Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jun 1;26(11):2708–2714. doi: 10.1093/nar/26.11.2708

Plant cytosolic tRNAHis possesses an exceptional C54 in the canonical TPsiC loop.

K Akama 1, Y Yukawa 1, M Sugiura 1, I Small 1
PMCID: PMC147610  PMID: 9592158

Abstract

A nuclear gene coding for tRNAHis from Arabidopsis has been reported to contain C54in the TPsiC loop, although the corresponding nucleotide is an invariant U or a derivative in nearly all other tRNAs. The only previously reported plant cytosolic tRNAHis sequence, from lupin, has U54. To re-examine plant cytosolic tRNAsHis and their genes we have used DNA and RNA sequence analyses, restriction enzyme digestion of PCR-amplified tRNA genes, RNA hybridization and in vivo aminoacylation assays. Our results suggest that Arabidopsis nuclear tRNAHis genes ubiquitously contain C54, as do those from tobacco, lupin and pea. The C54 nucleotide is maintained in the mature tRNAHis, which is aminoacylated in vivo , but to a relatively low level compared with other tRNAs examined. Finally, it was shown that an Arabidopsis tRNAHis gene with T54in place of C54 is over 5-fold more transcriptionally active than the wild-type gene using an in vitro system derived from plant nuclei. A possible role for this apparently sub-optimal tRNAHis sequence is suggested.

Full Text

The Full Text of this article is available as a PDF (229.3 KB).

Selected References

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

  1. Akama K., Nass A., Junker V., Beier H. Characterization of nuclear tRNA(Tyr) introns: their evolution from red algae to higher plants. FEBS Lett. 1997 Nov 10;417(2):213–218. doi: 10.1016/s0014-5793(97)01288-x. [DOI] [PubMed] [Google Scholar]
  2. Akama K., Tanifuji S. Nucleotide sequence of a putative pseudogene of histidine tRNA from Arabidopsis thaliana. Plant Mol Biol. 1989 Dec;13(6):721–722. doi: 10.1007/BF00016027. [DOI] [PubMed] [Google Scholar]
  3. Basavappa R., Sigler P. B. The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. EMBO J. 1991 Oct;10(10):3105–3111. doi: 10.1002/j.1460-2075.1991.tb07864.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Carneiro V. T., Dietrich A., Maréchal-Drouard L., Cosset A., Pelletier G., Small I. Characterization of some major identity elements in plant alanine and phenylalanine transfer RNAs. Plant Mol Biol. 1994 Dec;26(6):1843–1853. doi: 10.1007/BF00019497. [DOI] [PubMed] [Google Scholar]
  5. Choisne N., Carneiro V. T., Pelletier G., Small I. Implication of 5'-flanking sequence elements in expression of a plant tRNA(Leu) gene. Plant Mol Biol. 1998 Jan;36(1):113–123. doi: 10.1023/a:1005988004924. [DOI] [PubMed] [Google Scholar]
  6. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
  7. Ciampi M. S., Melton D. A., Cortese R. Site-directed mutagenesis of a tRNA gene: base alterations in the coding region affect transcription. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1388–1392. doi: 10.1073/pnas.79.5.1388. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ciechanover A., Wolin S. L., Steitz J. A., Lodish H. F. Transfer RNA is an essential component of the ubiquitin- and ATP-dependent proteolytic system. Proc Natl Acad Sci U S A. 1985 Mar;82(5):1341–1345. doi: 10.1073/pnas.82.5.1341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Deblaere R., Bytebier B., De Greve H., Deboeck F., Schell J., Van Montagu M., Leemans J. Efficient octopine Ti plasmid-derived vectors for Agrobacterium-mediated gene transfer to plants. Nucleic Acids Res. 1985 Jul 11;13(13):4777–4788. doi: 10.1093/nar/13.13.4777. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dower W. J., Miller J. F., Ragsdale C. W. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 1988 Jul 11;16(13):6127–6145. doi: 10.1093/nar/16.13.6127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Drabkin H. J., Helk B., RajBhandary U. L. The role of nucleotides conserved in eukaryotic initiator methionine tRNAs in initiation of protein synthesis. J Biol Chem. 1993 Nov 25;268(33):25221–25228. [PubMed] [Google Scholar]
  12. Fan H., Sugiura M. A plant basal in vitro system supporting accurate transcription of both RNA polymerase II- and III-dependent genes: supplement of green leaf component(s) drives accurate transcription of a light-responsive rbcS gene. EMBO J. 1995 Mar 1;14(5):1024–1031. doi: 10.1002/j.1460-2075.1995.tb07083.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gaëta B. A., Sharp S. J., Stewart T. S. Saturation mutagenesis of the Drosophila tRNA(Arg) gene B-Box intragenic promoter element: requirements for transcription activation and stable complex formation. Nucleic Acids Res. 1990 Mar 25;18(6):1541–1548. doi: 10.1093/nar/18.6.1541. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Ho Y. S., Kan Y. W. In vivo aminoacylation of human and Xenopus suppressor tRNAs constructed by site-specific mutagenesis. Proc Natl Acad Sci U S A. 1987 Apr;84(8):2185–2188. doi: 10.1073/pnas.84.8.2185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
  17. Kumar R., Maréchal-Drouard L., Akama K., Small I. Striking differences in mitochondrial tRNA import between different plant species. Mol Gen Genet. 1996 Sep 25;252(4):404–411. doi: 10.1007/BF02173005. [DOI] [PubMed] [Google Scholar]
  18. Maréchal-Drouard L., Kumar R., Remacle C., Small I. RNA editing of larch mitochondrial tRNA(His) precursors is a prerequisite for processing. Nucleic Acids Res. 1996 Aug 15;24(16):3229–3234. doi: 10.1093/nar/24.16.3229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Nameki N., Asahara H., Shimizu M., Okada N., Himeno H. Identity elements of Saccharomyces cerevisiae tRNA(His). Nucleic Acids Res. 1995 Feb 11;23(3):389–394. doi: 10.1093/nar/23.3.389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rich A., RajBhandary U. L. Transfer RNA: molecular structure, sequence, and properties. Annu Rev Biochem. 1976;45:805–860. doi: 10.1146/annurev.bi.45.070176.004105. [DOI] [PubMed] [Google Scholar]
  21. Sharp S. J., Schaack J., Cooley L., Burke D. J., Söll D. Structure and transcription of eukaryotic tRNA genes. CRC Crit Rev Biochem. 1985;19(2):107–144. doi: 10.3109/10409238509082541. [DOI] [PubMed] [Google Scholar]
  22. Traboni C., Ciliberto G., Cortese R. Mutations in Box B of the promoter of a eucaryotic tRNAPro gene affect rate of transcription, processing, and stability of the transcripts. Cell. 1984 Jan;36(1):179–187. doi: 10.1016/0092-8674(84)90087-4. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. Yukawa Y., Sugita M., Sugiura M. Efficient in vitro transcription of plant nuclear tRNA(Ser) genes in a nuclear extract from tobacco cultured cells. Plant J. 1997 Oct;12(4):965–970. doi: 10.1046/j.1365-313x.1997.12040965.x. [DOI] [PubMed] [Google Scholar]
  25. Zhou C., Abaigar L., Jong A. Y. A protocol for using T7 DNA polymerase in oligonucleotide site-directed mutagenesis. Biotechniques. 1990 May;8(5):503–503. [PubMed] [Google Scholar]
  26. Zhu S., Sobolev A. Y., Wek R. C. Histidyl-tRNA synthetase-related sequences in GCN2 protein kinase regulate in vitro phosphorylation of eIF-2. J Biol Chem. 1996 Oct 4;271(40):24989–24994. doi: 10.1074/jbc.271.40.24989. [DOI] [PubMed] [Google Scholar]
  27. von Pawel-Rammingen U., Aström S., Byström A. S. Mutational analysis of conserved positions potentially important for initiator tRNA function in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Apr;12(4):1432–1442. doi: 10.1128/mcb.12.4.1432. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES