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A hierarchical model for evolution of 23S ribosomal RNA


The emergence of the ribosome constituted a pivotal step in the evolution of life. This event happened nearly four billion years ago, and any traces of early stages of ribosome evolution are generally thought to have completely eroded away. Surprisingly, a detailed analysis of the structure of the modern ribosome reveals a concerted and modular scheme of its early evolution.

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Figure 1: Location of inter-domain A-minor interactions in the secondary structure of the E. coli 23S rRNA.
Figure 2: The location of the identified elements in the E. coli 23S rRNA secondary structure (a) and the network of D1 and D2 dependencies between them (b).
Figure 3: The aggrandizement of the 23S rRNA structure during its evolution.


  1. Stillman, B. (ed.) The Ribosome. Cold Spring Harbor Symposia on Quantative Biology (Cold Spring Harbor Laboratory Press, 2001)

    Google Scholar 

  2. Crick, F. H. The origin of the genetic code. J. Mol. Biol. 38, 367–369 (1968)

    Article  CAS  Google Scholar 

  3. Gilbert, W. The RNA world. Nature 319, 618 (1986)

    Article  ADS  Google Scholar 

  4. Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 A resolution. Science 292, 883–896 (2001)

    Article  ADS  CAS  Google Scholar 

  5. Ban, N. et al. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)

    Article  ADS  CAS  Google Scholar 

  6. Harms, J. et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679–688 (2001)

    Article  CAS  Google Scholar 

  7. Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006)

    Article  ADS  CAS  Google Scholar 

  8. Schuwirth, B. S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005)

    Article  ADS  CAS  Google Scholar 

  9. Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001)

    Article  ADS  CAS  Google Scholar 

  10. Noller, H. F., Hoffarth, V. & Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416–1419 (1992)

    Article  ADS  CAS  Google Scholar 

  11. Nissen, P. et al. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000)

    Article  ADS  CAS  Google Scholar 

  12. Gutell, R. R., Larsen, N. & Woese, C. R. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58, 10–26 (1994)

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Doudna, J. A. & Rath, V. L. Structure and function of the eukaryotic ribosome: the next frontier. Cell 109, 153–156 (2002)

    Article  CAS  Google Scholar 

  14. Cannone, J. J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002)

    Article  Google Scholar 

  15. Nissen, P. et al. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA 98, 4899–4903 (2001)

    Article  ADS  CAS  Google Scholar 

  16. Doherty, E. A., Batey, R. T., Masquida, B. & Doudna, J. A. A universal mode of helix packing in RNA. Nature Struct. Biol. 8, 339–343 (2001)

    Article  CAS  Google Scholar 

  17. Polacek, N. & Mankin, A. S. The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit. Rev. Biochem. Mol. Biol. 40, 285–311 (2005)

    Article  CAS  Google Scholar 

  18. Agmon, I., Bashan, A., Zarivach, R. & Yonath, A. Symmetry at the active site of the ribosome: structural and functional implications. Biol. Chem. 386, 833–844 (2005)

    Article  CAS  Google Scholar 

  19. 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 377, 309–314 (1995)

    Article  ADS  CAS  Google Scholar 

  20. Kim, D. F. & Green, R. Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol. Cell 4, 859–864 (1999)

    Article  CAS  Google Scholar 

  21. Hansen, J. L., Schmeing, T. M., Moore, P. B. & Steitz, T. A. Structural insights into peptide bond formation. Proc. Natl Acad. Sci. USA 99, 11670–11675 (2002)

    Article  ADS  CAS  Google Scholar 

  22. Zhang, B. & Cech, T. R. Peptide bond formation by in vitro selected ribozymes. Nature 390, 96–100 (1997)

    Article  ADS  CAS  Google Scholar 

  23. Savelsbergh, A. et al. Stimulation of the GTPase activity of translation elongation factor G by ribosomal protein L7/12. J. Biol. Chem. 275, 890–894 (2000)

    Article  CAS  Google Scholar 

  24. Kavran, J. M. & Steitz, T. A. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J. Mol. Biol. 371, 1047–1059 (2007)

    Article  CAS  Google Scholar 

  25. Nikulin, A. et al. Structure of the L1 protuberance in the ribosome. Nature Struct. Biol. 10, 104–108 (2003)

    Article  CAS  Google Scholar 

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We thank L. Brakier-Gingras, A. Mankin, S. Michnick and I. Ponomarenko for advice and comments. This work was supported by a grant from NSERC.

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Correspondence to Sergey V. Steinberg.

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Bokov, K., Steinberg, S. A hierarchical model for evolution of 23S ribosomal RNA. Nature 457, 977–980 (2009).

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