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Correlation Between Crystal and Solution Structures in tRNA. Yeast tRNAPhe and tRNAAsp the Models for Free and Messenger RNA Bound tRNAs

  • Richard Giegé
  • Anne-Catherine Dock
  • Philippe Dumas
  • Jean-Pierre Ebel
  • Pascale Romby
  • Eric Westhof
  • Dino Moras
Part of the NATO ASI Series book series (NSSA, volume 110)

Abstract

The three-dimensional structures of two elongator transfer RNAs are known in great details: first that of yeast tRNA(Phe) (1–4) and more recently that of yeast tRNA(Asp) (5–8). As seen in Figure 1, both molecules are folded in an L-shaped conformation, which is also found for initiator tRNAs (9,10). Since the conserved or semi-conserved residues (11) are involved in the tertiary interactions which stabilize this folding (1–10), the L-shaped structure represents the general structural organization of all tRNA molecules. Such structural similarity is satisfactory to explain common functions of tRNAs, namely the interaction with ribosomes, and in the case of elongator tRNAs with elongator factors, but not sufficient to account for specific functions. In that case specific structural features must be involved. Differences in the anticodon sequences account for the decoding of the genetic message on mRNA. Recognition by aminoacyl-tRNA synthetases, which leads to the specific ami noacylation of tRNAs is more complex. Because many aminoacyl-tRNA synthetases recognize isoacceptor tRNAs and catalyze tRNA mischarging (12), these features cannot be simple linear nucleotide sequences, but more likely structural domains found at the three-dimensional level.

Keywords

Yeast tRNA tRNA Molecule Anticodon Loop Anticodon Stem Anticodon Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    G.J. Quigley, A. Wang, N.C. Seeman, F.L. Suddath, A. Rich, J.L. Sussmann and S.H. Kim, Hydrogen bonding in yeast phenylalanine transfer RNA, Proc. Natl. Acad. Sci. U.S.A. 72: 4866–4870 (1975).CrossRefGoogle Scholar
  2. 2.
    A. Jack, J.E. Ladner and A. Klug, Crystal lographic refinement of yeast phenylalanine transfer RNA at 2.5 Å resolution, J. Mol. Biol. 108: 619–649 (1976).CrossRefGoogle Scholar
  3. 3.
    C.D. Stout, H. Mizuno, S.T. Rao, P. Swaminathan, J. Rubin, P. Brennan and M. Sundaralingam, Atomic coordinates and molecular conformation of yeast phenylalanine tRNA. An independant investigation, Acta Crys. B54: 1529–1544 (1978).Google Scholar
  4. 4.
    J.L. Sussmann, S.R. Holbrook, R.W. Warrant, G.M. Church and S.H. Kim, Crystal structure of yeast phenylalanine transfer RNA: crystallographic refinement, J. Mol. Biol. 123: 607–630 (1978).CrossRefGoogle Scholar
  5. 5.
    D. Moras, M.B. Comarmond, J. Fischer, R. Weiss, J.C. Thierry, J.P. Ebel and R. Giegé, Crystal structure of yeast tRNAAsp, Nature (London) 286: 669–674 (1980).CrossRefGoogle Scholar
  6. 6.
    E. Westhof, P. Dumas and D. Moras, Loop stereochemistry and dynamics in transfer RNA, J. Biomol. Struct. Dyn. 1: 337–359 (1983).Google Scholar
  7. 7.
    E. Westhof, P. Dumas and D. Moras, Crystallographic refinement of yeast aspartic acid transfer RNA, J. Mol. Biol. 184: 119–145 (1985).CrossRefGoogle Scholar
  8. 8.
    P. Dumas, J.P. Ebel, R. Giegé, D. Moras, J.C. Thierry and E. Westhof, Crystal structure of yeast tRNA(Asp): Atomic coordinates, Biochimie (Paris) 67: 597–606 (1985).Google Scholar
  9. 9.
    R.W. Schevitz, A.D. Podjarny, N. Krishnamachar, T.T. Hughes, P. Sigler and J.-L. Sussmann, Crystal structure of an eukaryotic initiator tRNA, Nature (London) 278: 188–190 (1979).CrossRefGoogle Scholar
  10. 10.
    N. Woo, B. Roe and A. Rich, Three-dimensional structure of Escherichia coli initiator tRNA(Met), Nature (London) 286: 346–351 (1980).CrossRefGoogle Scholar
  11. 11.
    M. Sprinzl, J. Moll, F. Meissner and T. Hartmann, Compilation of tRNA sequences, Nucl. Acids Res. 13: r1–r49 (1985).CrossRefGoogle Scholar
  12. 12.
    R. Giegé, D. Kern, J.P. Ebel, H. Grosjean, S. De Henau and H. Chantrenne, Incorrect aminoacylation involving tRNAs or valyl-tRNA synthetase from Bacillus stearothermophilus, Eur. J. Biochem. 45: 351–362 (1974).CrossRefGoogle Scholar
  13. 13.
    H.G. Gassen, Ligand induced conformational changes in ribonucleic acids, Prog. Nucl. Acid Res. Mol. Biol. 24: 57–86 (1980) and ref. therein.CrossRefGoogle Scholar
  14. 14.
    R. Rigler and W. Wintermeyer, Dynamics of tRNA, Ann. Rev. Biophys. Bioeng. 12: 475–505 (1983).CrossRefGoogle Scholar
  15. 15.
    D.A. Peattie, Direct chemical method for sequencing RNA, Proc. Natl. Acad. Sci. U.S.A. 76: 1760–1764 (1979).CrossRefGoogle Scholar
  16. 16.
    A.M. Maxam and W. Gilbert, Sequencing end-labeled DNA with base-specific chemical cleavages, Methods in Enzymology 65: 499–459 (1980).CrossRefGoogle Scholar
  17. 17.
    V.V. Vlassov, R. Giegé and J.P. Ebel, Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea, Eur. J. Biochem. 119: 51–59 (1981).CrossRefGoogle Scholar
  18. 18.
    P. Romby, D. Moras, M. Bergdoll, P. Dumas, V.V. Vlassov, E. Westhof, J.P. Ebel and R. Giegé, Yeast tRNA(Asp) tertiary structure in solution and areas of interaction of the tRNA with aspartyl-tRNA synthetase. A comparative study of the yeast phenylalanine system by phosphate alkylation experiments with ethylnitrosourea, J. Mol. Biol. 184: 455–471 (1985).CrossRefGoogle Scholar
  19. 19.
    D.A. Peattie and W. Gilbert, Chemical probes for higher-order structure in RNA, Proc. Nath Acad. Sci. U.S.A. 77: 4679–4682 (1980).CrossRefGoogle Scholar
  20. 20.
    P. Romby, R. Giegé, C. Houssier and H. Grosjean, Anticodon-anticodon interactions in solution. Studies of the self-association of yeast or Escherichia coli tRNA(Asp) and of their interactions with Escherichia coli tRNA(Val), J. Mol. Biol. 184: 107–118 (1985).CrossRefGoogle Scholar
  21. 21.
    D. Moras, A.C. Dock, P. Dumas, E. Westhof, P. Romby and R. Giegé, The versatile transfer RNA molecule: Crystallography of yeast tRNA(Asp). in “Nucleic Acids: The Vectors of Life”, B. Pullman and J. Jortner, eds., Reidel Publishing Company, Dordrecht: 403–414 (1983).CrossRefGoogle Scholar
  22. 22.
    G.J. Quigley, N.C. Seeman, A.H.J. Wang, F.L. Suddath and A. Rich, Yeast phenylalanine transfer RNA: Atomic coordinates and torsion angles, Nucl. Acids Res. 2: 2329–2341 (1975).CrossRefGoogle Scholar
  23. 23.
    M. Chen, R. Giegé, R. Lord and A. Rich, Raman spectra and structure of yeast phenylalanine transfer RNA in the crystalline state and in solution, Biochemistry 14: 4385–4391 (1975).CrossRefGoogle Scholar
  24. 24.
    G.T. Robillard, C.E. Tarr, F. Vosman and J.C. Berendsen, Similarity of the crystal and solution structure of yeast tRNA(Phe), Nature (London) 262: 363–369 (1976).CrossRefGoogle Scholar
  25. 25.
    S.R. Holbrook and S.H. Kim, Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA, Biopolymers 22: 1145–1166 (1983).CrossRefGoogle Scholar
  26. 26.
    N. Figueroa, G. Keith, S.L. Leroy, P. Plateau, S. Roy and M. Guéron, NMR study of slowly exchanging imino protons in yeast tRNA(Asp), Proc. Natl. Acad. Sci. U.S.A. 80: 4330–4333 (1983).CrossRefGoogle Scholar
  27. 27.
    R. Giegé, P. Romby, C. Florentz, J.P. Ebel, P. Dumas, E. Westhof and D. Moras, Solution conformation of tRNAs: Correlation with crystal structures, in “Nucleic Acids: The Vectors of Life”, B. Pullman and J. Jortner, eds., Reidel Publishing Company, Dordrecht: 415–426 (1983).CrossRefGoogle Scholar
  28. 28.
    M. Garret, B. Labouesse, S. Litvak, P. Romby, J.P. Ebel and R. Giegé, Tertiary structure of animal tRNA(Trp) in solution and interaction of tRNA(Trp) with tryphophanyl-tRNA synthetase, Eur. J. Biochem. 138: 67–75 (1983).CrossRefGoogle Scholar
  29. 29.
    C. Florentz, J.P. Briand, P. Romby, L. Hirth, J.P. Ebel and R. Giegé, The tRNA-like structure of turnip yellow mosaic virus RNA: Structural organization of the last 159 nucleotides from the 3’-OH terminus, EMBO J., 1: 269–276 (1982).Google Scholar
  30. 30.
    H. Guilley, G. Jonard, B. Kukla and K.E. Richards, Sequence of 1000 nucleotides at the 3’end of tobacco mosaic virus RNA, Nucl. Acids Res. 6: 1287–1308 (1979).CrossRefGoogle Scholar
  31. 31.
    P. Carbon, C. Ehresmann, B. Ehresmann and J.P. Ebel, The sequence of Escherichia coli ribosomal 16S RNA determined by new rapid gel methods, Febs Lett. 94: 152–156 (1978).CrossRefGoogle Scholar
  32. 32.
    D. Moras, A.C. Dock, P. Dumas, E. Westhof, P. Romby, J.P. Ebel and R. Giegé, The structure of yeast tRNA(Asp), a model for tRNA interacting with messenger RNA, J. Biomol. Struct. Dyn. submitted.Google Scholar
  33. 33.
    V. Schwartz, H. M. Menzel and H.G. Gassen, Codon-dependent rearrangement of the three-dimensional structure of phenylalanine tRNA, exposing the TUCG sequence for binding to the 50S ribosomal subunit, Biochemistry 15: 2484–2490 (1976).CrossRefGoogle Scholar
  34. 34.
    M. Sprinzl, T. Wagner, S. Lorenz and V.A. Erdmann, Regions of tRNA important for binding to the ribosomal A and P sites, Biochemistry 15: 3031–3039 (1976).CrossRefGoogle Scholar
  35. 35.
    P. Davenloo, M. Sprinzl and F. Cramer, Proton nuclear magnetic resonance of minor nucleosides in yeast phenylalanine transfer ribonucleic acid. Conformational changes as a consequence of aminoacylation, removal of the Y base, and codon-anticodon interaction, Biochemistry 18: 3189–3199 (1979).CrossRefGoogle Scholar
  36. 36.
    R. Wagner and R.A. Garret, Chemical evidence for a codon-induced allosteric change in tRNA(Lys) involving the 7-methylguanosine residue 46, Eur. J. Biochem. 97: 615–621 (1979).CrossRefGoogle Scholar
  37. 37.
    N. Farber and C.R. Cantor, Comparison of the structures of free and ribosome-bound tRNA(Phe) by using slow tritium exchange, Proc. Natl. Acad. Sci. U.S.A. 77: 5135–5139 (1980).CrossRefGoogle Scholar
  38. 38.
    T. Jorgenson, G. Siboskan, F. Wikman and B.F.C. Clark, Studies of the tRNA structure in different ribosomal sites, in: “11th International tRNA Workshop, Banz, Germany”, abstract CII-2 (1555).Google Scholar
  39. 39.
    B. Pace, E.A. Matthews, K.D. Johnson, C.R. Cantor, and N.R. Pace, Conserved 5S rRNA complement to tRNA is not required for protein synthesis, Proc. Natl. Acad. Sci. U.S.A. 79: 36–40 (1982).CrossRefGoogle Scholar
  40. 40.
    B. Helk and M. Sprinzl, Interaction of the T-loop of tRNA with the conserved CpGpUmpApApCp sequence of 16S RNA, in “11th. International tRNA Workshop Banz, Germany”, abstract CII-6 (1985).Google Scholar

Copyright information

© Plenum Press, New York 1986

Authors and Affiliations

  • Richard Giegé
    • 1
  • Anne-Catherine Dock
    • 1
  • Philippe Dumas
    • 1
  • Jean-Pierre Ebel
    • 1
  • Pascale Romby
    • 1
  • Eric Westhof
    • 1
  • Dino Moras
    • 1
  1. 1.Institut de Biologie Moléculaire et CellulaireCNRSStrasbourg CedexFrance

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