Skip to main content
NCBI home page
RNA logoLink to RNA
. 2001 Jan;7(1):54–63. doi: 10.1017/s1355838201001650

Interactions between 23S rRNA and tRNA in the ribosomal E site.

M Bocchetta 1, L Xiong 1, S Shah 1, A S Mankin 1
PMCID: PMC1370069  PMID: 11214181

Abstract

Interactions between tRNA or its analogs and 23S rRNA in the large ribosomal subunit were analyzed by RNA footprinting and by modification-interference selection. In the E site, tRNA protected bases G2112, A2392, and C2394 of 23S rRNA. Truncated tRNA, lacking the anticodon stem-loop, protected A2392 and C2394, but not G2112, and tRNA derivatives with a shortened 3' end protected only G2112, but not A2392 or C2394. Modification interference revealed C2394 as the only accessible nucleotide in 23S rRNA whose modification interferes with binding of tRNA in the large ribosomal subunit E site. The results suggest a direct contact between A76 of tRNA A76 and C2394 of 23S rRNA. Protections at G2112 may reflect interaction of this 23S rRNA region with the tRNA central fold.

Full Text

The Full Text of this article is available as a PDF (297.7 KB).

Selected References

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

  1. Ban N., Nissen P., Hansen J., Moore P. B., Steitz T. A. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905–920. doi: 10.1126/science.289.5481.905. [DOI] [PubMed] [Google Scholar]
  2. Bocchetta M., Xiong L., Mankin A. S. 23S rRNA positions essential for tRNA binding in ribosomal functional sites. Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3525–3530. doi: 10.1073/pnas.95.7.3525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cate J. H., Yusupov M. M., Yusupova G. Z., Earnest T. N., Noller H. F. X-ray crystal structures of 70S ribosome functional complexes. Science. 1999 Sep 24;285(5436):2095–2104. doi: 10.1126/science.285.5436.2095. [DOI] [PubMed] [Google Scholar]
  4. Francklyn C., Schimmel P. Aminoacylation of RNA minihelices with alanine. Nature. 1989 Feb 2;337(6206):478–481. doi: 10.1038/337478a0. [DOI] [PubMed] [Google Scholar]
  5. Frank J. The ribosome-structure and functional ligand-binding experiments using cryo-electron microscopy. J Struct Biol. 1998 Dec 15;124(2-3):142–150. doi: 10.1006/jsbi.1998.4071. [DOI] [PubMed] [Google Scholar]
  6. Geigenmüller U., Nierhaus K. H. Significance of the third tRNA binding site, the E site, on E. coli ribosomes for the accuracy of translation: an occupied E site prevents the binding of non-cognate aminoacyl-tRNA to the A site. EMBO J. 1990 Dec;9(13):4527–4533. doi: 10.1002/j.1460-2075.1990.tb07904.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gnirke A., Nierhaus K. H. tRNA binding sites on the subunits of Escherichia coli ribosomes. J Biol Chem. 1986 Nov 5;261(31):14506–14514. [PubMed] [Google Scholar]
  8. Grajevskaja R. A., Ivanov Y. V., Saminsky E. M. 70-S ribosomes of Escherichia coli have an additional site for deacylated tRNA binding. Eur J Biochem. 1982 Nov;128(1):47–52. doi: 10.1111/j.1432-1033.1982.tb06929.x. [DOI] [PubMed] [Google Scholar]
  9. Joseph S., Noller H. F. Mapping the rRNA neighborhood of the acceptor end of tRNA in the ribosome. EMBO J. 1996 Feb 15;15(4):910–916. [PMC free article] [PubMed] [Google Scholar]
  10. Keith G. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie. 1995;77(1-2):142–144. doi: 10.1016/0300-9084(96)88118-1. [DOI] [PubMed] [Google Scholar]
  11. Khaitovich P., Mankin A. S., Green R., Lancaster L., Noller H. F. Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc Natl Acad Sci U S A. 1999 Jan 5;96(1):85–90. doi: 10.1073/pnas.96.1.85. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kirillov S. V., Makarov E. M., Semenkov YuP Quantitative study of interaction of deacylated tRNA with Escherichia coli ribosomes. Role of 50 S subunits in formation of the E site. FEBS Lett. 1983 Jun 27;157(1):91–94. doi: 10.1016/0014-5793(83)81122-3. [DOI] [PubMed] [Google Scholar]
  13. Lill R., Lepier A., Schwägele F., Sprinzl M., Vogt H., Wintermeyer W. Specific recognition of the 3'-terminal adenosine of tRNAPhe in the exit site of Escherichia coli ribosomes. J Mol Biol. 1988 Oct 5;203(3):699–705. doi: 10.1016/0022-2836(88)90203-3. [DOI] [PubMed] [Google Scholar]
  14. Lill R., Robertson J. M., Wintermeyer W. Affinities of tRNA binding sites of ribosomes from Escherichia coli. Biochemistry. 1986 Jun 3;25(11):3245–3255. doi: 10.1021/bi00359a025. [DOI] [PubMed] [Google Scholar]
  15. Lill R., Robertson J. M., Wintermeyer W. Binding of the 3' terminus of tRNA to 23S rRNA in the ribosomal exit site actively promotes translocation. EMBO J. 1989 Dec 1;8(12):3933–3938. doi: 10.1002/j.1460-2075.1989.tb08574.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lill R., Robertson J. M., Wintermeyer W. tRNA binding sites of ribosomes from Escherichia coli. Biochemistry. 1984 Dec 18;23(26):6710–6717. doi: 10.1021/bi00321a066. [DOI] [PubMed] [Google Scholar]
  17. Lill R., Wintermeyer W. Destabilization of codon-anticodon interaction in the ribosomal exit site. J Mol Biol. 1987 Jul 5;196(1):137–148. doi: 10.1016/0022-2836(87)90516-x. [DOI] [PubMed] [Google Scholar]
  18. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Moazed D., Noller H. F. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell. 1989 May 19;57(4):585–597. doi: 10.1016/0092-8674(89)90128-1. [DOI] [PubMed] [Google Scholar]
  20. Moazed D., Noller H. F. Sites of interaction of the CCA end of peptidyl-tRNA with 23S rRNA. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3725–3728. doi: 10.1073/pnas.88.9.3725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Monro R. E., Marcker K. A. Ribosome-catalysed reaction of puromycin with a formylmethionine-containing oligonucleotide. J Mol Biol. 1967 Apr 28;25(2):347–350. doi: 10.1016/0022-2836(67)90146-5. [DOI] [PubMed] [Google Scholar]
  22. Noller H. F., Hoffarth V., Zimniak L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science. 1992 Jun 5;256(5062):1416–1419. doi: 10.1126/science.1604315. [DOI] [PubMed] [Google Scholar]
  23. Osswald M., Greuer B., Brimacombe R. Localization of a series of RNA-protein cross-link sites in the 23S and 5S ribosomal RNA from Escherichia coli, induced by treatment of 50S subunits with three different bifunctional reagents. Nucleic Acids Res. 1990 Dec 11;18(23):6755–6760. doi: 10.1093/nar/18.23.6755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Porse B. T., Thi-Ngoc H. P., Garrett R. A. The donor substrate site within the peptidyl transferase loop of 23 S rRNA and its putative interactions with the CCA-end of N-blocked aminoacyl-tRNA(Phe). J Mol Biol. 1996 Dec 6;264(3):472–483. doi: 10.1006/jmbi.1996.0655. [DOI] [PubMed] [Google Scholar]
  25. Rheinberger H. J., Sternbach H., Nierhaus K. H. Codon-anticodon interaction at the ribosomal E site. J Biol Chem. 1986 Jul 15;261(20):9140–9143. [PubMed] [Google Scholar]
  26. Rheinberger H. J., Sternbach H., Nierhaus K. H. Three tRNA binding sites on Escherichia coli ribosomes. Proc Natl Acad Sci U S A. 1981 Sep;78(9):5310–5314. doi: 10.1073/pnas.78.9.5310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rinke-Appel J., Jünke N., Osswald M., Brimacombe R. The ribosomal environment of tRNA: crosslinks to rRNA from positions 8 and 20:1 in the central fold of tRNA located at the A, P, or E site. RNA. 1995 Dec;1(10):1018–1028. [PMC free article] [PubMed] [Google Scholar]
  28. Samaha R. R., Green R., Noller H. F. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature. 1995 Sep 28;377(6547):309–314. doi: 10.1038/377309a0. [DOI] [PubMed] [Google Scholar]
  29. Sprinzl M., Sternbach H., von der Haar F., Cramer F. Enzymatic incorporation of ATP and CTP analogues into the 3' end of tRNA. Eur J Biochem. 1977 Dec;81(3):579–589. doi: 10.1111/j.1432-1033.1977.tb11985.x. [DOI] [PubMed] [Google Scholar]
  30. Stern S., Moazed D., Noller H. F. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 1988;164:481–489. doi: 10.1016/s0076-6879(88)64064-x. [DOI] [PubMed] [Google Scholar]
  31. Wintermeyer W., Schleich H. G., Zachau H. G. Incorporation of amines or hydrazines into tRNA replacing wybutine or dihydrouracil. Methods Enzymol. 1979;59:110–121. doi: 10.1016/0076-6879(79)59073-9. [DOI] [PubMed] [Google Scholar]
  32. Wower J., Kirillov S. V., Wower I. K., Guven S., Hixson S. S., Zimmermann R. A. Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites. J Biol Chem. 2000 Dec 1;275(48):37887–37894. doi: 10.1074/jbc.M005031200. [DOI] [PubMed] [Google Scholar]
  33. Wower J., Scheffer P., Sylvers L. A., Wintermeyer W., Zimmermann R. A. Topography of the E site on the Escherichia coli ribosome. EMBO J. 1993 Feb;12(2):617–623. doi: 10.1002/j.1460-2075.1993.tb05694.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Zubay G., Takanami M. Observations on the configuration of nucleotides near the 3'-hydroxy end of adapter RNA. Biochem Biophys Res Commun. 1964 Mar 26;15(3):207–213. doi: 10.1016/0006-291x(64)90147-0. [DOI] [PubMed] [Google Scholar]
  35. von Ahsen U., Noller H. F. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science. 1995 Jan 13;267(5195):234–237. doi: 10.1126/science.7528943. [DOI] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES