Mapping structural differences between 30S ribosomal subunit assembly intermediates

Nature Structural and Molecular Biology

Volumn 11, Issue 2, 2004, Pages 179-186

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

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME PROTEIN; RIBOSOME RNA;

ARTICLE; CHEMICAL MODIFICATION; ESCHERICHIA COLI; IN VITRO STUDY; LOW TEMPERATURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; RIBOSOME SUBUNIT; SEDIMENTATION;

ESCHERICHIA COLI; NUCLEIC ACID CONFORMATION; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0742322957     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb719     Document Type: Article

References (39)

1. Traub, P. & Nomura, M. Structure and function of E. coli ribosomes, V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins. Proc. Natl. Acad. Sci. USA 59, 777-784 (1968).
2. Mizushima, S. & Nomura, M. Assembly mapping of 30S ribosomal proteins in E. coli. Nature 226, 1214-1218 (1970).
3. Held, W.A., Mizushima, S. & Nomura, M. Reconstitution of Escherichia coli 30S ribosomal subunits from purified molecular components. J. Biol. Chem. 218, 5720-5730 (1973).
4. Culver, G.M. & Noller, H.F. Efficient reconstitution of functional Escherichia coli 30S ribosomal subunits from a complete set of recombinant small subunit ribosomal proteins. RNA 5, 832-843 (1999).
5. Held, W.A., Ballou, B., Mizushima, S. & Nomura, M. Assembly mapping of 30S ribosomal proteins from Escherichia coli. J. Biol. Chem. 249, 3103-3111 (1974).
6. Traub, P. & Nomura, M. Structure and function of E. coli ribosomes. VI. Mechanism of assembly of 30S ribosomes studied in vitro. J. Mol. Biol. 40, 391-413 (1969).
7. Held, W.A. & Nomura, M. Rate determining step in the reconstitution of Escherichia coli 30S ribosomal subunits. Biochemistry 12, 3273-3281 (1973).
8. Guthrie, C., Nashimoto, H. & Nomura, M. Structure and function of E. coli ribosomes, VIII. Cold-sensitive mutants defective in ribosome assembly. Proc. Natl. Acad. Sci. USA 63, 384-391 (1969).
9. Nashimoto, H., Held, W., Kaltschmidt, E. & Nomura, M. Structure and function of bacterial ribosomes. XII. Accumulation of 21S particles by some cold-sensitive mutants of E. coli. J. Mol. Biol. 62, 121-138 (1971).
10. Nierhaus, K.H., Bordasch, K. & Homann, H.E. Ribosomal proteins. XLIII. in vivo assembly of Escherichia coli ribosomal proteins. J. Mol. Biol. 74, 587-597 (1973).
11. Lindahl, L. Intermediates and time kinetics of the in vivo assembly of Escherichia coli ribosomes. J. Mol. Biol. 92, 15-37 (1975).
12. Alix, J.-H. & Guerin, M.-F. Mutant DnaK chaperones cause ribosome assembly defects in Escherichia coli. Proc. Natl. Acad. Sci. USA 90, 9725-9729 (1993).
13. Cate, J.H., Yusupov, M.M., Yusupova, G.Z., Earnest, T.N. & Noller, H.F. X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095-2104 (1999).
14. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327-339 (2000).
15. Moazed, D., Van Stolk, B.J., Douthwaite, S. & Noller, H.F. Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in the decoding region of 16S rRNA. J. Mol. Biol. 191, 483-493 (1986).
16. Merryman, C. & Noller, H.F. Footprinting and modification-interference analysis of binding sites on RNA. In RNA:Protein Interactions. A Practical Approach (ed. Smith, C.W.J.) 237-253 (Oxford Univ. Press, New York, 1993).
17. Powers, T. & Noller, H.F. A functional pseudoknot in 16S ribosomal RNA. EMBO J. 10, 2203-2214 (1991).
18. Vila, A., Viril-Farley, J. & Tapprich, W.E. Pseudoknot in the central domain of small subunit ribosomal RNA is essential for translation. Proc. Natl. Acad. Sci. USA 91, 11148-11152 (1994).
19. Poot, R.A., van den Worm, S.H., Pleij, C.W. & van Duin, J. Base complementarity in helix 2 of the central pseudoknot in 16S rRNA is essential for ribosome functioning. Nucleic Acids Res. 26, 549-553 (1998).
20. Cannone, J.J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002).
21. Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 Å resolution, Science 292, 883-896 (2001).
22. Dolan, M.A., Babin, P. & Wollenzien, P. Construction and analysis of base-paired regions of the 16S rRNA in the 30S ribosomal subunit determined by constraint satisfaction molecular modeling. J. Mol. Graph. Model. 19, 495-513 (2001).
23. Schluenzen, F. et al. Structure of functionally activated small ribosomal subunit at 3,3 angstroms resolution. Cell 102, 615-623 (2000).
24. Nikulin, A. et al. Crystal structure of the S15-rRNA complex. Nat. Struct. Biol. 7, 273-277 (2000).
25. Agalarov, S.C., Sridhar Prasad, G., Funke, P.M., Stout, C.D. & Williamson, J.R. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science 288, 107-113 (2000).
26. Brodersen, D.E., Clemons Jr., W.M., Carter, A.P., Wimberly, B.T. & Ramakrishnan, V. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16S RNA. J. Mol. Biol. 316, 725-768 (2002).
27. Powers, T. & Noller, H.F. Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1, 194-209 (1995).
28. Stern, S., Changchien, L.-M., Craven, G.R. & Noller, H.F. Interaction of proteins S16, S17 and S20 with 16S ribosomal RNA. J. Mol. Biol. 200, 291-299 (1988).
29. Powers, T., Changchien, L., Craven, G. & Noller, H. Probing the assembly of the 3′ major domain of 16S ribosomal RNA. Quaternary interactions involving ribosomal proteins S7, S9 and S19. J. Mol. Biol. 200, 309-319 (1988).
30. Powers, T., Stern, S., Changchien, L.M. & Noller, H.F. Probing the assembly of the 3′ major domain of 16S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14. J. Mol. Biol. 201, 697-716 (1988).
31. Moazed, D. & Noller, H.F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985-994 (1986).
32. Moazed, D. & Noller, H.F. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16S rRNA. J. Mol. Biol. 211, 135-145 (1990).
33. Yusupova, G.Z., Yusupov, M.M., Cate, J.H.D. & Noller, H.F. The path of the messenger RNA through the ribosome. Cell 106, 233-241 (2001).
34. Moazed, D., Samaha, R.R., Gualerzi, C. & Noller, H.F. Specific protection of 16S rRNA by translational initiation factors. J. Mol. Biol. 248, 207-210 (1995).
35. Moazed, D., Stern, S. & Noller, H.F. Rapid chemical probing of conformations in 16S ribosomal RNA and 30S ribosomal subunits using primer extension. J. Mol. Biol. 187, 399-416 (1986).
36. Culver, G.M. & Noller, H.F. In vitro reconstitution of 30S ribosomal subunits using complete set of recombinant proteins. Methods Enzymol. 318, 446-460 (2000).
37. Culver, G.M. Assembly of the 30S ribosomal subunit. Biopolymers 68, 234-249.
38. Carson, M. Ribbons. Methods Enzymol. 277, 493-505 (1997).
39. Brimacombe, R. The structure of ribosomal RNA: A three-dimensional jigsaw puzzle. Eur. J. Biochem. 230, 365-383 (1995).