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. 1982 Aug;151(2):1013–1021. doi: 10.1128/jb.151.2.1013-1021.1982

Aminoacyl-tRNAs from Physarum polycephalum: patterns of codon recognition.

D Hatfield, M Rice, C A Hession, P W Melera
PMCID: PMC220355  PMID: 7047488

Abstract

Isoacceptors of Physarum polycephalum Ala-, Arg-, Glu-, Gln-, Gly-, Ile-, Leu-, Lys-, Ser-, Thr-, and Val-tRNAs were resolved by reverse-phase chromatography and isolated, and their codon recognition properties were determined in a ribosomal binding assay. Codon assignments were made to most isoacceptors, and they are summarized along with those determined in other studies from Escherichia coli, yeasts, wheat germ, hymenoptera, Xenopus, and mammals. The patterns of codon recognition by isoacceptors from P. polycephalum are more similar to those of animals than to those of plants or lower fungi.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Berman H. M., Marcu D., Narayanan P. Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine. Nucleic Acids Res. 1978 Mar;5(3):893–903. doi: 10.1093/nar/5.3.893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bossi L., Ruth J. R. The influence of codon context on genetic code translation. Nature. 1980 Jul 10;286(5769):123–127. doi: 10.1038/286123a0. [DOI] [PubMed] [Google Scholar]
  3. Caskey C. T., Beaudet A., Nirenberg M. RNA codons and protein synthesis. 15. Dissimilar responses of mammalian and bacterial transfer RNA fractions to messenger RNA codons. J Mol Biol. 1968 Oct 14;37(1):99–118. doi: 10.1016/0022-2836(68)90076-4. [DOI] [PubMed] [Google Scholar]
  4. Chavancy G., Chevallier A., Fournier A., Garel J. P. Adaptation of iso-tRNA concentration to mRNA codon frequency in the eukaryote cell. Biochimie. 1979;61(1):71–78. doi: 10.1016/s0300-9084(79)80314-4. [DOI] [PubMed] [Google Scholar]
  5. Crick F. H. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. doi: 10.1016/s0022-2836(66)80022-0. [DOI] [PubMed] [Google Scholar]
  6. Di Natale P., Eilat D. Patterns of E. coli leucine tRNA isoacceptors following bacteriophage MS2 infection. Nucleic Acids Res. 1976 Apr;3(4):917–930. doi: 10.1093/nar/3.4.917. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gauss D. H., Sprinzl M. Compilation of tRNA sequences. Nucleic Acids Res. 1981 Jan 10;9(1):r1–23. [PMC free article] [PubMed] [Google Scholar]
  8. Goldman E., Hatfield G. W. Use of purified isoacceptor tRNAs for the study of codon-anticodon recognition in vitro with sequenced natural messenger RNA. Methods Enzymol. 1979;59:292–309. doi: 10.1016/0076-6879(79)59092-2. [DOI] [PubMed] [Google Scholar]
  9. Goldman E., Holmes W. M., Hatfield G. W. Specificity of codon recognition by Escherichia coli tRNALeu isoaccepting species determined by protein synthesis in vitro directed by phage RNA. J Mol Biol. 1979 Apr 25;129(4):567–585. doi: 10.1016/0022-2836(79)90469-8. [DOI] [PubMed] [Google Scholar]
  10. Hall L., Braun R. The organisation of genes for transfer RNA and ribosomal RNA in amoebae and plasmodia of Physarum polycephalum. Eur J Biochem. 1977 Jun 1;76(1):165–174. doi: 10.1111/j.1432-1033.1977.tb11582.x. [DOI] [PubMed] [Google Scholar]
  11. Hatfield D., Matthews C. R., Rice M. Aminoacyl-transfer RNA populations in mammalian cells chromatographic profiles and patterns of codon recognition. Biochim Biophys Acta. 1979 Oct 25;564(3):414–423. doi: 10.1016/0005-2787(79)90032-7. [DOI] [PubMed] [Google Scholar]
  12. Hatfield D., Nirenberg M. Binding of radioactive oligonucleotides to ribosomes. Biochemistry. 1971 Nov;10(23):4318–4323. doi: 10.1021/bi00799a025. [DOI] [PubMed] [Google Scholar]
  13. Hatfield D. Recognition of nonsense codons in mammalian cells. Proc Natl Acad Sci U S A. 1972 Oct;69(10):3014–3018. doi: 10.1073/pnas.69.10.3014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hatfield D., Rice M., Hoffman E. Patterns of codon recognition by isoacceptor amino acyl-tRNAs from Hymenoptera. Biochem Biophys Res Commun. 1978 Nov 14;85(1):436–444. doi: 10.1016/s0006-291x(78)80061-8. [DOI] [PubMed] [Google Scholar]
  15. Hatfield D., Rice M. Patterns of codon recognition by isoacceptor aminoacyl-tRNAs from wheat germ. Nucleic Acids Res. 1978 Oct;5(10):3491–3502. doi: 10.1093/nar/5.10.3491. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hereford L. M., Rosbash M. Number and distribution of polyadenylated RNA sequences in yeast. Cell. 1977 Mar;10(3):453–462. doi: 10.1016/0092-8674(77)90032-0. [DOI] [PubMed] [Google Scholar]
  17. Hudspeth M. E., Timberlake W. E., Goldberg R. B. DNA sequence organization in the water mold Achlya. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4332–4336. doi: 10.1073/pnas.74.10.4332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. doi: 10.1016/0022-2836(81)90363-6. [DOI] [PubMed] [Google Scholar]
  19. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 1981 Sep 25;151(3):389–409. doi: 10.1016/0022-2836(81)90003-6. [DOI] [PubMed] [Google Scholar]
  20. Jank P., Shindo-Okada N., Nishimura S., Gross H. J. Rabbit liver tRNA1Val:I. Primary structure and unusual codon recognition. Nucleic Acids Res. 1977 Jun;4(6):1999–2008. doi: 10.1093/nar/4.6.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kelmers A. D., Heatherly D. E. Columns for rapid chromatographic separation of small amounts of tracer-labeled transfer ribonucleic acids. Anal Biochem. 1971 Dec;44(2):486–495. doi: 10.1016/0003-2697(71)90236-3. [DOI] [PubMed] [Google Scholar]
  22. Kruse T. A., Clark B. F. The effect of specific structural modification on the biological activity of E. coli arginine tRNA. Nucleic Acids Res. 1978 Mar;5(3):879–892. doi: 10.1093/nar/5.3.879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lewin B. Units of transcription and translation: sequence components of heterogeneous nuclear RNA and messenger RNA. Cell. 1975 Feb;4(2):77–93. doi: 10.1016/0092-8674(75)90113-0. [DOI] [PubMed] [Google Scholar]
  24. Maizels N. Dictyostelium 17S, 25S, and 5S rDNAs lie within a 38,000 base pair repeated unit. Cell. 1976 Nov;9(3):431–438. doi: 10.1016/0092-8674(76)90088-x. [DOI] [PubMed] [Google Scholar]
  25. Melera P. W., Hession C. A. Starvation phase of Physarum polycephalum: characterization of transfer ribonucleic acid. Mol Cell Biol. 1981 Jan;1(1):13–20. doi: 10.1128/mcb.1.1.13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Melera P. W., Momeni C., Rusch H. P. Analysis of isoaccepting tRNAs during the growth phase mitotic cycle of Physarum polycephalum. Biochemistry. 1974 Sep 24;13(20):4139–4142. doi: 10.1021/bi00717a012. [DOI] [PubMed] [Google Scholar]
  27. Melera P. W., Rusch H. P. A characterization of ribonucleic acid in the myxomycete Physarum polycephalum. Exp Cell Res. 1973 Nov;82(1):197–209. doi: 10.1016/0014-4827(73)90262-0. [DOI] [PubMed] [Google Scholar]
  28. Melera P. W., Rusch H. P. Aminoacylation of transfer ribonucleic acid in vitro during the mitotic cycle of Physarum polycephalum. Biochemistry. 1973 Mar 27;12(7):1307–1311. doi: 10.1021/bi00731a010. [DOI] [PubMed] [Google Scholar]
  29. Mitra S. K., Ley A. N., Smith C. J. Specificity of AAG codon recognition by lysyl transfer ribonucleic acid from yeast. J Biol Chem. 1971 Sep 25;246(18):5854–5856. [PubMed] [Google Scholar]
  30. Mitra S. K., Lustig F., Akesson B., Axberg T., Elias P., Lagerkvist U. Relative efficiency of anticodons in reading the valine codons during protein synthesis in vitro. J Biol Chem. 1979 Jul 25;254(14):6397–6401. [PubMed] [Google Scholar]
  31. NIRENBERG M., LEDER P. RNA CODEWORDS AND PROTEIN SYNTHESIS. THE EFFECT OF TRINUCLEOTIDES UPON THE BINDING OF SRNA TO RIBOSOMES. Science. 1964 Sep 25;145(3639):1399–1407. doi: 10.1126/science.145.3639.1399. [DOI] [PubMed] [Google Scholar]
  32. Oashi Z., Saneyoshi M., Harada F., Hara H., Nishimura S. Presumed anticodon structure of glutamic acid tRNA from E. coli: a possible location of a 2-thiouridine derivative in the first position of the anticodon. Biochem Biophys Res Commun. 1970 Aug 24;40(4):866–872. doi: 10.1016/0006-291x(70)90983-6. [DOI] [PubMed] [Google Scholar]
  33. Philippsen P., Thomas M., Kramer R. A., Davis R. W. Unique arrangement of coding sequences for 5 S, 5.8 S, 18 S and 25 S ribosomal RNA in Saccharomyces cerevisiae as determined by R-loop and hybridization analysis. J Mol Biol. 1978 Aug 15;123(3):387–404. doi: 10.1016/0022-2836(78)90086-4. [DOI] [PubMed] [Google Scholar]
  34. Reeves R. H., Imura N., Schwam H., Weiss G. B., Schulman L. H., Chambers R. W. Transfer RNA, I. Isolation and characterization of a new yeast alanine transfer RNA. Proc Natl Acad Sci U S A. 1968 Aug;60(4):1450–1457. doi: 10.1073/pnas.60.4.1450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sekiya T., Takeishi K., Ukita T. Specificity of yeast glutamic acid transfer RNA for codon recognition. Biochim Biophys Acta. 1969 Jun 17;182(2):411–426. doi: 10.1016/0005-2787(69)90192-0. [DOI] [PubMed] [Google Scholar]
  36. Sen G. C., Ghosh H. P. Coding properties of isoaccepting lysine transfer RNA species from baker's yeast. Biochim Biophys Acta. 1973 Apr 21;308(7):106–116. doi: 10.1016/0005-2787(73)90127-5. [DOI] [PubMed] [Google Scholar]
  37. Smith C. J., Teh H. S., Ley A. N., D'Obrenan P. The nucleotide sequences and coding properties of the major and minor lysine transfer ribonucleic acids from the haploid yeast Saccharomyces cerevisiae S288C. J Biol Chem. 1973 Jun 25;248(12):4475–4485. [PubMed] [Google Scholar]
  38. Söll D., Cherayil J. D., Bock R. M. Studies on polynucleotides. LXXV. Specificity of tRNA for codon recognition as studied by the ribosomal binding technique. J Mol Biol. 1967 Oct 14;29(1):97–112. doi: 10.1016/0022-2836(67)90183-0. [DOI] [PubMed] [Google Scholar]
  39. Weissenbach J., Dirheimer G., Falcoff R., Sanceau J., Falcoff E. Yeast tRNALeu (anticodon U--A--G) translates all six leucine codons in extracts from interferon treated cells. FEBS Lett. 1977 Oct 1;82(1):71–76. doi: 10.1016/0014-5793(77)80888-0. [DOI] [PubMed] [Google Scholar]

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