Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1988 Aug;8(8):3332–3337. doi: 10.1128/mcb.8.8.3332

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.

Y Choffat 1, B Suter 1, R Behra 1, E Kubli 1
PMCID: PMC363568  PMID: 3145410

Abstract

In Saccharomyces cerevisiae, pseudouridine formation in the middle position of the tRNA(Tyr) anticodon (psi 35) is dependent on the presence of the intron in the tRNA(Tyr) gene (Johnson and Abelson, Nature 302:681-687, 1983). Drosophila melanogaster tRNA(Tyr) genes contain introns of three size classes: 20 or 21 base pairs (bp) (six genes), 48 bp (one gene), and 113 bp (one gene). As in yeast, removal of the intron led to loss of psi 35 in the anticodon when transcription was assayed in Xenopus laevis oocytes. All Drosophila intron sizes supported psi 35 formation. The same results were obtained with the homologous X. laevis tRNA(Tyr) genes containing introns of 12 or 13 bp or with a deleted intron. The introns of yeast (Nishikura and DeRobertis, J. Mol. Biol. 145:405-420, 1981), D. melanogaster, and X. laevis tRNA(Tyr) wild-type genes, while they all supported psi 35 synthesis, did not share any consensus sequences. As discussed, these results, taken together, suggest that for appropriate function the psi 35 enzyme in the X. laevis oocyte needs the presence of an unqualified intron in the tRNA gene and a tRNA(Tyr)-like structure in the unprocessed tRNA precursor.

Full text

PDF
3332

Images in this article

3334Image
on p.3334
3335Image
on p.3335

Selected References

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

  1. Attardi D. G., Margarit I., Tocchini-Valentini G. P. Structural alterations in mutant precursors of the yeast tRNALeu3 gene which behave as defective substrates for a highly purified splicing endoribonuclease. EMBO J. 1985 Dec 1;4(12):3289–3297. doi: 10.1002/j.1460-2075.1985.tb04079.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Björk G. R., Ericson J. U., Gustafsson C. E., Hagervall T. G., Jönsson Y. H., Wikström P. M. Transfer RNA modification. Annu Rev Biochem. 1987;56:263–287. doi: 10.1146/annurev.bi.56.070187.001403. [DOI] [PubMed] [Google Scholar]
  3. Capone J. P., Sharp P. A., RajBhandary U. L. Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene. EMBO J. 1985 Jan;4(1):213–221. doi: 10.1002/j.1460-2075.1985.tb02338.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. De Robertis E. M., Olson M. V. Transcription and processing of cloned yeast tyrosine tRNA genes microinjected into frog oocytes. Nature. 1979 Mar 8;278(5700):137–143. doi: 10.1038/278137a0. [DOI] [PubMed] [Google Scholar]
  5. Dente L., Cesareni G., Cortese R. pEMBL: a new family of single stranded plasmids. Nucleic Acids Res. 1983 Mar 25;11(6):1645–1655. doi: 10.1093/nar/11.6.1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Freier S. M., Kierzek R., Jaeger J. A., Sugimoto N., Caruthers M. H., Neilson T., Turner D. H. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. doi: 10.1073/pnas.83.24.9373. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gouilloud E., Clarkson S. G. A dispersed tyrosine tRNA gene from Xenopus laevis with high transcriptional activity in vitro. J Biol Chem. 1986 Jan 5;261(1):486–494. [PubMed] [Google Scholar]
  8. Green C. J., Kammen H. O., Penhoet E. E. Purification and properties of a mammalian tRNA pseudouridine synthase. J Biol Chem. 1982 Mar 25;257(6):3045–3052. [PubMed] [Google Scholar]
  9. Grosjean H. J., de Henau S., Crothers D. M. On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A. 1978 Feb;75(2):610–614. doi: 10.1073/pnas.75.2.610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. 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]
  11. Laski F. A., Alzner-DeWeerd B., RajBhandary U. L., Sharp P. A. Expression of a X. laevis tRNATyr gene in mammalian cells. Nucleic Acids Res. 1982 Aug 11;10(15):4609–4626. doi: 10.1093/nar/10.15.4609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lee M. C., Knapp G. Transfer RNA splicing in Saccharomyces cerevisiae. Secondary and tertiary structures of the substrates. J Biol Chem. 1985 Mar 10;260(5):3108–3115. [PubMed] [Google Scholar]
  13. 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]
  14. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Nishikura K., De Robertis E. M. RNA processing in microinjected Xenopus oocytes. Sequential addition of base modifications in the spliced transfer RNA. J Mol Biol. 1981 Jan 15;145(2):405–420. doi: 10.1016/0022-2836(81)90212-6. [DOI] [PubMed] [Google Scholar]
  16. Nishikura K., Kurjan J., Hall B. D., De Robertis E. M. Genetic analysis of the processing of a spliced tRNA. EMBO J. 1982;1(2):263–268. doi: 10.1002/j.1460-2075.1982.tb01157.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. O'Farrell P. Z., Cordell B., Valenzuela P., Rutter W. J., Goodman H. M. Structure and processing of yeast precursor tRNAs containing intervening sequences. Nature. 1978 Aug 3;274(5670):438–445. doi: 10.1038/274438a0. [DOI] [PubMed] [Google Scholar]
  18. Ogden R. C., Lee M. C., Knapp G. Transfer RNA splicing in Saccharomyces cerevisiae: defining the substrates. Nucleic Acids Res. 1984 Dec 21;12(24):9367–9382. doi: 10.1093/nar/12.24.9367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Robinson R. R., Davidson N. Analysis of a drosophila tRNA gene cluster: two tRNALeu genes contain intervening sequences. Cell. 1981 Jan;23(1):251–259. doi: 10.1016/0092-8674(81)90289-0. [DOI] [PubMed] [Google Scholar]
  20. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Silberklang M., Gillum A. M., RajBhandary U. L. Use of in vitro 32P labeling in the sequence analysis of nonradioactive tRNAs. Methods Enzymol. 1979;59:58–109. doi: 10.1016/0076-6879(79)59072-7. [DOI] [PubMed] [Google Scholar]
  22. Strobel M. C., Abelson J. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol Cell Biol. 1986 Jul;6(7):2663–2673. doi: 10.1128/mcb.6.7.2663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Suter B., Altwegg M., Choffat Y., Kubli E. The nucleotide sequence of two homogeneic Drosophila melanogaster tRNATyr isoacceptors: application of a rapid tRNA anticodon sequencing method using S-1 nuclease. Arch Biochem Biophys. 1986 May 15;247(1):233–237. doi: 10.1016/0003-9861(86)90552-7. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Swerdlow H., Guthrie C. Structure of intron-containing tRNA precursors. Analysis of solution conformation using chemical and enzymatic probes. J Biol Chem. 1984 Apr 25;259(8):5197–5207. [PubMed] [Google Scholar]
  26. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  27. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis: a simple method using two oligonucleotide primers and a single-stranded DNA template. DNA. 1984 Dec;3(6):479–488. doi: 10.1089/dna.1.1984.3.479. [DOI] [PubMed] [Google Scholar]
  28. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. doi: 10.1093/nar/9.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES