A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. II. The RNA-Protein interaction data

Journal of Molecular Biology

Volumn 271, Issue 4, 1997, Pages 545-565

  Mueller, Florian ^a   Brimacombe, Richard ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Computer modelling; Electron microscopic reconstruction; Neutron scattering map; Protein foot printing; RNA protein cross linking

Indexed keywords

HYDROXYL RADICAL; PROTEIN S; RIBOSOME PROTEIN; RIBOSOME RNA; RNA 16S; TRANSFER RNA;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; CROSS LINKING; CRYOELECTRON MICROSCOPY; ESCHERICHIA COLI; IMMUNOELECTRON MICROSCOPY; NEUTRON SCATTERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN RNA BINDING; RIBOSOME SUBUNIT; RNA CONFORMATION; RNA STRUCTURE; STEREOCHEMISTRY;

ESCHERICHIA COLI;

EID: 0030821676     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1211     Document Type: Article

References (48)

1. Alexander R. W., Muralikrishna P., Cooperman B. S. Ribosomal components neighbouring the conserved 518-533 loop of 16 S rRNA in 30 S subunits. Biochemistry. 33:1994;12109-12118.
2. Allen G., Capasso R., Gualerzi C. Identification of the amino acid residues of proteins S5 and S8 adjacent to each other in the 30 S ribosomal subunit of E. coli. J. Biol. Chem. 254:1979;9800-9806.
3. Allmang C., Mougel M., Westhof E., Ehresmann B., Ehresmann C. Role of conserved nucleotides in building the 16 S rRNA binding site of E. coli ribosomal protein S8. Nucl. Acids Res. 22:1994;3708-3714.
4. Batey R. T., Williamson J. R. Interaction of the B. stearothermophilus ribosomal protein S15 with 16 S rRNA. II. Specificity determinants of RNA-protein recognition. J. Mol. Biol. 261:1996;550-567.
5. Berglund H., Rak A., Serganov A., Garber M., Härd T. Solution structure of the ribosomal RNA binding protein S15 from T. thermophilus. Nature Struct. Biol. 4:1997;20-23.
6. Brimacombe R. RNA-protein interactions in the E. coli ribosome. Biochimie. 73:1991;927-936.
7. Brimacombe R. The structure of ribosomal RNA; a three-dimensional jigsaw puzzle. Eur. J. Biochem. 230:1995;365-383.
8. Brimacombe R., Atmadja J., Stiege W., Schüler D. A detailed model of the three-dimensional structure of E. coli 16 S ribosomal RNA in situ in the 30 S subunit. J. Mol. Biol. 199:1988;115-136.
9. Capel M. S., Kjeldgaard M., Engelman D. M., Moore P. B. Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of E. coli. J. Mol. Biol. 200:1988;65-87.
10. Davies C., Ramakrishnan V., White S. W. Ribosomal protein S8 from B. stearothermophilus at 1.9 Å resolution; structural evidence for specific S8-RNA and S8-protein interactions within the 30 S ribosomal subunit. Structure. 4:1996;1093-1104.
11. Dragon F., Brakier-Gingras L. Interaction of E. coli ribosomal protein S7 with 16 S rRNA. Nucl. Acids Res. 21:1993;1199-1203.
12. Fink D. L., Chen R. O., Noller H. F., Altman R. B. Computational methods for defining the allowed conformational space of 16 S rRNA based on chemical foot-printing data. RNA. 2:1996;851-866.
13. Frank J., Penczek P., Grassucci R., Srivastava S. Three-dimensional reconstruction of the 70 S E. coli ribosome in ice; the distribution of ribosomal RNA. J. Cell Biol. 115:1991;597-605.
14. 15N NMR. Biochemistry. 32:1993;12812-12820.
15. Greuer B., Osswald M., Brimacombe R., Stöffler G. RNA-protein cross-linking in E. coli ribosomal subunits; determination of sites on 16 S RNA that are cross-linked to proteins S3, S4, S7, S9, S10, S11, S17, S18 and S21 by treatment with bis -(2-chloroethyl)-methylamine. Nucl. Acids Res. 15:1987;3241-3255.
16. Heileck G. M., Noller H. F. Site-directed hydroxyl radical probing of the rRNA neighbourhood of ribosomal protein S5. Science. 272:1996;1659-1662.
17. Hoffman D. W., Davies C., Gerchman S. E., Kycia J. H., Porter S. J., White S. W., Ramakrishnan V. Crystal structure of prokaryotic ribosomal protein L9; a bi-lobed RNA-binding protein. EMBO J. 13:1994;205-212.
18. Kyriatsoulis A., Maly P., Greuer B., Brimacombe R., Stöffler G., Frank R., Blöcker H. RNA-protein cross-linking in E. coli ribosomal subunits; localization of sites on 16 S RNA which are cross-linked to proteins S17 and S21 by treatment with 2-iminothiolane. Nucl. Acids Res. 14:1986;1171-1186.
19. Malhotra F., Harvey S. C. A quantitative model of the E. coli 16 S RNA in the 30 S ribosomal subunit. J. Mol. Biol. 240:1994;308-340.
20. Mueller F., Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 Å J. Mol. Biol. 271:1997;524-544.
21. Mueller F., Döring T., Erdemir T., Greuer B., Jünke N., Osswald M., Rinke-Appel J., Stade K., Thamm S., Brimacombe R. Getting closer to an understanding of the three-dimensional structure of ribosomal RNA. Biochem. Cell Biol. 73:1995;767-773.
22. Mueller F., Stark H., van Heel M., Rinke-Appel J., Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. III. The topography of the functional centre. J. Mol. Biol. 271:1997;566-587.
23. Oakes M., Henderson E., Scheinman A., Clark M., Lake J. A. Ribosome structure, function and evolution; mapping ribosomal RNA, proteins and functional sites in three-dimensions. Structure, Function and Genetics of Ribosomes. 1986;Springer-Verlag, New York.
24. Ofengand J., Ciesiolka J., Denman R., Nurse K. Structural and functional interactions of the tRNA-ribosome complex. Hardesty B., Kramer G. Structure, Function and Genetics of Ribosomes. 1986;Springer-Verlag, New York.
25. Olson H. M., Olah T. V., Cooperman B. S., Glitz D. G. Immune electron microscopic localization of dinitrophenol-modified ribosomal protein S19 in reconstituted E. coli 30 S subunits using antibodies to dinitrophenol. J. Biol. Chem. 263:1988;4801-4806.
26. Osswald M., Greuer B., Brimacombe R., Stöffler G., Bäumert H., Fasold H. RNA-protein cross-linking in E. coli 30 S ribosomal subunits; determination of sites on 16 S RNA that are cross-linked to proteins S3, S4, S5, S8, S9, S11, S13, S19 and S21 by treatment with p-azidophenyl acetimidate. Nucl. Acids Res. 15:1987;3221-3240.
27. Osswald M., Döring T., Brimacombe R. The ribosomal neighbourhood of the central fold of tRNA; cross-links from position 47 of tRNA located at the A, P or E site. Nucl. Acids Res. 23:1995;4645-4641.
28. Piepersberg W., Böck A., Yaguchi M., Wittmann H. G. Genetic position and amino acid replacements of several mutations in ribosomal protein S5 from E. coli. Mol. Gen. Genet. 143:1975;43-52.
29. Powers T., Noller H. F. Selective perturbation of G530 of 16 S rRNA by translational miscoding agents and a streptomycin-dependence mutation in protein S12. J. Mol. Biol. 235:1994;156-172.
30. Powers T., Noller H. F. Hydroxyl radical footprinting of ribosomal proteins on 16 S rRNA. RNA. 1:1995;194-209.
31. Valto 16 S RNA at the ribosomal P site; identification of cross-linked residues. Proc. Natl Acad. Sci. USA. 79:1982;5450-5454.
32. Ramakrishnan V. Distribution of protein and RNA in the 30 S ribosomal subunit. Science. 231:1986;1562-1564.
33. Ramakrishnan V., White S. W. The structure of ribosomal protein S5 reveals sites of interaction with 16 S rRNA. Nature. 358:1992;768-771.
34. Rinke-Appel J., Jünke N., Osswald M., Brimacombe R. The ribosomal environment of tRNA; cross-links to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P or E site. RNA. 1:1995;1018-1028.
35. fMetin the P site of the E. coli ribosome. Biochemistry. 32:1993;12802-12811.
36. Schwedler G., Albrecht-Ehrlich R., Rak K. H. Immunoelectron microscopic localization of proteins BS8, BS9, BS20, BL3 and BL21 on the surface of 30 S and 50S subunits from B. stearothermophilus. Eur. J. Biochem. 217:1993;361-369.
37. Stark H., Orlova E. V., Rinke-Appel J., Jünke N., Mueller F., Rodnina M., Wintermeyer W., Brimacombe R., van Heel M. Arrangement of tRNAs in pre- and post-translocational ribosomes revealed by electron cryomicroscopy. Cell. 88:1997;19-28.
38. Stern S., Weiser B., Noller H. F. Model for the three-dimensional folding of 16 S ribosomal RNA. J. Mol. Biol. 204:1988;447-481.
39. Stöffler G., Stöffler-Meilicke M. Immuno electron microscopy on E. coli ribosomes. Hardesty B., Kramer G. Structure, Function and Genetics of Ribosomes. 1986;Springer-Verlag, New York.
40. Stöffler-Meilicke M., Stöffler G. Topography of the ribosomal proteins from E. coli within the intact subunits as determined by immuno electron microscopy and protein-protein cross-linking. Hill W. E., Dahlberg A. E., Garrett R. A., Moore P. B., Schlessinger D., Warner J. R. The Ribosome; Structure, Function and Evolution. 1990;ASM Press, Washington DC.
41. Stuhrmann H. B., Koch M. H. J., Parfait R., Haas J., Ibel K., Crichton R. R. Determination of the distribution of protein and nucleic acid in the 70 S ribosomes of E. coli and their 30 S subunits by neutron scattering. J. Mol. Biol. 119:1978;203-212.
42. Traut R. R., Lambert J. M., Boileau G., Kenny J. W. Protein topography of E. coli ribosomal subunits as inferred from protein cross-linking. Chambliss G., Craven G. R., Davies J., Davis K., Kahan L., Nomura M. Ribosomes, Structure, Function and Genetics. 1980;University Park Press, Baltimore.
43. Urlaub H., Thiede B., Müller E. C., Brimacombe R., Wittmann-Liebold B. Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in E. coli 30 S subunits by a new approach using MALDI-MS combined with N-terminal micro-sequencing. J. Biol. Chem. 272:1997;14547-14555.
44. Wiener L., Schüler D., Brimacombe R. Protein binding sites on E. coli 16 S ribosomal RNA; RNA regions that are protected by proteins S7, S9 and S19, and by proteins S8, S15 and S17. Nucl. Acids Res. 16:1988;1233-1250.
45. Wittmann-Liebold B. Ribosomal proteins; their structure and evolution. Hardesty B., Kramer G. Structure, Function and Genetics of Ribosomes. 1986;Springer-Verlag, New York.
46. Wower I., Brimacombe R. The localization of multiple cross-link sites on 16 S RNA which are cross-linked to proteins S7 and S8 in E. coli ribosomal subunits by treatment with 2-iminothiolane. Nucl. Acids Res. 11:1983;1419-1437.
47. Wower J., Malloy T. A., Hixson S. S., Zimmermann R. A. Probing tRNA binding sites on the E. coli 30 S ribosomal subunit with photoreactive analogs of the anticodon arm. Biochim. Biophys. Acta. 1050:1990;38-44.
48. Zwieb C., Brimacombe R. RNA-protein cross-linking in E. coli ribosomal subunits; precise localization of the nucleotide in 16 S RNA which is coupled to protein S7 by UV-irradiation. Nucl. Acids Res. 6:1979;1775-1790.