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The Folding of RNA in the 30S Subunit of Escherichia coli Ribosomes

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Structure, Function, and Genetics of Ribosomes

Part of the book series: Springer Series in Molecular Biology ((SSMOL))

Abstract

The structure of the ribosome has been studied by many different techniques and at many levels of complexity. An approach that we have followed extensively in recent years is to break the organelle into fragments and to investigate each fragment individually. The objective is to convert the large and complex particle into several smaller, less complex, and more manageable units, while preserving, as far as possible, the original native structure in the degree demanded by the nature of the information sought.

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References

  • Atmajda, J., Brimacombe, R., Maden, B.E.H. (1984). Xenopus laevis 18 S ribosomal RNA; experimental determination of secondary structural elements, and locations of methyl groups in the secondary structure model. Nucl. Acids Res. 12: 2649–2667.

    Article  Google Scholar 

  • Chiaruttini, C., Expert-Bezan£on, A., Hayes, D., Thurlow, D.L., Ehresmann, B. (1982). Protein-RNA crosslinking in E. coli 30 S ribosomal subunits. Identification of a 16 S rRNA fragment crosslinked to protein S12 by the use of the chemical crosslinking reagent l-ethyl-3-dimethyl-aminopropylcarbodiimide. Nucl. Acids Res. 10: 7657–7676.

    Article  PubMed  CAS  Google Scholar 

  • Cotter, R.I., McPhie, P., Gratzer, W.B. (1976). Internal organization of the ribosome. Nature 216: 864–868.

    Article  Google Scholar 

  • Cox, R.A. (1977). Structure and function of prokaryotic and eukaryotic ribosomes. Prog. Biophys. Mol. Biol. 32: 193–231.

    Article  PubMed  CAS  Google Scholar 

  • Douthwaite, S., Christensen, A., Garrett, R.A. (1983). Higher order structure in the 3′-minor domain of small subunit ribosomal RNAs from a gram negative bacterium, a gram positive bacterium and a eukaryote. J. Mol. Biol. 169: 249–279.

    Article  PubMed  CAS  Google Scholar 

  • Dunn, J.M., Wong, K.P. (1979). Molecular mechanism of in vitro 30S ribosome assembly. I. Conformational changes of the 16S RNA. J. Biol. Chem. 254: 7705–7711.

    PubMed  CAS  Google Scholar 

  • Ehresmann, C., Stiegler, P., Carbon, P., Ungewickell, E., Garrett, R.A. (1980). The topography of the 5′ end of 16-S RNA in the presence and absence of ribosomal proteins S4 and S20. Eur. J. Biochem. 103: 439–446.

    Article  PubMed  CAS  Google Scholar 

  • Eilam, Y., Elson, D. (1971). Unfolding of the 30S ribosomal subunit of E. coli and the conformation of the unfolded subunit. Parallel sedimentation and optical rotatory dispersion studies. Biochemistry 10: 1489–1495.

    Article  PubMed  CAS  Google Scholar 

  • Elson, D., Spitnik-Elson, P., Avital, S., Abramowitz, R. (1979). Binding of magnesium ions and ethidium bromide: comparison of ribosomes and free ribosomal RNA. Nucl. Acids Res. 7: 465–480.

    Article  PubMed  CAS  Google Scholar 

  • Expert-Bezancon, A., Milet, M., Carbon, P. (1983). Precise localization of several covalent RNA-RNA cross-links in E. coli 16S RNA. Eur. J. Biochem. 136: 267–274.

    Article  PubMed  CAS  Google Scholar 

  • Glotz, C., Brimacombe, R. (1980). An experimentally derived model for the secondary structure of the 16 S ribosomal RNA from E. coli. Nucl. Acids Res. 8: 2377–2395.

    Article  PubMed  CAS  Google Scholar 

  • Glotz, C., Zwieb, C., Brimacombe, R., Edwards, K., Kossel, H. (1981). Secondary structure of the large subunit ribosomal RNA from E. coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes. Nucl. Acids Res. 9: 3287–3306.

    Article  PubMed  CAS  Google Scholar 

  • Herr, W., Chapman, N.M., Noller, H.F. (1979). Mechanism of ribosomal subunit association: discrimination of specific sites in 16S RNA essential for association activity. J. Mol. Biol. 130: 433–449.

    Article  PubMed  CAS  Google Scholar 

  • Klein, B.F., King, T.C., Schlessinger, D. (1983). Structure of partially denatured E. coli 23 S ribosomal RNA determined by electron microscopy. J. Mol. Biol. 168: 809–830.

    Article  PubMed  CAS  Google Scholar 

  • Korn, A.P., Spitnik-Elson, P., Elson, D. (1982). The topology of the 30S ribosomal subunit and a proposal for the surface distribution of its RNA by dark field electron microscopy. J. Biol. Chem. 257: 7155–7160.

    PubMed  CAS  Google Scholar 

  • Korn, A.P., Spitnik-Elson, P., Elson, D. (1985). Identification of the collarlike structure of the 30 S ribosomal subunit from E. coli by dark field electron microscopy. Eur. J. Cell Biol. 39: 56–61.

    PubMed  CAS  Google Scholar 

  • Luhrmann, R., Stoffler-Meilicke, M., Stoffler, G. (1981). Localization of the 3′ end of 16 S rRNA in E. coli 30 S ribosomal subunits by immuno electron microscopy. Mol. Gen. Genet. 182: 369–376.

    Article  PubMed  CAS  Google Scholar 

  • Mackie, G.A., Zimmermann, R.A. (1975). Characterization of fragments of 16S RNA protected against pancreatic ribonuclease digestion by ribosomal protein S4. J. Biol. Chem. 250: 4100–4112.

    PubMed  CAS  Google Scholar 

  • Maly, P., Brimacombe, R. (1983). Refined secondary structure models for the 16S and 23 S ribosomal RNA of E. coli. Nucl. Acids Res. 11: 7263–7286.

    Article  PubMed  CAS  Google Scholar 

  • Nelles, L., Fang, B.L., Volckaert, G., Vandenberghe, A., De Wachter, R. (1984). Nucleotide sequence of a crustacean 18 S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucl. Acids Res. 12: 8749–8768.

    Article  PubMed  CAS  Google Scholar 

  • Noller, H.F., Woese, C.R. (1981). Secondary structure of 16S ribosomal RNA. Science 212: 403–411.

    Article  PubMed  CAS  Google Scholar 

  • Olson, H.M., Glitz, D.G. (1979). Ribosomal structure: localization of 3′ end of RNA in small subunit by immunoelectronmicroscopy. Proc. Natl. Acad. Sci. USA 76: 3769–3773.

    Article  PubMed  CAS  Google Scholar 

  • Politz, S.M., Glitz, D.G. (1977). Ribosome structure: localization of N6, N6-dimeth-yladenosine by electron microscopy of a ribosome-antibody complex. Proc. Natl. Acad. Sci. USA 74: 1468–1472.

    Article  PubMed  CAS  Google Scholar 

  • Ross, A., Brimacombe, R. (1979). Experimental determination of interacting sequences in ribosomal RNA. Nature 281: 271–276.

    Article  PubMed  CAS  Google Scholar 

  • Santer, M., Santer, U. (1973). Action of ribonuclease T1 on 30S ribosomes of E. coli and its role in sequence studies on 16S ribonucleic acid. J. Bacteriol. 116: 1304–1313.

    PubMed  CAS  Google Scholar 

  • Serdyuk, I.N., Agalarov, S.C., Sedelnikova, S.E., Spirin, A.S., May, R.P. (1983). Shape and compactness of the isolated ribosomal 16S RNA and its complexes with ribosomal proteins. J. Mol. Biol. 169: 409–425.

    Article  PubMed  CAS  Google Scholar 

  • Shatsky, I.N., Mochalova, L.V., Kojouharova, M.S., Bogdanov, A.A., Vasiliev, V.D. (1979). Localization of the 3′ end of E. coli 16 S RNA by electron microscopy of antibody-labelled subunits. J. Mol. Biol. 133: 501–515.

    Article  PubMed  CAS  Google Scholar 

  • Spitnik-Elson, P., Elson, D. (1979). The fragmentation of ribosomes. Meth. Enzymol. 59: 461–481.

    Article  PubMed  CAS  Google Scholar 

  • Spitnik-Elson, P., Elson, D., Avital, S., Abramowitz, R. (1982a). A ribonucleoprotein fragment of the 30 S ribosome of E. coli: evidence for long range RNA-RNA interactions. Nucl. Acids Res. 10: 1995–2006.

    Article  PubMed  CAS  Google Scholar 

  • Spitnik-Elson, P., Elson, D., Avital, S., Abramowitz, R. (1982b). A ribonucleoprotein fragment of the 30 S ribosome of E. coli containing two contiguous domains of the 16S RNA. Nucl. Acids Res. 10: 4483–4492.

    Article  PubMed  CAS  Google Scholar 

  • Spitnik-Elson, P., Elson, D., Avital, S., Abramowitz, R. (1985). Long range RNA- RNA interactions in the 30 S ribosomal subunit of E. coli. Nucl. Acids Res. 13: 4719–4738.

    Article  PubMed  CAS  Google Scholar 

  • Stiegler, P., Carbon, P., Zuker, M., Ebel, J.P., Ehresmann, C. (1981). Structural organization of the 16 S ribosomal RNA from E. coli. Topography and secondary structure. Nucl. Acids Res. 9: 2153–2171.

    Article  PubMed  CAS  Google Scholar 

  • Thammana, P., Cantor, C.R., Wollenzien, P.L., Hearst, J.E. (1979). Crosslinking studies on the organization of the 16 S ribosomal RNA within the 30 S E. coli subunit. J. Mol. Biol. 135: 271–283.

    Article  PubMed  CAS  Google Scholar 

  • Thomas, G.J., Jr., Prescott, B., Hamilton, M.G. (1980). Raman spectra and conformational properties of ribosomes during various stages of disassembly. Biochemistry 19: 3604–3613.

    Article  PubMed  CAS  Google Scholar 

  • Thompson, J.F., Hearst, J.E. (1983). Structure of E. coli 16S RNA elucidated by psoralen crosslinking. Cell 32: 1355–1365.

    Article  PubMed  CAS  Google Scholar 

  • Ungewickell, E., Garrett, R.A., Ehresmann, C., Stiegler, P., Fellner, P. (1975). An investigation of the 16 S RNA binding sites of ribosomal proteins S4, S8, S15 and S 20 from E. coli. Eur. J. Biochem. 51: 165–180.

    Article  PubMed  CAS  Google Scholar 

  • Van Holde, K.E., Hill, W.E. (1974). General physical properties of ribosomes. In: Ribosomes, ed. Nomura, M., Tissieres, A., Lengyel, P. Cold Spring Harbor Laboratory, New York, pp. 53–91.

    Google Scholar 

  • Vigne, R., Jordan, B.R. (1971). Conformational analysis of RNA molecules by partial RNAse digestion and two dimensional acrylamide gel electrophoresis. Application to E. coli 5S RNA. Biochimie 53: 981–986.

    Article  PubMed  CAS  Google Scholar 

  • Woese, C.R., Gutell, R., Gupta, R., Noller, H.F. (1983). Detailed analysis of the higher-order structure of 16S-like ribosomal RNAs. Microbiol. Rev. 47: 621–669.

    PubMed  CAS  Google Scholar 

  • Wollenzien, P.L., Cantor, C.R. (1982). Gel electrophoretic technique for separating crosslinked RNAs. J. Mol. Biol. 159: 151–166.

    Article  PubMed  CAS  Google Scholar 

  • Wower, I., Brimacombe, R. (1983). The localization of multiple sites on 16 S RNA which are cross-linked to proteins S7 and S8 in E. coli 30 S ribosomal subunits by treatment with 2-iminothiolane. Nucl. Acids Res. 11: 1419–1437.

    Article  PubMed  CAS  Google Scholar 

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Spitnik-Elson, P., Elson, D. (1986). The Folding of RNA in the 30S Subunit of Escherichia coli Ribosomes. In: Hardesty, B., Kramer, G. (eds) Structure, Function, and Genetics of Ribosomes. Springer Series in Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4612-4884-2_13

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  • DOI: https://doi.org/10.1007/978-1-4612-4884-2_13

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4612-9346-0

  • Online ISBN: 978-1-4612-4884-2

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