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. 1997 Nov 1;25(21):4194–4200. doi: 10.1093/nar/25.21.4194

The tRNATyr-isoacceptors and their genes in the ciliate Tetrahymena thermophila: cytoplasmic tRNATyr has a QPsiA anticodon and is coded by multiple intron-containing genes.

V Junker 1, T Teichmann 1, A Hekele 1, C Fingerhut 1, H Beier 1
PMCID: PMC147040  PMID: 9336446

Abstract

In the ciliated protozoa Tetrahymena thermophila introns have been detected in rRNA and mRNAs until now. We have isolated and sequenced seven tRNATyr genes from the T.thermophila nuclear genome. All of these genes contain introns of identical length and sequence. The 11 bp long intervening sequences are located 1 nt 3' to the anticodon as found in other eukaryotic nuclear tRNA genes. Tetrahymena tRNATyr genes are efficiently transcribed in HeLa cell nuclear extract. Moreover, processing and splicing occurred in HeLa as well as in wheat germ extracts, supporting the notion that Tetrahymena tRNATyr introns can be classified as authentic tRNA introns. We have also isolated cytoplasmic tRNATyr from Tetrahymena cells. This tRNATyr isoacceptor has a QPsiA anticodon and is not a UAG suppressor as shown in in vitro translation studies. Since UAG and UAA codons are used as glutamine codons in Tetrahymena macronuclear DNA, the presence of a strong natural UAG suppressor such as tRNATyr with GPsiA anticodon should cause misreading of the glutamine as tyrosine codons and the absence of the latter had thus been predicted. Furthermore we have studied the organization of tRNATyr genes in the genome of T.thermophila and have found two types of tRNATyr gene arrangement. A minimum of 12 tRNATyr genes are present as single copies in genomic DNA HindIII restriction fragments ranging in size from 0.6 to 7 kb. Additionally one cluster of tRNATyr genes consisting of six members has been detected in a 2.3 kb HindIII fragment.

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Selected References

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  1. Beier H., Barciszewska M., Krupp G., Mitnacht R., Gross H. J. UAG readthrough during TMV RNA translation: isolation and sequence of two tRNAs with suppressor activity from tobacco plants. EMBO J. 1984 Feb;3(2):351–356. doi: 10.1002/j.1460-2075.1984.tb01810.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beier H., Barciszewska M., Sickinger H. D. The molecular basis for the differential translation of TMV RNA in tobacco protoplasts and wheat germ extracts. EMBO J. 1984 May;3(5):1091–1096. doi: 10.1002/j.1460-2075.1984.tb01934.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Caron F. Deviations from the 'universal' genetic code. Microbiol Sci. 1986 Feb;3(2):36–40. [PubMed] [Google Scholar]
  4. Choffat Y., Suter B., Behra R., Kubli E. Pseudouridine modification in the tRNA(Tyr) anticodon is dependent on the presence, but independent of the size and sequence, of the intron in eucaryotic tRNA(Tyr) genes. Mol Cell Biol. 1988 Aug;8(8):3332–3337. doi: 10.1128/mcb.8.8.3332. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Csank C., Taylor F. M., Martindale D. W. Nuclear pre-mRNA introns: analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. Nucleic Acids Res. 1990 Sep 11;18(17):5133–5141. doi: 10.1093/nar/18.17.5133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Culbertson M. R., Winey M. Split tRNA genes and their products: a paradigm for the study of cell function and evolution. Yeast. 1989 Nov-Dec;5(6):405–427. doi: 10.1002/yea.320050602. [DOI] [PubMed] [Google Scholar]
  7. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Endoh H., Nagahashi S., Okada N. Tetrahymena pyriformis DNA fragment with a gene cluster for 3 putative serine tRNAs and an asparagine tRNA. Nucleic Acids Res. 1989 Dec 11;17(23):10122–10122. doi: 10.1093/nar/17.23.10122. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Filipowicz W., Shatkin A. J. Origin of splice junction phosphate in tRNAs processed by HeLa cell extract. Cell. 1983 Feb;32(2):547–557. doi: 10.1016/0092-8674(83)90474-9. [DOI] [PubMed] [Google Scholar]
  10. Fuchs T., Beier D., Beier H. The tRNA(Tyr) multigene family of Nicotiana rustica: genome organization, sequence analyses and expression in vitro. Plant Mol Biol. 1992 Dec;20(5):869–878. doi: 10.1007/BF00027158. [DOI] [PubMed] [Google Scholar]
  11. Geiduschek E. P., Tocchini-Valentini G. P. Transcription by RNA polymerase III. Annu Rev Biochem. 1988;57:873–914. doi: 10.1146/annurev.bi.57.070188.004301. [DOI] [PubMed] [Google Scholar]
  12. Goodman H. M., Olson M. V., Hall B. D. Nucleotide sequence of a mutant eukaryotic gene: the yeast tyrosine-inserting ochre suppressor SUP4-o. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5453–5457. doi: 10.1073/pnas.74.12.5453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Green C. J., Sohel I., Vold B. S. The discovery of new intron-containing human tRNA genes using the polymerase chain reaction. J Biol Chem. 1990 Jul 25;265(21):12139–12142. [PubMed] [Google Scholar]
  14. Grivell L. A. Molecular evolution. Deciphering divergent codes. Nature. 1986 Nov 13;324(6093):109–110. doi: 10.1038/324109a0. [DOI] [PubMed] [Google Scholar]
  15. Hanyu N., Kuchino Y., Nishimura S., Beier H. Dramatic events in ciliate evolution: alteration of UAA and UAG termination codons to glutamine codons due to anticodon mutations in two Tetrahymena tRNAs. EMBO J. 1986 Jun;5(6):1307–1311. doi: 10.1002/j.1460-2075.1986.tb04360.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hatfield D. L., Smith D. W., Lee B. J., Worland P. J., Oroszlan S. Structure and function of suppressor tRNAs in higher eukaryotes. Crit Rev Biochem Mol Biol. 1990;25(2):71–96. doi: 10.3109/10409239009090606. [DOI] [PubMed] [Google Scholar]
  17. Hattori M., Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. doi: 10.1016/0003-2697(86)90403-3. [DOI] [PubMed] [Google Scholar]
  18. Johnson G. D., Pirtle I. L., Pirtle R. M. The nucleotide sequence of tyrosine tRNAQ* psi A from bovine liver. Arch Biochem Biophys. 1985 Jan;236(1):448–453. doi: 10.1016/0003-9861(85)90647-2. [DOI] [PubMed] [Google Scholar]
  19. Johnson P. F., Abelson J. The yeast tRNATyr gene intron is essential for correct modification of its tRNA product. Nature. 1983 Apr 21;302(5910):681–687. doi: 10.1038/302681a0. [DOI] [PubMed] [Google Scholar]
  20. Katze J. R., Mosteller R. D. Inhibition of nucleoside Q formation in transfer ribonucleic acid during methionine starvation of relaxed-control Escherichia coli. J Bacteriol. 1976 Jan;125(1):205–210. doi: 10.1128/jb.125.1.205-210.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kaçar Y., Beier H., Gross H. J. The presence of tRNA pseudogenes in mammalia and plants and their absence in yeast may account for different specificities of pre-tRNA processing enzymes. Gene. 1995 Apr 14;156(1):129–132. doi: 10.1016/0378-1119(95)00079-l. [DOI] [PubMed] [Google Scholar]
  22. Kimmel A. R., Gorovsky M. A. Numbers of 5S and tRNA genes in macro- and micronuclei of Tetrahymena pyriformis. Chromosoma. 1976 Mar 10;54(4):327–337. doi: 10.1007/BF00292813. [DOI] [PubMed] [Google Scholar]
  23. Kruger K., Grabowski P. J., Zaug A. J., Sands J., Gottschling D. E., Cech T. R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell. 1982 Nov;31(1):147–157. doi: 10.1016/0092-8674(82)90414-7. [DOI] [PubMed] [Google Scholar]
  24. Kuchino Y., Hanyu N., Tashiro F., Nishimura S. Tetrahymena thermophila glutamine tRNA and its gene that corresponds to UAA termination codon. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4758–4762. doi: 10.1073/pnas.82.14.4758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Landin R. M., Boisnard M., Petrissant G. Correlation between the presence of tRNA His GUG and the erythropoietic function in foetal sheep liver. Nucleic Acids Res. 1979 Nov 24;7(6):1635–1648. doi: 10.1093/nar/7.6.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. MacPherson J. M., Roy K. L. Two human tyrosine tRNA genes contain introns. Gene. 1986;42(1):101–106. doi: 10.1016/0378-1119(86)90155-1. [DOI] [PubMed] [Google Scholar]
  27. Morin G. B., Cech T. R. Phylogenetic relationships and altered genome structures among Tetrahymena mitochondrial DNAs. Nucleic Acids Res. 1988 Jan 11;16(1):327–346. doi: 10.1093/nar/16.1.327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pederson D. S., Yao M. C., Kimmel A. R., Gorovsky M. A. Sequence organization within and flanking clusters of 5S ribosomal RNA genes in Tetrahymena. Nucleic Acids Res. 1984 Mar 26;12(6):3003–3021. doi: 10.1093/nar/12.6.3003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Prescott D. M. The DNA of ciliated protozoa. Microbiol Rev. 1994 Jun;58(2):233–267. doi: 10.1128/mr.58.2.233-267.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sprinzl M., Steegborn C., Hübel F., Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1996 Jan 1;24(1):68–72. doi: 10.1093/nar/24.1.68. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Stange N., Beier D., Beier H. Expression of nuclear tRNA(Tyr) genes from Arabidopsis thaliana in HeLa cell and wheat germ extracts. Plant Mol Biol. 1991 May;16(5):865–875. doi: 10.1007/BF00015078. [DOI] [PubMed] [Google Scholar]
  32. Stange N., Beier D., Beier H. Intron excision from tRNA precursors by plant splicing endonuclease requires unique features of the mature tRNA domain. Eur J Biochem. 1992 Nov 15;210(1):193–203. doi: 10.1111/j.1432-1033.1992.tb17408.x. [DOI] [PubMed] [Google Scholar]
  33. Stange N., Beier H. A cell-free plant extract for accurate pre-tRNA processing, splicing and modification. EMBO J. 1987 Sep;6(9):2811–2818. doi: 10.1002/j.1460-2075.1987.tb02577.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Stange N., Gross H. J., Beier H. Wheat germ splicing endonuclease is highly specific for plant pre-tRNAs. EMBO J. 1988 Dec 1;7(12):3823–3828. doi: 10.1002/j.1460-2075.1988.tb03267.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Stanley J., Vassilenko S. A different approach to RNA sequencing. Nature. 1978 Jul 6;274(5666):87–89. doi: 10.1038/274087a0. [DOI] [PubMed] [Google Scholar]
  36. Suter B., Kubli E. tRNA(Tyr) genes of Drosophila melanogaster: expression of single-copy genes studied by S1 mapping. Mol Cell Biol. 1988 Aug;8(8):3322–3331. doi: 10.1128/mcb.8.8.3322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Teichmann T., Urban C., Beier H. The tRNA(Ser)-isoacceptors and their genes in Nicotiana rustica: genome organization, expression in vitro and sequence analyses. Plant Mol Biol. 1994 Mar;24(6):889–901. doi: 10.1007/BF00014443. [DOI] [PubMed] [Google Scholar]
  38. Tourancheau A. B., Tsao N., Klobutcher L. A., Pearlman R. E., Adoutte A. Genetic code deviations in the ciliates: evidence for multiple and independent events. EMBO J. 1995 Jul 3;14(13):3262–3267. doi: 10.1002/j.1460-2075.1995.tb07329.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Valle R. P., Morch M. D. Stop making sense: or Regulation at the level of termination in eukaryotic protein synthesis. FEBS Lett. 1988 Aug 1;235(1-2):1–15. doi: 10.1016/0014-5793(88)81225-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. White B. N., Tener G. M. Activity of a transfer RNA modifying enzyme during the development of Drosophila and its relationship to the su(s) locus. J Mol Biol. 1973 Mar 15;74(4):635–651. doi: 10.1016/0022-2836(73)90054-5. [DOI] [PubMed] [Google Scholar]
  41. Zerfass K., Beier H. Pseudouridine in the anticodon G psi A of plant cytoplasmic tRNA(Tyr) is required for UAG and UAA suppression in the TMV-specific context. Nucleic Acids Res. 1992 Nov 25;20(22):5911–5918. doi: 10.1093/nar/20.22.5911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. van Tol H., Beier H. All human tRNATyr genes contain introns as a prerequisite for pseudouridine biosynthesis in the anticodon. Nucleic Acids Res. 1988 Mar 25;16(5):1951–1966. doi: 10.1093/nar/16.5.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. van Tol H., Stange N., Gross H. J., Beier H. A human and a plant intron-containing tRNATyr gene are both transcribed in a HeLa cell extract but spliced along different pathways. EMBO J. 1987 Jan;6(1):35–41. doi: 10.1002/j.1460-2075.1987.tb04715.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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