 and surrounding elements of 16 S rRNA in the 70 S ribosome from combined use of directed hydroxyl radical probing and X-ray crystallography RNA 6 2000 717 729
48. O. Weichenrieder, C. Stehlin, U. Kapp, D. Birse, P.A. Timmins, K. Strub, and S. Cusack Hierarchical assembly of the Alu domain of the mammalian signal recognition particle RNA 7 2001 731 740
49. C. Merryman, and H.F. Noller Footprinting and modification-interference analysis of binding sites on RNA C.W.J Smith RNA:Protein Interactions. A Practical Approach 1998 Oxford University Press New York
50. M. Carson Ribbons Methods Enzymol. 277 1997 493 505