Structure and functions of 5S rRNA.

• Authors: Mirosława Z Barciszewska , Maciej Szymański , Volker A Erdmann , Jan Barciszewski
• Languages of publication: EN

Abstracts

EN

The ribosome is a macromolecular assembly that is responsible for protein biosynthesis in all organisms. It is composed of two-subunit, ribonucleoprotein particles that translate the genetic material into an encoded polypeptides. The small subunit is the site of codon-anticodon interaction between the messenger RNA (mRNA) and transfer RNA (tRNA) substrates, and the large subunit catalyses peptide bond formation. The peptidyltransferase activity is fulfilled by 23S rRNA, which means that ribosome is a ribozyme. 5S rRNA is a conserved component of the large ribosomal subunit that is thought to enhance protein synthesis by stabilizing ribosome structure. This paper shortly summarises new results obtained on the structure and function of 5S rRNA.

Keywords

EN

50S subunit structure; ribosomal 5S RNA; 5S rRNA; crystal structure

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2001
• Volume: 48
• Issue: 1
• Pages: 191-198

Dates

published

2001

received

2000-11-7

revised

2001-01-8

accepted

2001-03-2

Contributors

author

Mirosława Z Barciszewska

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Maciej Szymański

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Volker A Erdmann

• Institut für Biochemie, Freie Universität Berlin, Berlin, Germany

author

Jan Barciszewski

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• 1. Porse, B.T. & Garrett, R.A. (1999) Ribosomal mechanics, antibiotics, and GTP hydrolysis. Cell 97, 423-426.
• 2. Garrett, R. (1999) Mechanics of the ribosome. Nature 400, 811-812.
• 3. Davies, C. & White, S.W. (2000) Electrons and X-rays gang up on the ribosome. Structure Fold Des. 8, R41-R45.
• 4. Green, R. & Puglisi, J.D. (1999) The ribosome revealed. Nat. Struct. Biol. 6, 999-1003.
• 5. Agrawal, R.K. & Frank, J. (1999) Structural studies of the translational apparatus. Curr. Opin. Struct. Biol. 9, 215-221.
• 6. Ban, N., Nissen, P., Penczek, P., Hansen, J., Capel, M., Moore, P.B. & Steitz, T.A. (1999) Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature 400, 841-847.
• 7. Clemons, W.M., May, J.L.C., Wimberly, B.T., McCutcheon, J.P., Capel, M.S. & Ramakrishan, V. (1999) Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature 400, 833-840.
• 8. Cate, J.H., Yusupov, M.M., Yusupova, G.Zh., Earnest, T.N. & Noller, H.F. (1999) X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095-2104.
• 9. Spahn, Ch.M.T., Grassucci, R.A., Penczek, P. & Frank, J. (1999) Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy. Structure 7, 1567- 1573.
• 10. Stark, H., Rodnina, M.V., Wieden, H.-J., van Heel, M. & Wintermeyer, W. (2000) Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100, 301-309.
• 11. Gabashvili, I.S., Agrawal, R.K., Spahn, Ch.M.T., Grassucci, R.A., Svergun, D.I., Frank, J. & Penczek, P. (2000) Solution structure of the E. coli 70S ribosome at 11.5 Å resolution. Cell 100, 537-549.
• 12. Gray, M.W., Burger, G. & Lang, B.F (1999) Mitochondrial evolution. Science 283, 1476-1481.
• 13. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905-920.
• 14. Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930.
• 15. Szymański, M., Barciszewska, M., Barciszewski, J. & Erdmann, V.A. (2000) 5S ribosomal RNA database Y2K. Nucleic Acids Res. 28, 166-167.
• 16. Barciszewska, M.Z., Szymański, M., Erdmann, V.A. & Barciszewski, J. (2000) 5S ribosomal RNA. Biomacromolecules 1, 297-302.
• 17. Kirpekar, F., Douthwaite, S. & Roepstorff, P. (2000) Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 6, 296-306.
• 18. Funari, S.S., Rapp, G., Perbrandt, M., Dierks, K., Vallazza, M., Betzel, C., Erdmann, V.A. & Svergun, D.I. (2000) Structure of free Thermus flavus 5S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering. J. Biol. Chem. 275, 31283- 31288.
• 19. Mueller, F., Sommer, I., Baranov, P., Matadeen, R., Stoldt, M., Wohnert, J., Gorlach, M., van Heel, M. & Brimacombe, R. (2000) The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 Å resolution. J. Mol. Biol. 298, 35-59.
• 20. Sergiev, P.V., Bogdanov, A.A., Dahlberg, A.E. & Dontsova, O. (2000) Mutations at position A960 of E. coli 23 S ribosomal RNA influence the structure of 5 S ribosomal RNA and the peptidyltransferase region of 23 S ribosomal RNA. J. Mol. Biol. 299, 379-389.
• 21. Khaitovich, P. & Mankin, A.S. (2000) Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5S rRNA. J. Mol. Biol. 291, 1025-1034.
• 22. Lorenz, S., Perbandt, M., Lippmann, C., Moore, K., DeLucas, L.J., Betzel, C. & Erdmann, V.A. (2000) Crystallization of engineered Thermus flavus 5S rRNA under earth and microgravity conditions. Acta Crystallogr. D. Biol. Crystallogr. 56, 498-500.
• 23. Bloemink, M.J. & Moore, P.B. (1999) Phosphorylation of ribosomal protein L18 is required for its folding and binding to 5S rRNA. Biochemistry 38, 13385-13390.
• 24. Claussen, M., Rudt, F. & Pieler, T. (1999) Functional modules in ribosomal protein L5 for ribonucleoprotein complex formation and nucleocytoplasmic transport. J. Biol. Chem. 274, 33951-33958.
• 25. Rosorius, O., Fries, B., Stauber, R.H., Hirschmann, N., Bevec, D. & Hauber, J. (2000) Human ribosomal protein L5 contains defined nuclear localization and export signals. J. Biol. Chem. 275, 12061-12068.
• 26. Park, J.W. & Bae, Y.S. (1999) Phosphorylation of ribosomal protein L5 by protein kinase CKII decreases its 5S rRNA binding activity. Biochem. Biophys. Res. Commun. 263, 475-481.
• 27. Stoldt, M., Wohnert, J., Ohlenschlager, O., Gorlach, M. & Brown, L.R. (1999) The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition. EMBO J. 18, 6508-6521.
• 28. Lu, M. & Steitz, T.A. (2000) Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8 Å resolution. Proc. Natl. Acad. Sci. U.S.A. 97, 2023-2028.
• 29. Neely, L.S., Lee, B.M., Xu, J., Wright, P.E. & Gottesfeld, J.M. (1999) Identification of a minimal domain of 5 S ribosomal RNA sufficient for high affinity interactions with the RNA-specific zinc fingers of transcription factor IIIA. J. Mol. Biol. 291, 549-560.
• 30. Jensen, L.R. & Frederiksen, S. (2000) The 5S rRNA genes in Macaca fascicularis are organized in two large tandem repeats. Biochim. Biophys. Acta, 1492, 537-542.
• 31. Cairns, C.A. & White, R.J. (1998) p53 is a general repressor of RNA polymerase III transcription. EMBO J. 17, 3112-3223.
• 32. Yu, A., Fan, H.Y., Liao, D., Bailey, A.D. & Weiner, A.M. (2000) Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2, and 5S genes. Mol. Cell. 5, 801-810.
• 33. Conconi, A., Liu, X., Koriazova, L., Ackerman, E.J. & Smerdon, M.J. (1999) Tight correlation between inhibition of DNA repair in vitro and transcription factor IIIA binding in 5S ribosomal RNA gene. EMBO J. 18, 1387-1396.
• 34. Liu, X., Mann, D.B., Suquet, C., Springer, D.L. & Smerdon, M.J. (2000) Ultraviolet damage and nucleosome folding of the 5S ribosomal RNA gene. Biochemistry 39, 557-566.
• 35. Liu, X. & Smerdon, M.J. (2000) Nucleotide excision repair of the 5 S ribosomal RNA gene assembled into a nucleosome. J. Biol. Chem. 275, 23729-23735.
• 36. Vitolo, J.M., Thiriet, C. & Hayes, J.J. (2000) The H3-H4 N-terminal tail domains are the primary mediators of transcription factor IIIA access to 5S DNA within a nucleosome. Mol. Cell. Biol. 20, 2167-2175.
• 37. Mathews, D.H., Sabina, J., Zuker, M. & Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
• 38. Ding, Y. & Lawrence, C.E. (1999) A Bayesian statistical algorithm for secondary structure prediction. Comput. Chem. 23, 387-400.
• 39. Zuker, M. (2000) Calculating nucleic acids secondary structure. Curr. Opin. Struct. Biol. 10, 303- 310.