Skip to main content
Log in

The ribosome moves: RNA mechanics and translocation

  • Perspective
  • Published:

From Nature Structural & Molecular Biology

View current issue Submit your manuscript

Abstract

During protein synthesis, mRNA and tRNAs must be moved rapidly through the ribosome while maintaining the translational reading frame. This process is coupled to large- and small-scale conformational rearrangements in the ribosome, mainly in its rRNA. The free energy from peptide-bond formation and GTP hydrolysis is probably used to impose directionality on those movements. We propose that the free energy is coupled to two pawls, namely tRNA and EF-G, which enable two ratchet mechanisms to act separately and sequentially on the two ribosomal subunits.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Figure 1: Conformational states and large-scale motions during ribosomal translocation.
Figure 2: Movement of the tRNA ASL on the 30S subunit.
Figure 3: Origins of 30S head-domain rotation.
Figure 4: tRNA constrains the conformational freedom of the ribosome.
Figure 5: Integrating kinetic and structural studies on translocation.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

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

    Article  CAS  Google Scholar 

  2. Demeshkina, N., Jenner, L., Westhof, E., Yusupov, M. & Yusupova, G. A new understanding of the decoding principle on the ribosome. Nature 484, 256–259 (2012).

    Article  CAS  Google Scholar 

  3. Nissen, P., Hansen, J., Ban, N., Moore, P.B. & Steitz, T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000).

    Article  CAS  Google Scholar 

  4. Frank, J. & Agrawal, R.K. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406, 318–322 (2000).

    Article  CAS  Google Scholar 

  5. Horan, L.H. & Noller, H.F. Intersubunit movement is required for ribosomal translocation. Proc. Natl. Acad. Sci. USA 104, 4881–4885 (2007).

    Article  CAS  Google Scholar 

  6. Moazed, D. & Noller, H.F. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342, 142–148 (1989).

    Article  CAS  Google Scholar 

  7. Cornish, P.V., Ermolenko, D.N., Noller, H.F. & Ha, T. Spontaneous intersubunit rotation in single ribosomes. Mol. Cell 30, 578–588 (2008).

    Article  CAS  Google Scholar 

  8. Sharma, H. et al. Kinetics of spontaneous and EF-G-accelerated rotation of ribosomal subunits. Cell Rep. 16, 2187–2196 (2016).

    Article  CAS  Google Scholar 

  9. Gavrilova, L.P., Kostiashkina, O.E., Koteliansky, V.E., Rutkevitch, N.M. & Spirin, A.S. Factor-free (“non-enzymic”) and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol. 101, 537–552 (1976).

    Article  CAS  Google Scholar 

  10. Gavrilova, L.P. & Spirin, A.S. Stimulation of “non-enzymic” translocation in ribosomes by p-chloromercuribenzoate. FEBS Lett. 17, 324–326 (1971).

    Article  CAS  Google Scholar 

  11. Fredrick, K. & Noller, H.F. Catalysis of ribosomal translocation by sparsomycin. Science 300, 1159–1162 (2003).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  13. Spahn, C.M. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23, 1008–1019 (2004).

    Article  CAS  Google Scholar 

  14. Ratje, A.H. et al. Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Nature 468, 713–716 (2010).

    Article  CAS  Google Scholar 

  15. Zhou, J., Lancaster, L., Donohue, J.P. & Noller, H.F. Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science 340, 1236086 (2013).

    Article  Google Scholar 

  16. Ramrath, D.J. et al. Visualization of two transfer RNAs trapped in transit during elongation factor G-mediated translocation. Proc. Natl. Acad. Sci. USA 110, 20964–20969 (2013).

    Article  CAS  Google Scholar 

  17. Zhou, J., Lancaster, L., Donohue, J.P. & Noller, H.F. How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation. Science 345, 1188–1191 (2014).

    Article  CAS  Google Scholar 

  18. Mohan, S. & Noller, H.F. Recurring RNA structural motifs underlie the mechanics of L1 stalk movement. Nat. Commun. 8, 14285 (2017).

    Article  CAS  Google Scholar 

  19. Bock, L.V., Blau, C., Vaiana, A.C. & Grubmüller, H. Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. Nucleic Acids Res. 43, 6747–6760 (2015).

    Article  CAS  Google Scholar 

  20. Mohan, S., Donohue, J.P. & Noller, H.F. Molecular mechanics of 30S subunit head rotation. Proc. Natl. Acad. Sci. USA 111, 13325–13330 (2014).

    Article  CAS  Google Scholar 

  21. Lescoute, A. & Westhof, E. Topology of three-way junctions in folded RNAs. RNA 12, 83–93 (2006).

    Article  CAS  Google Scholar 

  22. Réblová, K., Sponer, J. & Lankas, F. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res. 40, 6290–6303 (2012).

    Article  Google Scholar 

  23. Trabuco, L.G. et al. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J. Mol. Biol. 402, 741–760 (2010).

    Article  CAS  Google Scholar 

  24. Fei, J., Kosuri, P., MacDougall, D.D. & Gonzalez, R.L. Jr. Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation. Mol. Cell 30, 348–359 (2008).

    Article  CAS  Google Scholar 

  25. Cornish, P.V. et al. Following movement of the L1 stalk between three functional states in single ribosomes. Proc. Natl. Acad. Sci. USA 106, 2571–2576 (2009).

    Article  CAS  Google Scholar 

  26. Valle, M. et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat. Struct. Biol. 10, 899–906 (2003).

    Article  CAS  Google Scholar 

  27. Schmeing, T.M. et al. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326, 688–694 (2009).

    Article  CAS  Google Scholar 

  28. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077 (2006).

    Article  CAS  Google Scholar 

  29. Lill, R., Robertson, J.M. & Wintermeyer, W. Affinities of tRNA binding sites of ribosomes from Escherichia coli. Biochemistry 25, 3245–3255 (1986).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  32. Liu, Q. & Fredrick, K. Contribution of intersubunit bridges to the energy barrier of ribosomal translocation. Nucleic Acids Res. 41, 565–574 (2013).

    Article  CAS  Google Scholar 

  33. Komoda, T. et al. The A-site finger in 23 S rRNA acts as a functional attenuator for translocation. J. Biol. Chem. 281, 32303–32309 (2006).

    Article  CAS  Google Scholar 

  34. Wasserman, M.R., Alejo, J.L., Altman, R.B. & Blanchard, S.C. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation. Nat. Struct. Mol. Biol. 23, 333–341 (2016).

    Article  CAS  Google Scholar 

  35. Spirin, A.S. [On the mechanism of ribosome function. The hypothesis of locking-unlocking of subparticles]. Dokl. Akad. Nauk SSSR 179, 1467–1470 (1968).

    CAS  PubMed  Google Scholar 

  36. Savelsbergh, A. et al. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol. Cell 11, 1517–1523 (2003).

    Article  CAS  Google Scholar 

  37. Gao, Y.G. et al. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326, 694–699 (2009).

    Article  CAS  Google Scholar 

  38. Khade, P.K. & Joseph, S. Messenger RNA interactions in the decoding center control the rate of translocation. Nat. Struct. Mol. Biol. 18, 1300–1302 (2011).

    Article  CAS  Google Scholar 

  39. Liu, G. et al. EF-G catalyzes tRNA translocation by disrupting interactions between decoding center and codon-anticodon duplex. Nat. Struct. Mol. Biol. 21, 817–824 (2014).

    Article  CAS  Google Scholar 

  40. 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  CAS  Google Scholar 

  41. 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 

  42. Julián, P. et al. Structure of ratcheted ribosomes with tRNAs in hybrid states. Proc. Natl. Acad. Sci. USA 105, 16924–16927 (2008).

    Article  Google Scholar 

  43. Agirrezabala, X. et al. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell 32, 190–197 (2008).

    Article  CAS  Google Scholar 

  44. Wang, L., Altman, R.B. & Blanchard, S.C. Insights into the molecular determinants of EF-G catalyzed translocation. RNA 17, 2189–2200 (2011).

    Article  CAS  Google Scholar 

  45. Woese, C. Molecular mechanics of translation: a reciprocating ratchet mechanism. Nature 226, 817–820 (1970).

    Article  CAS  Google Scholar 

  46. Spirin, A.S. The ribosome as a conveying thermal ratchet machine. J. Biol. Chem. 284, 21103–21119 (2009).

    Article  CAS  Google Scholar 

  47. Frank, J. & Gonzalez, R.L. Jr. Structure and dynamics of a processive Brownian motor: the translating ribosome. Annu. Rev. Biochem. 79, 381–412 (2010).

    Article  CAS  Google Scholar 

  48. Spirin, A.S. Ribosomal translocation: facts and models. Prog. Nucleic Acid Res. Mol. Biol. 32, 75–114 (1985).

    Article  CAS  Google Scholar 

  49. Dorner, S., Brunelle, J.L., Sharma, D. & Green, R. The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nat. Struct. Mol. Biol. 13, 234–241 (2006).

    Article  CAS  Google Scholar 

  50. Dunkle, J.A. et al. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science 332, 981–984 (2011).

    Article  CAS  Google Scholar 

  51. Brilot, A.F., Korostelev, A.A., Ermolenko, D.N. & Grigorieff, N. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. Proc. Natl. Acad. Sci. USA 110, 20994–20999 (2013).

    Article  CAS  Google Scholar 

  52. Lin, J., Gagnon, M.G., Bulkley, D. & Steitz, T.A. Conformational changes of elongation factor G on the ribosome during tRNA translocation. Cell 160, 219–227 (2015).

    Article  CAS  Google Scholar 

  53. Salsi, E., Farah, E., Netter, Z., Dann, J. & Ermolenko, D.N. Movement of elongation factor G between compact and extended conformations. J. Mol. Biol. 427, 454–467 (2015).

    Article  CAS  Google Scholar 

  54. Belardinelli, R. et al. Choreography of molecular movements during ribosome progression along mRNA. Nat. Struct. Mol. Biol. 23, 342–348 (2016).

    Article  CAS  Google Scholar 

  55. Tourigny, D.S., Fernández, I.S., Kelley, A.C. & Ramakrishnan, V. Elongation factor G bound to the ribosome in an intermediate state of translocation. Science 340, 1235490 (2013).

    Article  Google Scholar 

  56. Jenner, L.B., Demeshkina, N., Yusupova, G. & Yusupov, M. Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat. Struct. Mol. Biol. 17, 555–560 (2010).

    Article  CAS  Google Scholar 

  57. Guo, Z. & Noller, H.F. Rotation of the head of the 30S ribosomal subunit during mRNA translocation. Proc. Natl. Acad. Sci. USA 109, 20391–20394 (2012).

    Article  CAS  Google Scholar 

  58. Ermolenko, D.N. & Noller, H.F. mRNA translocation occurs during the second step of ribosomal intersubunit rotation. Nat. Struct. Mol. Biol. 18, 457–462 (2011).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Harry F Noller or Srividya Mohan.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Noller, H., Lancaster, L., Zhou, J. et al. The ribosome moves: RNA mechanics and translocation. Nat Struct Mol Biol 24, 1021–1027 (2017). https://doi.org/10.1038/nsmb.3505

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.3505

  • Springer Nature America, Inc.

This article is cited by

Navigation