Conversion of Aminoacylation Specificity from TRNA(Tyr) to TRNA(Ser) in Vitro

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1990 Dec 11

PMID 2263446

Citations 47

Authors

H Himeno

T Hasegawa

T Ueda

K Watanabe

M Shimizu

Affiliations

Soon will be listed here.

Abstract

The discrimination mechanism between tRNA(Ser) and tRNA(Tyr) was studied using various in vitro transcripts of E. coli tRNATyr variants. The insertion of only two nucleotides into the variable stem of tRNA(Tyr) generates serine charging activity. The acceptor activities of some of the tRNA(Tyr) mutants with insertions in the long variable arm were enhanced by changes in nucleotides at positions 9 and/or 20B, which are possible elements for dictating the orientation of the long variable arm. These findings suggest that the long variable arm is involved in recognition by seryl-tRNA synthetase in spite of sequence and length variations shown within tRNA(Ser) isoacceptors, and eventually serves as a determinant for selection from other tRNA species. Changing the anticodon from GUA to the serine anticodon GGA resulted in a marked decrease in tyrosine charging activity, but this mutant did not show any serine charging activity. The discriminator base, the fourth base from the 3' end of tRNA, was also important for aminoacylation with tyrosine. Complete specificity change in vitro was facilitated by insertion of three nucleotides into the variable arm plus two nucleotide changes at positions 9 and 73.

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References

Himeno H, Hasegawa T, Ueda T, Watanabe K, Miura K, Shimizu M . Role of the extra G-C pair at the end of the acceptor stem of tRNA(His) in aminoacylation. Nucleic Acids Res. 1989; 17(19):7855-63. PMC: 334892. DOI: 10.1093/nar/17.19.7855. View

Leinfelder W, Zehelein E, Mandrand-Berthelot M, Bock A . Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature. 1988; 331(6158):723-5. DOI: 10.1038/331723a0. View

Rich A, Schimmel P . Structural organization of complexes of transfer RNAs with aminoacyl transfer RNA synthetases. Nucleic Acids Res. 1977; 4(5):1649-65. PMC: 343779. DOI: 10.1093/nar/4.5.1649. View

Grodberg J, Dunn J . ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. J Bacteriol. 1988; 170(3):1245-53. PMC: 210899. DOI: 10.1128/jb.170.3.1245-1253.1988. View

Normanly J, Abelson J . tRNA identity. Annu Rev Biochem. 1989; 58:1029-49. DOI: 10.1146/annurev.bi.58.070189.005121. View

Sampson J, Uhlenbeck O . Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc Natl Acad Sci U S A. 1988; 85(4):1033-7. PMC: 279695. DOI: 10.1073/pnas.85.4.1033. View

Seong B, Lee C, RajBhandary U . Suppression of amber codons in vivo as evidence that mutants derived from Escherichia coli initiator tRNA can act at the step of elongation in protein synthesis. J Biol Chem. 1989; 264(11):6504-8. View

Uemura H, Imai M, Ohtsuka E, Ikehara M, Soll D . E. coli initiator tRNA analogs with different nucleotides in the discriminator base position. Nucleic Acids Res. 1982; 10(20):6531-9. PMC: 326942. DOI: 10.1093/nar/10.20.6531. View

Schimmel P . Parameters for the molecular recognition of transfer RNAs. Biochemistry. 1989; 28(7):2747-59. DOI: 10.1021/bi00433a001. View

10.

Schulman L, Abelson J . Recent excitement in understanding transfer RNA identity. Science. 1988; 240(4859):1591-2. DOI: 10.1126/science.2454505. View

11.

Brennan T, Sundaralingam M . Structlre of transfer RNA molecules containing the long variable loop. Nucleic Acids Res. 1976; 3(11):3235-50. PMC: 343166. DOI: 10.1093/nar/3.11.3235. View

12.

Moras D, Comarmond M, Fischer J, Weiss R, Thierry J, Ebel J . Crystal structure of yeast tRNAAsp. Nature. 1980; 288(5792):669-74. DOI: 10.1038/288669a0. View

13.

Messing J . New M13 vectors for cloning. Methods Enzymol. 1983; 101:20-78. DOI: 10.1016/0076-6879(83)01005-8. View

14.

Grosjean H, Nicoghosian K, Haumont E, Soll D, Cedergren R . Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Res. 1985; 13(15):5697-706. PMC: 321899. DOI: 10.1093/nar/13.15.5697. View

15.

Robertus J, Ladner J, Finch J, Rhodes D, Brown R, Clark B . Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974; 250(467):546-51. DOI: 10.1038/250546a0. View

16.

Rould M, Perona J, Soll D, Steitz T . Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. Science. 1989; 246(4934):1135-42. DOI: 10.1126/science.2479982. View

17.

Ghysen A, Celis J . Mischarging single and double mutants of Escherichia coli sup3 tyrosine transfer RNA. J Mol Biol. 1974; 83(3):333-51. DOI: 10.1016/0022-2836(74)90283-6. View

18.

Schulman L, Pelka H . The anticodon contains a major element of the identity of arginine transfer RNAs. Science. 1989; 246(4937):1595-7. DOI: 10.1126/science.2688091. View

19.

Normanly J, Ogden R, Horvath S, Abelson J . Changing the identity of a transfer RNA. Nature. 1986; 321(6067):213-9. DOI: 10.1038/321213a0. View

20.

BARE L, Uhlenbeck O . Aminoacylation of anticodon loop substituted yeast tyrosine transfer RNA. Biochemistry. 1985; 24(9):2354-60. DOI: 10.1021/bi00330a034. View