Biopolym. Cell. 2000; 16(2):115-123.
Structure and Function of Biopolymers
Study of tertiary structure elements of tRNASer from Thermus thermophilus in solution
1Kovalenko O. P., 1Kriklivyi I. A., 1Tukalo M. A.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Reactivity of phosphates and bases in tRNASer T. thermophilus has been studied by chemical modification methods. Ethylnitrosourea has been used to modify phosphate groups, guanosines and cytidines have been modified by dimethylsulphate, adenosines – by diethylpyrocarbonate. The same tertiary interactions exist in the solution structure of tRNASer T. thermophilus as in the crystal one.

References

[1] Biou V, Yaremchuk A, Tukalo M, Cusack S. The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 1994;263(5152):1404-10.
[2] Gieg? R, Florentz C, Garcia A, Grosjean H, Perret V, Puglisi J, Th?obald-Dietrich A, Ebel JP. Exploring the aminoacylation function of transfer RNA by macromolecular engineering approaches. Involvement of conformational features in the charging process of yeast tRNA(Asp). Biochimie. 1990;72(6-7):453-61. Review.
[3] Holbrook SR, Sussman JL, Warrant RW, Kim SH. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J Mol Biol. 1978;123(4):631-60.
[4] Westhof E, Dumas P, Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J Mol Biol. 1985;184(1):119-45.
[5] Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thierry JC, Moras D. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science. 1991;252(5013):1682-9.
[6] Rould MA, Perona JJ, S?ll D, Steitz TA. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989;246(4934):1135-42.
[7] Nissen P, Thirup S, Kjeldgaard M, Nyborg J. The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure. 1999;7(2):143-56.
[8] Brennan T, Sundaralingam M. Structlre of transfer RNA molecules containing the long variable loop. Nucleic Acids Res. 1976;3(11):3235-50.
[9] Dock-Bregeon AC, Westhof E, Gieg? R, Moras D. Solution structure of a tRNA with a large variable region: yeast tRNASer. J Mol Biol. 1989;206(4):707-22.
[10] Asahara H, Himeno H, Tamura K, Nameki N, Hasegawa T, Shimizu M. Escherichia coli seryl-tRNA synthetase recognizes tRNA(Ser) by its characteristic tertiary structure. J Mol Biol. 1994;236(3):738-48.
[11] Petrushenko ZM, Tukalo MA, Gudzera OI, Rozhko OT, Matsuka GKh. Determination of interacting segments of tRNA(Leu) from cow mammary glands with homologous aminoacyl-tRNA-synthetase by a chemical modification method. Bioorg Khim. 1990;16(12):1647-52.
[12] Dietrich A, Romby P, Mar?chal-Drouard L, Guillemaut P, Gieg? R. Solution conformation of several free tRNALeu species from bean, yeast and Escherichia coli and interaction of these tRNAs with bean cytoplasmic Leucyl-tRNA synthetase. A phosphate alkylation study with ethylnitrosourea. Nucleic Acids Res. 1990;18(9):2589-97.
[13] McClain WH. Rules that govern tRNA identity in protein synthesis. J Mol Biol. 1993;234(2):257-80.
[14] Normanly J, Abelson J. tRNA identity. Annu Rev Biochem. 1989;58:1029-49.
[15] Tamura K, Asahara H, Himeno H, Hasegawa T, Shimizu M. Identity elements of Escherichia coli tRNA(Ala). J Mol Recognit. 1991;4(4):129-32.
[16] Asahara H, Himeno H, Tamura K, Hasegawa T, Watanabe K, Shimizu M. Recognition nucleotides of Escherichia coli tRNA(Leu) and its elements facilitating discrimination from tRNASer and tRNA(Tyr). J Mol Biol. 1993;231(2):219-29.
[17] Asahara H, Nameki N, Hasegawa T. In vitro selection of RNAs aminoacylated by Escherichia coli leucyl-tRNA synthetase. J Mol Biol. 1998;283(3):605-18.
[18] Petrushenko ZM, Tukalo MA, Matsuka GKh. A study of the conformation of tRNA(IAGLeu) from the cow mammary gland using chemical modification methods. Bioorg Khim. 1988;14(1):31-6.
[19] Watanabe Y, Tsurui H, Ueda T, Furushima R, Takamiya S, Kita K, Nishikawa K, Watanabe K. Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem. J Biol Chem. 1994;269(36):22902-6.
[20] Watanabe Y, Kawai G, Yokogawa T, Hayashi N, Kumazawa Y, Ueda T, Nishikawa K, Hirao I, Miura K, Watanabe K. Higher-order structure of bovine mitochondrial tRNA(SerUGA): chemical modification and computer modeling. Nucleic Acids Res. 1994;22(24):5378-84.
[21] Cusack S, Yaremchuk A, Tukalo M. The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J. 1996;15(11):2834-42.
[22] Romby P, Gieg? R, Houssier C, Grosjean H. Anticodon-anticodon interactions in solution. Studies of the self-association of yeast or Escherichia coli tRNAAsp and of their interactions with Escherichia coli tRNAVal. J Mol Biol. 1985;184(1):107-118.
[23] Nureki O, Niimi T, Muto Y, Kanno H, Kohno T, Muramat-su T, Kawai G, Miyazawa T, Giege R, Florentz C, Yokoyama S. Conformational change of tRNA upon interaction of the identity-determinant set with aminoacyl-tRNA synВ­thetase. The translational apparatus. New York; London: Plenum press, 1993: 59-78.
[24] Petrushenko ZM, Kovalenko OP, Malchenko NN, Krikliviy IA, Yaremchuk AD, Tukalo MA. The primary structure of tRNASer from Thermus thermophilus. Biopolym Cell. 1997; 13(3):202-8.
[25] Silberklang M, Gillum AM, RajBhandary UL. The use of nuclease P1 in sequence analysis of end group labeled RNA. Nucleic Acids Res. 1977;4(12):4091-108.
[26] Vlassov VV, Gieg? R, Ebel JP. Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur J Biochem. 1981;119(1):51-9.
[27] Vlassov VV, Giege R, Ebel JP. The tertiary structure of yeast tRNAPhe in solution studied by phosphodiester bond modification with ethylnitrosourea. FEBS Lett. 1980;120(1):12-6.
[28] Romby P, Moras D, Dumas P, Ebel JP, Gieg? R. Comparison of the tertiary structure of yeast tRNA(Asp) and tRNA(Phe) in solution. Chemical modification study of the bases. J Mol Biol. 1987;195(1):193-204.
[29] Peattie DA. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A. 1979;76(4):1760-4.
[30] Metzger AU, Heckl M, Willbold D, Breitschopf K, RajBhandary UL, R?sch P, Gross HJ. Structural studies on tRNA acceptor stem microhelices: exchange of the discriminator base A73 for G in human tRNALeu switches the acceptor specificity from leucine to serine possibly by decreasing the stability of the terminal G1-C72 base pair. Nucleic Acids Res. 1997;25(22):4551-6.
[31] Quigley GJ, Rich A. Structural domains of transfer RNA molecules. Science. 1976;194(4267):796-806.
[32] Romby P, Carbon P, Westhof E, Ehresmann C, Ebel JP, Ehresmann B, Gieg? R. Importance of conserved residues for the conformation of the T-loop in tRNAs. J Biomol Struct Dyn. 1987;5(3):669-87.
[33] Ehresmann C, Baudin F, Mougel M, Romby P, Ebel JP, Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987;15(22):9109-28.