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Ribosome Structure, Function, and Evolution: Mapping Ribosomal RNA, Proteins, and Functional Sites in Three Dimensions

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Structure, Function, and Genetics of Ribosomes

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

Abstract

Major advances have been made in recent years in our understanding of the structure, function, and evolution of ribosomes. One notes that the overall three-dimensional structures of ribosomes and ribosomal subunits are known; the primary and secondary structures of the rRNA are known for many diverse organisms; the approximate locations of many ribosomal proteins and of some sequences of the ribosomal RNAs are known; many aspects of ribosome function have been related to ribosome structure; and, finally, comparative studies of ribosomes have revealed some of the early steps in the evolution of ribosomes and of the cells that contain them.

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References

  • Bernabeu, C., Lake, J.A. (1982a) Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: immune mapping of the nascent chain. Proc. Natl. Acad. Sci. USA 79: 3111–3115.

    Article  PubMed  CAS  Google Scholar 

  • Bernabeu, C., Lake, J.A. (1982b). Packing of 70S ribosomes in dimers found at low ionic strength. J. Mol. Biol 160: 369373.

    Google Scholar 

  • Bernabeu, C., Tobin, E., Fowler, A., Zabin, I., Lake, J.A. (1983) Nascent polypeptide chains exit the ribosome in the same relative position in both eucaryotes and procaryotes. J. Cell Biol 96: 1471–1474.

    Article  PubMed  CAS  Google Scholar 

  • Boublik, M., Hellmann, W. (1978). Comparison of Artemia salina and Escherichia coli ribosome structure by electron microscopy. Proc. Natl. Acad. Sci. USA 75: 2829–2833.

    Article  CAS  Google Scholar 

  • Boublik, M., Hellmann, W., Roth, E.H. (1976). Localization of ribosomal proteins L7L12 in the 50S subunit of Escherichia coli ribosomes by electron microscopy. J. Mol. Biol 107: 479–490.

    Article  PubMed  CAS  Google Scholar 

  • Clark, W., Lake, J.A. (1983). Unusual rRNA-linked complex of 50S ribosomal subunits isolated from an Escherichia coli RNase III mutant. J. Bact 157: 971–974.

    Google Scholar 

  • Clark, M.W., Leonard, K., Lake, J.A. (1982). Ribosomal crystalline arrays of large subunits from Escherichia coli. Science, 216: 999–1000.

    Article  PubMed  CAS  Google Scholar 

  • Dabbs, E.R., Ehrlich, R., Hasenbank, R., Schroeter, B.-H., Stöffler-Meilicke, M., Stöffler, G. (1981). Mutants of Escherichia coli lacking ribosomal protein LI. J. Mol. Biol 149: 553–578.

    Article  PubMed  CAS  Google Scholar 

  • Emanuilov, I., Sabatini, D.D. (1981). Surface features and handedness of a model for the eukaryotic small ribosomal subunit. Ultrastructure Research 76: 263–276.

    Article  Google Scholar 

  • Emanuilov, I., Sabatini, D.D., Lake, J.A., Freienstein, C. (1978). Localization of eukaryotic initiation factor 3 on native small ribosomal subunits. Proc. Natl. Acad. Sci. USA 75: 1389–1393.

    Article  PubMed  CAS  Google Scholar 

  • Evstafieva, A.G., Shatsky, I.N., Bogdanov, A.A., Semenkov, Y.P., Vasiliev, V.D. (1983). Localization of 5′ and 3′ ends of the ribosome bound segment of template polynucleotides by immune electron microscopy. EMBO Journal 2: 799–804.

    PubMed  CAS  Google Scholar 

  • Frank, J., Verschoor, A., Boublik, M. (1981). Computer averaging of electron micrographs of 40S ribosomal subunits. Science 214: 1353–1355.

    Article  PubMed  CAS  Google Scholar 

  • Girshovich, A.S., Kurtschaliov, T.V., Ovchinnikov, Yu. A., Vasiliev, V.D. (1981). Localization of the elongation factor G on Escherichia coli ribosome. FEBS Letters 130: 54–59.

    Article  PubMed  CAS  Google Scholar 

  • Henderson, E.H., Oakes, M., Clark, M., Lake, J.A., Matheson, A., Zillig, W. (1984). A new ribosome structure. Science 225: 510–512.

    Article  PubMed  CAS  Google Scholar 

  • Johnson, A.E., Fairclough, R.H., Cantor, C.R. (1977). Some approaches for the study of ribosome-tRNA interactions. In: Nucleic Acid-Protein Recognition, ed. Vogel, H.J., Academic Press, New York, pp. 469–490.

    Google Scholar 

  • Kahan, L., Winkelmann, D.A., Lake, J.A. (1981). Ribosomal proteins S3, S6, S8 and S10 of Escherichia coli localized on the external surface of the small subunit by immune electron microscopy. J. Mol. Biol 145: 193–214.

    Article  PubMed  CAS  Google Scholar 

  • Kastner, B., Stöffler-Meilicke, M., Stöffler, G. (1981). Arrangement of the subunits in the ribosome of Escherichia coli: demonstration by immunoelectron microscopy. Proc. Natl. Acad. Sci. USA 78: 6652–6656.

    Article  PubMed  CAS  Google Scholar 

  • Keren-Zur, M., Boublik, M., Ofengand, J. (1979). Localization of the decoding region on the 30S Escherichia coli ribosomal subunit by affinity immunoelectron microscopy. Proc. Nat. Acad. Sci. USA 76: 1054–1058.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Pendergast, M., Kahan, L., Nomura, M. (1974b). Localization of Escherichia coli ribosomal proteins S4 and S14 by electron microscopy of anti-body-labeled subunits. Proc. Natl. Acad. Sci 71: 4688–4692.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A. (1976). Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes. J. Mol. Biol 105: 131–159.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A. (1977). Aminoacyl-tRNA binding at the recognition site is the first step of the elongation cycle of protein synthesis. Proc. Natl. Acad. Sci. USA 74: 1903–1907.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A. (1979). Ribosome structure and tRNA binding sites. In: Transfer RNA: structure, properties and recognition. Cold Spring Harbor Press, New York, pp. 393–411.

    Google Scholar 

  • Lake, J.A. (1979a). Ribosome structure and functional sites. In: Ribosomes, structure, function and genetics, eds. Chambliss et al., University Park Press, Baltimore, pp. 201–236.

    Google Scholar 

  • Lake, J.A. (1981a). The Ribosome. Scientific American 245: 84–97.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A. (1981b). Protein synthesis in prokaryotes and eukaryotes: the structural bases. In: Electron Microscopy of Proteins, ed. Harris, R., Academic Press, London, pp. 167–195.

    Google Scholar 

  • Lake, J.A. (1982). Ribosomal subunit orientations determined in the monomeric ribosome by single and by double-labeling immune electron microscopy. J. Mol. Biol 161: 89–106.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A. (1985). Evolving ribosome structure: domains in archaebacteria, eubacteria, eocytes and eukaryotes. Ann. Rev. Biochem 54: 507–530.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Clark, M.W., Henderson, E., Fay, S., Oakes, M., Scheinman, A., Thornber, P., Mah, R.A. (1985). Eubacteria, halobacteria, and the origin of photosynthesis: the photocytes. Proc. Natl. Acad. Sci. USA 82: 3716–3720.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Henderson, E., Oakes, M., Clark, M.W. (1984). Eocytes: a new ribo-some structure indicates a kingdom with a close relationship to eukaryotes. Proc. Natl. Acad. Sci. USA 81: 3786–3790.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Henderson, E., Clark, M.C., Matheson, A. (1982). Mapping evolution with ribosome structure: intralineage constancy and interlineage variation. Proc. Natl. Acad. Sci. USA 79: 5948–5952.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Kahan, L. (1975). Ribosomal proteins S5, Sll, S13 and S19 localized by electron microscopy of antibody-labeled subunits. J. Mol. Biol 99: 631–644.

    Article  PubMed  CAS  Google Scholar 

  • Lake, J.A., Nonomura, Y., Sabatini, D.D. (1974a). Ribosome structure as studied by electron microscopy. In: Ribosomes, eds. Nomura, M. et al., Cold Spring Harbor Press, New York, pp. 543–557.

    Google Scholar 

  • Lake, J.A., Pendergast, M., Kahan, L., Nomura, M. (1974c). Ribosome structure: three dimensional distribution of proteins S14 and S4. J. Supramolec. Struct 2: 189–195.

    Article  CAS  Google Scholar 

  • Lake, J.A., Strycharz, W.A. (1981). Ribosomal proteins LI, L17, L27 from Escherichia coli localized at single sites on the large subunit by immune electron microscopy. J. Mol. Biol 153: 979–992.

    Article  PubMed  CAS  Google Scholar 

  • Langer, J.A., Jurnak, F., Lake, J.A. (1984). Elongation factor Tuternary complex binds to small ribosomal subunits in a functionally active state. Biochemistry 23: 6171–6178.

    Article  PubMed  CAS  Google Scholar 

  • Lotti, M., Dabbs, E.R., Hasenbank, R., Stoffler-Meilicke, M., Stoffler, G. (1983). Characterization of a mutant from Escherichia coli lacking protein LI 5 and localization of protein LI5 by immunoelectron microscopy. Mol. Gen. Genet 192: 295–300.

    Article  PubMed  CAS  Google Scholar 

  • Lutsch, G., Noll, F., Theise, H., Enzmann, G., Bielka, H. (1979). Localization of proteins SI, S2, SI6 and S23 on the surface of small subunits of rat liver ribosomes by immune electron microscopy. Mol. Gen. Genet 176: 281–291.

    PubMed  CAS  Google Scholar 

  • Marquis, D., Fahnestock, S., Henderson, E., Woo, D., Schwinge, S., Clark, M., Lake, J.A. (1981). The L1/L12 stalk, a conserved feature of the prokaryotic ribosome, is attached to the large subunit through its N-terminus. J. Mol. Biol 150: 121–132.

    Article  PubMed  CAS  Google Scholar 

  • Moore, P.B., Engelman, D.M., Langer, J.A., Ramakrishnan, V.R., Schindler, D.G., Schoenborn, B.P., Siller, I.-Y., Yabuki, S. (1982). Neutron scattering and the 30S ribosomal subunits of Escherichia coli. In: Brookhaven National Laboratories Neutron Symposium.

    Book  Google Scholar 

  • Noller, H.F., Lake, J.A. (1984). Ribosome structure and function: localization of rRNA. In: Membrane Structure and Function, vol. 6, ed. Bittar, E. John Wiley and Sons, New York, pp. 217–297.

    Google Scholar 

  • Nomura, M., Mizushima, S., Ozaki, M., Traub, P., Lowry, C.V. (1969). Structure and function of ribosomes and their molecular components. Cold Spring Harbor Symp. Quant. Biol 34: 49–61.

    PubMed  CAS  Google Scholar 

  • Oakes, M., Clark, M., Henderson, E., Lake, J.A. (1986). DNA hybridization electron microscopy: ribosomal RNA nucleotides 1392–1407 are exposed in the cleft of the small subunit. Proc. Natl. Acad. Sci. USA 83: 275–279.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Olson, H.M., Grant, P.G., Cooperman, B.S., Glitz, D.H. (1982) Immunoelectron microscopic localization of puromycin binding on the large subunit of the Escherichia coli ribosome. J. Biol. Chem 257: 2649–2656.

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Shatsky, I.N., Evstafieva, A.G., Bystrova, A.A., Bogdanov, A.A., Vasiliev, V.D. (1980). Topography of RNA in the ribosome: location of the 3′-end of 5S RNA on the central protuberance of the 50S subunit. FEBS Lett. 121: 97–100.

    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 Escherichia coli 16S RNA by electron microscopy of antibody-labelled subunits. J. Mol. Biol 133: 501–515.

    Article  PubMed  CAS  Google Scholar 

  • Stöffler-Meilicke, M., Epe, B., Steinhauser, K.G., Wooley, P., Stöffler, G. (1983). Immunoelectron microscopy of ribosomes carrying a fluorescence label in a defined position. Location of proteins SI7 and L6 in the ribosome of Escherichia coli. FEBS Lett. 163: 94–98.

    Article  PubMed  Google Scholar 

  • Stöffler-Meilicke, Stöffler, G., Odom, O.W., Zinn, A., Kramer, G., Hardesty, B. (1982). Localization of 3′-ends of 5S and 23S rRNA’s in reconstituted subunits of Escherichia coli ribosomes. Proc. Natl. Acad. Sei. USA 78: 5538–5542.

    Google Scholar 

  • Stöffler-Meilicke, M., Noah, M., Stöffler, G. (1983) Location of eight ribosomal proteins on the surface of the 50S subunit from Escherichia coli. Proc. Natl. Acad. Sci. USA 80: 6780–6787.

    Article  PubMed  Google Scholar 

  • Strycharz, W.A., Nomura, M., Lake, J.A. (1978). Ribosomal proteins L7/L12 localized at a single region of the large subunit by immune electron microscopy. J. Mol. Biol 126: 123–140.

    Article  PubMed  CAS  Google Scholar 

  • Tischendorf, G.W., Zeichardt, M., Stöffler, G. (1974). Determination of the location of proteins L14, L17, L18, L19, L22, and L23 on the surface of the 50S ribosomal subunit of Escherichia coli by immune electron microscopy. Mol. Gen. Genet 134: 187–208.

    Article  PubMed  CAS  Google Scholar 

  • Tischendorf, G.W., Zeichardt, H., Stöffler, G. (1975). Architecture of the Escherichia coli ribosome as determined by immune electron microscopy. Proc. Natl. Acad. Sci. USA 72: 4820–4824.

    Article  PubMed  CAS  Google Scholar 

  • Trempe, M.R., Ohgi, K., Glitz, D.G. (1982). Localization of 7-Methylguanosine in the small subunits of Escherichia coli and chloroplast ribosomes by immunoelectron microscopy. J. Biol. Chem 257: 9822–9829.

    PubMed  CAS  Google Scholar 

  • Unwin, P.N.T. (1979). Attachment of ribosome crystals to intracellular membranes. J. Mol. Biol 132: 69–84.

    Article  PubMed  CAS  Google Scholar 

  • Vasiliev, V.D. (1974) Morphology of the ribosomal 30S subparticle according to electron microscopic data. Acta Biol. Med. Germ 33: 779–793.

    PubMed  CAS  Google Scholar 

  • Vasiliev, V.D., Seiivanova, O.M., Ryazantsev, S.N. (1983b). Structure of the Escherichia coli 50S ribosomal subunit. J. Mol. Biol 171: 561–569.

    Article  PubMed  CAS  Google Scholar 

  • Vasiliev, V.D., Seiivanova, O.M., Baranov, V.l., Spirin, A.S. (1983a). Structural study of translating 70S ribosomes from Escherichia coli I. Electron microscopy. FEBS Lett. 1557: 167–172.

    Article  Google Scholar 

  • Wabl, M.R. (1974). Microscopic localization of two proteins on the surface of the 50S ribosomal subunit of Escherichia coli using specific antibody markers. J. Mol. Biol 84: 241–247.

    Article  PubMed  CAS  Google Scholar 

  • Winkelman, D., Kahan, L., Lake, J.A. (1982). Ribosomal protein S4 is an internal protein: localization by immune electron microscopy on protein deficient subribosomal particles. Proc. Natl. Acad. Sci. USA 79: 5189–5198.

    Article  Google Scholar 

  • Woese, C.R. (1981). Archaebacteria. Sci. Am 244: 98–122.

    Article  CAS  Google Scholar 

  • Woese, C.R., Fox, G.E. (1977). Phylogenic structure of the prokaryotic domain: the primary kingdom. Proc. Natl. Acad. Sci. USA 74: 5088–5090.

    Article  PubMed  CAS  Google Scholar 

  • Yuki, A., Brimacombe, R. (1975). Nucleotide sequences of Escherichia coli 16-S RNA associated with ribosomal proteins S7, S9, S10, S14 and S19. Eur. J. Biochem 56: 23–27.

    Article  PubMed  CAS  Google Scholar 

  • Zillig, W., Schnabel, R., Stetter, K.O. (1985). Archaebacteria and the origin of the eukaryotic cytoplasm. Curr. Topics Microbiol 114: 1–18.

    CAS  Google Scholar 

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Oakes, M., Henderson, E., Scheinman, A., Clark, M., Lake, J.A. (1986). Ribosome Structure, Function, and Evolution: Mapping Ribosomal RNA, Proteins, and Functional Sites in Three Dimensions. 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_3

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  • DOI: https://doi.org/10.1007/978-1-4612-4884-2_3

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