Skip to main content
NCBI home page
RNA logoLink to RNA
. 1998 Mar;4(3):276–284.

A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme.

P Y Shi 1, A M Weiner 1, N Maizels 1
PMCID: PMC1369617  PMID: 9510330

Abstract

The CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase] catalyzes the addition and regeneration of the 3'-terminal CCA sequence of tRNAs. We show that the CCA-adding enzyme will specifically add a CCA terminus to synthetic full-length tDNA and to DNA oligonucleotides corresponding to the "top half" of tRNA-the acceptor stem and TpsiC stem-loop of tRNA. CCA addition to the top half tDNA minihelices requires a 2' as well as a 3' OH at the 3' terminus of the tDNA. Addition also depends on the length of the base paired stem, and is facilitated by, but is not dependent upon, the presence of a TpsiC loop. These results provide further evidence for independent functions of the top and bottom halves of tRNA, and support the hypothesis that these two structurally distinct and functionally independent domains evolved independently.

Full Text

The Full Text of this article is available as a PDF (728.5 KB).

Selected References

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

  1. Allain F. H., Varani G. Structure of the P1 helix from group I self-splicing introns. J Mol Biol. 1995 Jul 14;250(3):333–353. doi: 10.1006/jmbi.1995.0381. [DOI] [PubMed] [Google Scholar]
  2. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  3. Cudny H., Lupski J. R., Godson G. N., Deutscher M. P. Cloning, sequencing, and species relatedness of the Escherichia coli cca gene encoding the enzyme tRNA nucleotidyltransferase. J Biol Chem. 1986 May 15;261(14):6444–6449. [PubMed] [Google Scholar]
  4. Dahm S. C., Uhlenbeck O. C. Characterization of deoxy- and ribo-containing oligonucleotide substrates in the hammerhead self-cleavage reaction. Biochimie. 1990 Nov;72(11):819–823. doi: 10.1016/0300-9084(90)90191-i. [DOI] [PubMed] [Google Scholar]
  5. Dickerson R. E., Drew H. R., Conner B. N., Wing R. M., Fratini A. V., Kopka M. L. The anatomy of A-, B-, and Z-DNA. Science. 1982 Apr 30;216(4545):475–485. doi: 10.1126/science.7071593. [DOI] [PubMed] [Google Scholar]
  6. Evans J. A., Deutscher M. P. Polyamine stimulation and cation requirements of rabbit liver tRNA nucleotidyltransferase. J Biol Chem. 1976 Nov 10;251(21):6646–6652. [PubMed] [Google Scholar]
  7. Giegé R. Interplay of tRNA-like structures from plant viral RNAs with partners of the translation and replication machineries. Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12078–12081. doi: 10.1073/pnas.93.22.12078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hardt W. D., Schlegl J., Erdmann V. A., Hartmann R. K. Kinetics and thermodynamics of the RNase P RNA cleavage reaction: analysis of tRNA 3'-end variants. J Mol Biol. 1995 Mar 24;247(2):161–172. doi: 10.1006/jmbi.1994.0130. [DOI] [PubMed] [Google Scholar]
  9. Holm L., Sander C. DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci. 1995 Sep;20(9):345–347. doi: 10.1016/s0968-0004(00)89071-4. [DOI] [PubMed] [Google Scholar]
  10. Holmes C. E., Hecht S. M. Fe.bleomycin cleaves a transfer RNA precursor and its "transfer DNA" analog at the same major site. J Biol Chem. 1993 Dec 5;268(34):25909–25913. [PubMed] [Google Scholar]
  11. James J. K., Tinoco I., Jr The solution structure of a d[C(TTCG)G] DNA hairpin and comparison to the unusually stable RNA analogue. Nucleic Acids Res. 1993 Jul 11;21(14):3287–3293. doi: 10.1093/nar/21.14.3287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Keith G., Pixa G., Fix C., Dirheimer G. Primary structure of three tRNAs from brewer's yeast: tRNAPro2, tRNAHis1 and tRNAHis2. Biochimie. 1983 Nov-Dec;65(11-12):661–672. doi: 10.1016/s0300-9084(84)80030-9. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Li Z., Gillis K. A., Hegg L. A., Zhang J., Thurlow D. L. Effects of nucleotide substitutions within the T-loop of precursor tRNAs on interaction with ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and yeast. Biochem J. 1996 Feb 15;314(Pt 1):49–53. doi: 10.1042/bj3140049. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lim A. C., Barton J. K. Chemical probing of tDNAPhe with transition metal complexes: a structural comparison of RNA and DNA. Biochemistry. 1993 Oct 19;32(41):11029–11034. doi: 10.1021/bi00092a012. [DOI] [PubMed] [Google Scholar]
  16. Liu F., Altman S. Requirements for cleavage by a modified RNase P of a small model substrate. Nucleic Acids Res. 1996 Jul 15;24(14):2690–2696. doi: 10.1093/nar/24.14.2690. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Martin G., Keller W. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 1996 May 15;15(10):2593–2603. [PMC free article] [PubMed] [Google Scholar]
  18. McClain W. H., Guerrier-Takada C., Altman S. Model substrates for an RNA enzyme. Science. 1987 Oct 23;238(4826):527–530. doi: 10.1126/science.2443980. [DOI] [PubMed] [Google Scholar]
  19. Musier-Forsyth K., Schimmel P. Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature. 1992 Jun 11;357(6378):513–515. doi: 10.1038/357513a0. [DOI] [PubMed] [Google Scholar]
  20. Oh B. K., Pace N. R. Interaction of the 3'-end of tRNA with ribonuclease P RNA. Nucleic Acids Res. 1994 Oct 11;22(20):4087–4094. doi: 10.1093/nar/22.20.4087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Paquette J., Nicoghosian K., Qi G. R., Beauchemin N., Cedergren R. The conformation of single-stranded nucleic acids tDNA versus tRNA. Eur J Biochem. 1990 Apr 30;189(2):259–265. doi: 10.1111/j.1432-1033.1990.tb15485.x. [DOI] [PubMed] [Google Scholar]
  22. Perreault J. P., Altman S. Important 2'-hydroxyl groups in model substrates for M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli. J Mol Biol. 1992 Jul 20;226(2):399–409. doi: 10.1016/0022-2836(92)90955-j. [DOI] [PubMed] [Google Scholar]
  23. Perreault J. P., Pon R. T., Jiang M. Y., Usman N., Pika J., Ogilvie K. K., Cedergren R. The synthesis and functional evaluation of RNA and DNA polymers having the sequence of Escherichia coli tRNA(fMet). Eur J Biochem. 1989 Dec 8;186(1-2):87–93. doi: 10.1111/j.1432-1033.1989.tb15181.x. [DOI] [PubMed] [Google Scholar]
  24. Puglisi E. V., Puglisi J. D., Williamson J. R., RajBhandary U. L. NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end. Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11467–11471. doi: 10.1073/pnas.91.24.11467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Rao A. L., Dreher T. W., Marsh L. E., Hall T. C. Telomeric function of the tRNA-like structure of brome mosaic virus RNA. Proc Natl Acad Sci U S A. 1989 Jul;86(14):5335–5339. doi: 10.1073/pnas.86.14.5335. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Rudinger J., Blechschmidt B., Ribeiro S., Sprinzl M. Minimalist aminoacylated RNAs as efficient substrates for elongation factor Tu. Biochemistry. 1994 May 17;33(19):5682–5688. doi: 10.1021/bi00185a003. [DOI] [PubMed] [Google Scholar]
  27. Schimmel P., Giegé R., Moras D., Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8763–8768. doi: 10.1073/pnas.90.19.8763. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schimmel P., Ribas de Pouplana L. Transfer RNA: from minihelix to genetic code. Cell. 1995 Jun 30;81(7):983–986. doi: 10.1016/s0092-8674(05)80002-9. [DOI] [PubMed] [Google Scholar]
  29. Shi J. P., Martinis S. A., Schimmel P. RNA tetraloops as minimalist substrates for aminoacylation. Biochemistry. 1992 Jun 2;31(21):4931–4936. doi: 10.1021/bi00136a002. [DOI] [PubMed] [Google Scholar]
  30. Shi P. Y., Brinton M. A., Veal J. M., Zhong Y. Y., Wilson W. D. Evidence for the existence of a pseudoknot structure at the 3' terminus of the flavivirus genomic RNA. Biochemistry. 1996 Apr 2;35(13):4222–4230. doi: 10.1021/bi952398v. [DOI] [PubMed] [Google Scholar]
  31. Shi P. Y., Maizels N., Weiner A. M. Recovery of soluble, active recombinant protein from inclusion bodies. Biotechniques. 1997 Dec;23(6):1036–1038. doi: 10.2144/97236bm15. [DOI] [PubMed] [Google Scholar]
  32. Svärd S. G., Kagardt U., Kirsebom L. A. Phylogenetic comparative mutational analysis of the base-pairing between RNase P RNA and its substrate. RNA. 1996 May;2(5):463–472. [PMC free article] [PubMed] [Google Scholar]
  33. Thurlow D. L., Pulido G. M., Millar K. J. Unidentified open reading frames in the genome of Methanococcus jannaschii are similar in sequence to an archaebacterial gene for tRNA nucleotidyltransferase. J Mol Evol. 1997 Jun;44(6):686–689. doi: 10.1007/pl00013143. [DOI] [PubMed] [Google Scholar]
  34. Weiner A. M., Maizels N. tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7383–7387. doi: 10.1073/pnas.84.21.7383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Yang J. H., Usman N., Chartrand P., Cedergren R. Minimum ribonucleotide requirement for catalysis by the RNA hammerhead domain. Biochemistry. 1992 Jun 2;31(21):5005–5009. doi: 10.1021/bi00136a013. [DOI] [PubMed] [Google Scholar]
  36. Yue D., Maizels N., Weiner A. M. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996 Sep;2(9):895–908. [PMC free article] [PubMed] [Google Scholar]
  37. Zhu L., Deutscher M. P. tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J. 1987 Aug;6(8):2473–2477. doi: 10.1002/j.1460-2075.1987.tb02528.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES