Abstract
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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References
Stillman, B. (ed.) The Ribosome. Cold Spring Harbor Symposia on Quantative Biology (Cold Spring Harbor Laboratory Press, 2001)
Crick, F. H. The origin of the genetic code. J. Mol. Biol. 38, 367–369 (1968)
Gilbert, W. The RNA world. Nature 319, 618 (1986)
Yusupov, M. M. et al. Crystal structure of the ribosome at 5.5 A resolution. Science 292, 883–896 (2001)
Ban, N. et al. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905–920 (2000)
Harms, J. et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107, 679–688 (2001)
Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006)
Schuwirth, B. S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005)
Ogle, J. M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001)
Noller, H. F., Hoffarth, V. & Zimniak, L. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416–1419 (1992)
Nissen, P. et al. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000)
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)
Doudna, J. A. & Rath, V. L. Structure and function of the eukaryotic ribosome: the next frontier. Cell 109, 153–156 (2002)
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)
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)
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)
Polacek, N. & Mankin, A. S. The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit. Rev. Biochem. Mol. Biol. 40, 285–311 (2005)
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)
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)
Kim, D. F. & Green, R. Base-pairing between 23S rRNA and tRNA in the ribosomal A site. Mol. Cell 4, 859–864 (1999)
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)
Zhang, B. & Cech, T. R. Peptide bond formation by in vitro selected ribozymes. Nature 390, 96–100 (1997)
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)
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)
Nikulin, A. et al. Structure of the L1 protuberance in the ribosome. Nature Struct. Biol. 10, 104–108 (2003)
Acknowledgements
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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Bokov, K., Steinberg, S. A hierarchical model for evolution of 23S ribosomal RNA. Nature 457, 977–980 (2009). https://doi.org/10.1038/nature07749
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DOI: https://doi.org/10.1038/nature07749
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