Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1994 Jan 1;13(1):241–248. doi: 10.1002/j.1460-2075.1994.tb06254.x

The length and the secondary structure of the D-stem of human selenocysteine tRNA are the major identity determinants for serine phosphorylation.

X Q Wu 1, H J Gross 1
PMCID: PMC394798  PMID: 8306966

Abstract

Selenocysteine tRNA [tRNA(Ser)Sec] has been shown to be serylated by tRNA(Ser) synthetase. The serine moiety of seryl-tRNA(Ser)Sec in vertebrates is further phosphorylated by a kinase, in addition to being converted into selenocysteine. Using site-directed mutagenesis we have introduced a number of mutations into T7 RNA polymerase transcripts of human tRNA(Ser)Sec. Our results show that most of the unique structural features of tRNA(Ser)(Sec), like the 5'-triphosphate, the 9 bp long acceptor stem and the anticodon, are not identity elements for phosphorylation of human seryl-tRNA(Ser)Sec. However, the length and secondary structure of the D-stem (6 bp in contrast with 4 bp in the canonical serine tRNA) of human tRNA(Ser)Sec, but not its sequence, are the major identity determinants which discriminate this tRNA from common tRNA(Ser) and identify it as the substrate for phosphorylation by seryl-tRNA(Ser)Sec kinase. This notion is confirmed by the fact that normal seryl-tRNA(Ser), which is not a substrate for serine phosphorylation, becomes a substrate if two additional base pairs are introduced into its D-stem.

Full text

PDF
245

Selected References

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

  1. Baron C., Westhof E., Böck A., Giegé R. Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser). J Mol Biol. 1993 May 20;231(2):274–292. doi: 10.1006/jmbi.1993.1282. [DOI] [PubMed] [Google Scholar]
  2. Berry M. J., Banu L., Larsen P. R. Type I iodothyronine deiodinase is a selenocysteine-containing enzyme. Nature. 1991 Jan 31;349(6308):438–440. doi: 10.1038/349438a0. [DOI] [PubMed] [Google Scholar]
  3. Böck A., Forchhammer K., Heider J., Baron C. Selenoprotein synthesis: an expansion of the genetic code. Trends Biochem Sci. 1991 Dec;16(12):463–467. doi: 10.1016/0968-0004(91)90180-4. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Carbon P., Krol A. Transcription of the Xenopus laevis selenocysteine tRNA(Ser)Sec gene: a system that combines an internal B box and upstream elements also found in U6 snRNA genes. EMBO J. 1991 Mar;10(3):599–606. doi: 10.1002/j.1460-2075.1991.tb07987.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Diamond A., Dudock B., Hatfield D. Structure and properties of a bovine liver UGA suppressor serine tRNA with a tryptophan anticodon. Cell. 1981 Aug;25(2):497–506. doi: 10.1016/0092-8674(81)90068-4. [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. Dock-Bregeon A. C., Westhof E., Giegé R., Moras D. Solution structure of a tRNA with a large variable region: yeast tRNASer. J Mol Biol. 1989 Apr 20;206(4):707–722. doi: 10.1016/0022-2836(89)90578-0. [DOI] [PubMed] [Google Scholar]
  9. Forchhammer K., Leinfelder W., Boesmiller K., Veprek B., Böck A. Selenocysteine synthase from Escherichia coli. Nucleotide sequence of the gene (selA) and purification of the protein. J Biol Chem. 1991 Apr 5;266(10):6318–6323. [PubMed] [Google Scholar]
  10. Forchhammer K., Leinfelder W., Böck A. Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature. 1989 Nov 23;342(6248):453–456. doi: 10.1038/342453a0. [DOI] [PubMed] [Google Scholar]
  11. Hatfield D., Diamond A., Dudock B. Opal suppressor serine tRNAs from bovine liver form phosphoseryl-tRNA. Proc Natl Acad Sci U S A. 1982 Oct;79(20):6215–6219. doi: 10.1073/pnas.79.20.6215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Heider J., Leinfelder W., Böck A. Occurrence and functional compatibility within Enterobacteriaceae of a tRNA species which inserts selenocysteine into protein. Nucleic Acids Res. 1989 Apr 11;17(7):2529–2540. doi: 10.1093/nar/17.7.2529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. 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 Oct 11;17(19):7855–7863. doi: 10.1093/nar/17.19.7855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kato N., Hoshino H., Harada F. Minor serine tRNA containing anticodon NCA (C4 RNA) from human and mouse cells. Biochem Int. 1983 Nov;7(5):635–645. [PubMed] [Google Scholar]
  15. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lee B. J., Kang S. G., Hatfield D. Transcription of Xenopus selenocysteine tRNA Ser (formerly designated opal suppressor phosphoserine tRNA) gene is directed by multiple 5'-extragenic regulatory elements. J Biol Chem. 1989 Jun 5;264(16):9696–9702. [PubMed] [Google Scholar]
  17. Lee B. J., Rajagopalan M., Kim Y. S., You K. H., Jacobson K. B., Hatfield D. Selenocysteine tRNA[Ser]Sec gene is ubiquitous within the animal kingdom. Mol Cell Biol. 1990 May;10(5):1940–1949. doi: 10.1128/mcb.10.5.1940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lee B. J., Worland P. J., Davis J. N., Stadtman T. C., Hatfield D. L. Identification of a selenocysteyl-tRNA(Ser) in mammalian cells that recognizes the nonsense codon, UGA. J Biol Chem. 1989 Jun 15;264(17):9724–9727. [PubMed] [Google Scholar]
  19. Lee B. J., de la Peña P., Tobian J. A., Zasloff M., Hatfield D. Unique pathway of expression of an opal suppressor phosphoserine tRNA. Proc Natl Acad Sci U S A. 1987 Sep;84(18):6384–6388. doi: 10.1073/pnas.84.18.6384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lee C. P., Mandal N., Dyson M. R., RajBhandary U. L. The discriminator base influences tRNA structure at the end of the acceptor stem and possibly its interaction with proteins. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7149–7152. doi: 10.1073/pnas.90.15.7149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lee C. P., Seong B. L., RajBhandary U. L. Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J Biol Chem. 1991 Sep 25;266(27):18012–18017. [PubMed] [Google Scholar]
  22. Leinfelder W., Forchhammer K., Veprek B., Zehelein E., Böck A. In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product. Proc Natl Acad Sci U S A. 1990 Jan;87(2):543–547. doi: 10.1073/pnas.87.2.543. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Leinfelder W., Stadtman T. C., Böck A. Occurrence in vivo of selenocysteyl-tRNA(SERUCA) in Escherichia coli. Effect of sel mutations. J Biol Chem. 1989 Jun 15;264(17):9720–9723. [PubMed] [Google Scholar]
  24. Leinfelder W., Zehelein E., Mandrand-Berthelot M. A., Böck A. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature. 1988 Feb 25;331(6158):723–725. doi: 10.1038/331723a0. [DOI] [PubMed] [Google Scholar]
  25. MARCKER K., SANGER F. N-FORMYL-METHIONYL-S-RNA. J Mol Biol. 1964 Jun;8:835–840. doi: 10.1016/s0022-2836(64)80164-9. [DOI] [PubMed] [Google Scholar]
  26. Mizutani T., Hashimoto A. Purification and properties of suppressor seryl-tRNA: ATP phosphotransferase from bovine liver. FEBS Lett. 1984 Apr 24;169(2):319–322. doi: 10.1016/0014-5793(84)80342-7. [DOI] [PubMed] [Google Scholar]
  27. Mizutani T., Kurata H., Yamada K. Study of mammalian selenocysteyl-tRNA synthesis with [75Se]HSe. FEBS Lett. 1991 Sep 2;289(1):59–63. doi: 10.1016/0014-5793(91)80908-l. [DOI] [PubMed] [Google Scholar]
  28. Mizutani T., Narihara T., Hashimoto A. Purification and properties of bovine liver seryl-tRNA synthetase. Eur J Biochem. 1984 Aug 15;143(1):9–13. doi: 10.1111/j.1432-1033.1984.tb08331.x. [DOI] [PubMed] [Google Scholar]
  29. Mizutani T. Some evidence of the enzymatic conversion of bovine suppressor phosphoseryl-tRNA to selenocysteyl-tRNA. FEBS Lett. 1989 Jul 3;250(2):142–146. doi: 10.1016/0014-5793(89)80707-0. [DOI] [PubMed] [Google Scholar]
  30. Mizutani T., Tachibana Y. Possible incorporation of phosphoserine into globin readthrough protein via bovine opal suppressor phosphoseryl-tRNA. FEBS Lett. 1986 Oct 20;207(1):162–166. doi: 10.1016/0014-5793(86)80032-1. [DOI] [PubMed] [Google Scholar]
  31. O'Neill V. A., Eden F. C., Pratt K., Hatfield D. L. A human opal suppressor tRNA gene and pseudogene. J Biol Chem. 1985 Feb 25;260(4):2501–2508. [PubMed] [Google Scholar]
  32. Schön A., Böck A., Ott G., Sprinzl M., Söll D. The selenocysteine-inserting opal suppressor serine tRNA from E. coli is highly unusual in structure and modification. Nucleic Acids Res. 1989 Sep 25;17(18):7159–7165. doi: 10.1093/nar/17.18.7159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schön A., Kannangara C. G., Gough S., Söll D. Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature. 1988 Jan 14;331(6152):187–190. doi: 10.1038/331187a0. [DOI] [PubMed] [Google Scholar]
  34. Sharp S. J., Stewart T. S. The characterization of phosphoseryl tRNA from lactating bovine mammary gland. Nucleic Acids Res. 1977 Jul;4(7):2123–2136. doi: 10.1093/nar/4.7.2123. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Shen Q., Chu F. F., Newburger P. E. Sequences in the 3'-untranslated region of the human cellular glutathione peroxidase gene are necessary and sufficient for selenocysteine incorporation at the UGA codon. J Biol Chem. 1993 May 25;268(15):11463–11469. [PubMed] [Google Scholar]
  36. Sprinzl M., Dank N., Nock S., Schön A. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2127–2171. doi: 10.1093/nar/19.suppl.2127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Stadtman T. C. Selenium biochemistry. Annu Rev Biochem. 1990;59:111–127. doi: 10.1146/annurev.bi.59.070190.000551. [DOI] [PubMed] [Google Scholar]
  38. Steinberg S., Misch A., Sprinzl M. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1993 Jul 1;21(13):3011–3015. doi: 10.1093/nar/21.13.3011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Sturchler C., Westhof E., Carbon P., Krol A. Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec). Nucleic Acids Res. 1993 Mar 11;21(5):1073–1079. doi: 10.1093/nar/21.5.1073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Varshney U., Lee C. P., RajBhandary U. L. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J Biol Chem. 1991 Dec 25;266(36):24712–24718. [PubMed] [Google Scholar]
  41. Wilcox M., Nirenberg M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc Natl Acad Sci U S A. 1968 Sep;61(1):229–236. doi: 10.1073/pnas.61.1.229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Zawadzki V., Gross H. J. Rapid and simple purification of T7 RNA polymerase. Nucleic Acids Res. 1991 Apr 25;19(8):1948–1948. doi: 10.1093/nar/19.8.1948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Zinoni F., Birkmann A., Leinfelder W., Böck A. Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon. Proc Natl Acad Sci U S A. 1987 May;84(10):3156–3160. doi: 10.1073/pnas.84.10.3156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zinoni F., Heider J., Böck A. Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4660–4664. doi: 10.1073/pnas.87.12.4660. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES