Skip to main content
SpringerLink
Log in

Studying the Structural Organization of Polyribosomes with Alexander S. Spirin

  • Published:
Biochemistry (Moscow) Aims and scope Submit manuscript

Abstract

“Would it be possible to analyze molecular mechanisms and structural organisation of polyribosome assemblies using cryo electron tomography?” – we asked through a longstanding collaboration between my research group and that of Alexander S. Spirin. Indeed, it was: we found that double-row polyribosomes can have both circular and linear arrangements of their mRNA [Afonina, Z. A., et al. (2013) Biochemistry (Moscow)], we figured out how eukaryotic ribosomes assemble on an mRNA to form supramolecular left-handed helices [Myasnikov, A. G., et al. (2014) Nat. Commun.], that the circularization of polyribosomes is poly-A and cap-independent [Afonina, Z. A., et al. (2014) Nucleic Acids Res.], and that intermediary polyribosomes with open structures exist after a transition from a juvenile phase to strongly translating polysomes of medium size [Afonina, Z. A., et al. (2015) Nucleic Acids Res.] until they form densely packed helical structures with reduced activity. Our joint fruitful exchanges, hence, led to major advances in the field, which are reviewed here from a personal and historical perspective in memory of Alexander S. Spirin.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

Similar content being viewed by others

Abbreviations

cryo-EM:

cryo electron microcopy

cryo-ET:

cryo electron tomography

References

  1. Warner, J. R., Rich, A., and Hall, C. E. (1962) Electron microscope studies of ribosomal clusters synthesizing hemoglobin, Science, 138, 1399-1403, https://doi.org/10.1126/science.138.3548.1399.

    Article  CAS  PubMed  Google Scholar 

  2. Warner, J. R., Knopf, P. M., and Rich, A. (1963) A multiple ribosomal structure in protein synthesis, Proc. Natl. Acad. Sci. USA, 49, 122-129, https://doi.org/10.1073/pnas.49.1.122.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Wooding, F. B. (1968) Ribosome helices in mature cells, J. Ultrastruct. Res., 24, 157-164, https://doi.org/10.1016/S0022-5320(68)80025-5.

    Article  CAS  PubMed  Google Scholar 

  4. Kopeina, G. S., Afonina, Zh. A., Gromova, K. V., Shirokov, V. A., Vasiliev, V. D., and Spirin, A. S. (2008) Step-wise formation of eukaryotic double-row polyribosomes and circular translation of polysomal mRNA, Nucleic Acids Res., 36, 2476-2488, https://doi.org/10.1093/nar/gkm1177.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Medalia, O., Weber, I., Frangakis, A. S., Nicastro, D., Gerisch, G., Baumeister, W. (2002) Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography, Science, 298, 1209-1213, https://doi.org/10.1126/science.1076184.

    Article  CAS  PubMed  Google Scholar 

  6. Spirin, A. S., Baranov, V. I., Ryabova, L. A., Ovodov, S., Alakhov, Y. B. (1988) A continuous cell-free translation system capable of producing polypeptides in high yield, Science, 242, 1162-1164, https://doi.org/10.1126/science.3055301.

    Article  CAS  PubMed  Google Scholar 

  7. Shirokov, V. A., Kommer, A. A., Kolb, V. A., and Spirin, A. S. (2007) Continuous-exchange protein-synthesizing systems, in Methods in Molecular Biology, In vitro Transcription and Translation Protocols (Grandi, G., ed.) Humana Press Inc., Totowa, NJ, 375, pp. 19-55, https://doi.org/10.1007/978-1-59745-388-2_2.

  8. Myasnikov, A. G., Afonina, Z., and Klaholz, B. P. (2013) Single particle and molecular assembly analysis of polyribosomes by single- and double-tilt cryo electron tomography, Ultramicroscopy, 126, 33-39, https://doi.org/10.1016/j.ultramic.2012.12.009.

    Article  CAS  PubMed  Google Scholar 

  9. Afonina, Z. A., Myasnikov, A. G., Khabibullina, N. F., Belorusova, A. Yu., Ménétret, J.-F., et al. (2013) Topology of mRNA chain in isolated eukaryotic double-row polyribosomes, Biochemistry (Moscow), 78, 445-454, https://doi.org/10.1134/S0006297913050027.

    Article  CAS  Google Scholar 

  10. Myasnikov, A. G., Afonina, Z. A., Ménétret, J.-F., Shirokov, V. A., Spirin, A. S., and Klaholz, B. P. (2014) The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes, Nat. Commun., 5, 5294, https://doi.org/10.1038/ncomms6294.

    Article  CAS  PubMed  Google Scholar 

  11. Orlov, I., Myasnikov, A. G., Andronov, L., Natchiar, S. K., Khatter, H., et al. (2017) The integrative role of cryo electron microscopy in molecular and cellular structural biology, Biol. Cell, 109, 81-93, https://doi.org/10.1111/boc.201600042.

    Article  CAS  PubMed  Google Scholar 

  12. Afonina, Z. A., Myasnikov, A. G., Shirokov, V. A., Klaholz, B. P., Spirin, A. S. (2014) Formation of circular polyribosomes on eukaryotic mRNA without cap-structure and poly(A)-tail: a cryo electron tomography study, Nucleic Acids Res., 42, 9461-9469, https://doi.org/10.1093/nar/gku599.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Afonina, Z. A., Myasnikov, A. G., Shirokov, V. A., Klaholz, B. P., and Spirin, A. S. (2015) Conformation transitions of eukaryotic polyribosomes during multi-round translation, Nucleic Acids Res., 43, 618-628, https://doi.org/10.1093/nar/gku1270.

    Article  CAS  PubMed  Google Scholar 

  14. Ortiz, J. O., Förster, F., Kürner, J., Linaroudis, A. A., and Baumeister, W. (2006) Mapping 70S ribosomes in intact cells by cryo electron tomography and pattern recognition, J. Struct. Biol., 156, 334-341, https://doi.org/10.1016/j.jsb.2006.04.014.

    Article  CAS  PubMed  Google Scholar 

  15. Brandt, F., Carlson, L. A., Hartl, F. U., Baumeister, W., Grünewald, K. (2010) The three-dimensional organization of polyribosomes in intact human cells, Mol. Cell, 39, 560-569, https://doi.org/10.1016/j.molcel.2010.08.003.

    Article  CAS  PubMed  Google Scholar 

  16. Brandt, F., Etchells, S. A., Ortiz, J. O., Elcock, A. H., Hartl, U., and Baumeister, W. (2009) The native 3D organization of bacterial polysomes, Cell, 136, 261-271, https://doi.org/10.1016/j.cell.2008.11.016.

    Article  CAS  PubMed  Google Scholar 

  17. Simonetti, A., Marzi, S., Myasnikov, A. G., Ménétret, J.-F., and Klaholz, B. P. (2011) Insights into translation initiation and termination complexes and into the polysome architecture, in Ribosomes (Rodnina, M. V., Wintermeyer, W., and Green, R., eds.) Springer, Vienna, https://doi.org/10.1007/978-3-7091-0215-2_10.

  18. Ménétret, J.-F., Khatter, H., Simonetti, A., Orlov, I., Myasnikov, A. G., et al. (2013) Integrative structure–function analysis of large nucleoprotein complexes, in RNA Structure and Folding (Klostermeier, D., and Hammann, C., eds.), https://doi.org/10.1515/9783110284959.

  19. Klaholz, B. P. (2019) Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis, Acta Cryst., D75, 878-881, https://doi.org/10.1107/S2059798319013391.

    Article  Google Scholar 

  20. Tegunov, D., Xue, L., Dienemann, C., Cramer, P., and Mahamid, J. (2021) Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells, Nat. Methods, 18, 186-193, https://doi.org/10.1038/s41592-020-01054-7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

I thank past and present members of my research group at CBI/IGBMC for dedicated research and members of the integrated structural biology platform at the CBI/IGBMC for support. I acknowledge support by Centre National pour la Recherche Scientifique (CNRS), Institut National pour la Recherche Médicale (Inserm), Association pour la Recherche sur le Cancer (ARC), Institut National du Cancer (INCa), the Fondation pour la Recherche Médicale (FRM), Ligue nationale contre le cancer (Ligue), Agence National pour la Recherche (ANR), and USIAS of the University of Strasbourg (USIAS-2018-012). The electron microscope facility was supported by the Région Grand Est and by the French Infrastructure for Integrated Structural Biology (FRISBI) and Instruct-ERIC.

Author information

Authors and Affiliations

  1. Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 67404, Illkirch, France

    Bruno P. Klaholz

  2. Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404, Illkirch, France

    Bruno P. Klaholz

  3. Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404, Illkirch, France

    Bruno P. Klaholz

  4. Université de Strasbourg, 67081, Strasbourg, France

    Bruno P. Klaholz

Authors
  1. Bruno P. Klaholz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bruno P. Klaholz.

Ethics declarations

The author declares no conflicts of interest in financial or any other sphere. This article does not contain any studies involving human participants or animals performed by the author.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Klaholz, B.P. Studying the Structural Organization of Polyribosomes with Alexander S. Spirin. Biochemistry Moscow 86, 1053–1059 (2021). https://doi.org/10.1134/S0006297921090030

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006297921090030

Keywords

Search

Navigation