Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Dynamic switch of the signal recognition particle from scanning to targeting

Nature Structural & Molecular Biology volume 19, pages 1332–1337 (2012)Cite this article

Subjects

Abstract

Ribosomes synthesizing inner membrane proteins in Escherichia coli are targeted to the membrane by the signal recognition particle (SRP) pathway. By rapid kinetic analysis we show that after initial binding to the ribosome, SRP undergoes dynamic fluctuations in search of additional interactions. Non-translating ribosomes, or ribosomes synthesizing non-membrane proteins, do not provide these contacts, allowing SRPs to dissociate rapidly. A nascent peptide in the exit tunnel stabilizes SRPs in a standby state. Binding to the emerging signal-anchor sequence (SAS) of a nascent membrane protein halts the fluctuations of SRP, resulting in complex stabilization and recruitment of the SRP receptor. We propose a kinetic model where SRP rapidly scans all ribosomes until it encounters a ribosome exposing an SAS. Binding to the SAS switches SRP into the targeting mode, in which dissociation is slow and docking of the SRP receptor is accelerated.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Kinetics of SRP–ribosome interaction.
Figure 2: Influence of the Lep peptide on the kinetics of SRP–ribosome interaction.
Figure 3: Influence of the Lep peptide on the kinetic stability of SRP–RNC complexes.
Figure 4: Kinetics of FtsY interaction with ribosome-bound SRP.
Figure 5: Schematic of the SRP cycle derived from kinetics.

Similar content being viewed by others

References

  1. Bibi, E. Early targeting events during membrane protein biogenesis in Escherichia coli. Biochim. Biophys. Acta 1808, 841–850 (2011).

    Article  CAS  Google Scholar 

  2. Grudnik, P., Bange, G. & Sinning, I. Protein targeting by the signal recognition particle. Biol. Chem. 390, 775–782 (2009).

    Article  CAS  Google Scholar 

  3. Luirink, J., von Heijne, G., Houben, E. & de Gier, J.W. Biogenesis of inner membrane proteins in Escherichia coli. Annu. Rev. Microbiol. 59, 329–355 (2005).

    Article  CAS  Google Scholar 

  4. Bornemann, T., Jöckel, J., Rodnina, M.V. & Wintermeyer, W. Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel. Nat. Struct. Mol. Biol. 15, 494–499 (2008).

    Article  CAS  Google Scholar 

  5. Zhang, X., Rashid, R., Wang, K. & Shan, S.O. Sequential checkpoints govern substrate selection during cotranslational protein targeting. Science 328, 757–760 (2010).

    Article  CAS  Google Scholar 

  6. Jensen, C.G. & Pedersen, S. Concentrations of 4.5S RNA and Ffh protein in Escherichia coli: the stability of Ffh protein is dependent on the concentration of 4.5S RNA. J. Bacteriol. 176, 7148–7154 (1994).

    Article  CAS  Google Scholar 

  7. Gu, S.Q., Peske, F., Wieden, H.J., Rodnina, M.V. & Wintermeyer, W. The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9, 566–573 (2003).

    Article  CAS  Google Scholar 

  8. Buskiewicz, I.A., Jockel, J., Rodnina, M.V. & Wintermeyer, W. Conformation of the signal recognition particle in ribosomal targeting complexes. RNA 15, 44–54 (2009).

    Article  CAS  Google Scholar 

  9. Halic, M. et al. Signal recognition particle receptor exposes the ribosomal translocon binding site. Science 312, 745–747 (2006).

    Article  CAS  Google Scholar 

  10. Zheng, N. & Gierasch, L.M. Domain interactions in E. coli SRP: stabilization of M domain by RNA is required for effective signal sequence modulation of NG domain. Mol. Cell 1, 79–87 (1997).

    Article  CAS  Google Scholar 

  11. Bradshaw, N., Neher, S.B., Booth, D.S. & Walter, P. Signal sequences activate the catalytic switch of SRP RNA. Science 323, 127–130 (2009).

    Article  CAS  Google Scholar 

  12. Jagath, J.R., Rodnina, M.V., Lentzen, G. & Wintermeyer, W. Interaction of guanine nucleotides with the signal recognition particle from Escherichia coli. Biochemistry 37, 15408–15413 (1998).

    Article  CAS  Google Scholar 

  13. Peluso, P. et al. Role of 4.5S RNA in assembly of the bacterial signal recognition particle with its receptor. Science 288, 1640–1643 (2000).

    Article  CAS  Google Scholar 

  14. Schaffitzel, C. & Ban, N. Generation of ribosome nascent chain complexes for structural and functional studies. J. Struct. Biol. 158, 463–471 (2007).

    Article  CAS  Google Scholar 

  15. Bhushan, S. et al. SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center. PLoS Biol. 9, e1000581 (2011).

    Article  CAS  Google Scholar 

  16. Saraogi, I., Zhang, D., Chandrasekaran, S. & Shan, S.O. Site-specific fluorescent labeling of nascent proteins on the translating ribosome. J. Am. Chem. Soc. 133, 14936–14939 (2011).

    Article  CAS  Google Scholar 

  17. Janda, C.Y. et al. Recognition of a signal peptide by the signal recognition particle. Nature 465, 507–510 (2010).

    Article  CAS  Google Scholar 

  18. Hainzl, T., Huang, S., Merilainen, G., Brannstrom, K. & Sauer-Eriksson, A.E. Structural basis of signal-sequence recognition by the signal recognition particle. Nat. Struct. Mol. Biol. 18, 389–391 (2011).

    Article  CAS  Google Scholar 

  19. Egea, P.F. et al. Substrate twinning activates the signal recognition particle and its receptor. Nature 427, 215–221 (2004).

    Article  CAS  Google Scholar 

  20. Focia, P.J., Shepotinovskaya, I.V., Seidler, J.A. & Freymann, D.M. Heterodimeric GTPase core of the SRP targeting complex. Science 303, 373–377 (2004).

    Article  CAS  Google Scholar 

  21. Estrozi, L.F., Boehringer, D., Shan, S.O., Ban, N. & Schaffitzel, C. Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor. Nat. Struct. Mol. Biol. 18, 88–90 (2011).

    Article  CAS  Google Scholar 

  22. Mircheva, M. et al. Predominant membrane localization is an essential feature of the bacterial signal recognition particle receptor. BMC Biol. 7, 76 (2009).

    Article  Google Scholar 

  23. Braig, D. et al. Signal sequence-independent SRP-SR complex formation at the membrane suggests an alternative targeting pathway within the SRP cycle. Mol. Biol. Cell 22, 2309–2323 (2011).

    Article  CAS  Google Scholar 

  24. Stjepanovic, G. et al. Lipids trigger a conformational switch that regulates signal recognition particle (SRP)-mediated protein targeting. J. Biol. Chem. 286, 23489–23497 (2011).

    Article  CAS  Google Scholar 

  25. Zhang, X., Schaffitzel, C., Ban, N. & Shan, S.O. Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proc. Natl. Acad. Sci. USA 106, 1754–1759 (2009).

    Article  CAS  Google Scholar 

  26. Shen, K., Zhang, X. & Shan, S.O. Synergistic actions between the SRP RNA and translating ribosome allow efficient delivery of the correct cargos during cotranslational protein targeting. RNA 17, 892–902 (2011).

    Article  CAS  Google Scholar 

  27. Zhang, X., Kung, S. & Shan, S.O. Demonstration of a multistep mechanism for assembly of the SRP x SRP receptor complex: implications for the catalytic role of SRP RNA. J. Mol. Biol. 381, 581–593 (2008).

    Article  CAS  Google Scholar 

  28. Buskiewicz, I., Kubarenko, A., Peske, F., Rodnina, M.V. & Wintermeyer, W. Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY. RNA 11, 947–957 (2005).

    Article  CAS  Google Scholar 

  29. Buskiewicz, I. et al. Conformations of the signal recognition particle protein Ffh from Escherichia coli as determined by FRET. J. Mol. Biol. 351, 417–430 (2005).

    Article  CAS  Google Scholar 

  30. Kramer, G. et al. L23 protein functions as a chaperone docking site on the ribosome. Nature 419, 171–174 (2002).

    Article  CAS  Google Scholar 

  31. Rodnina, M.V. & Wintermeyer, W. GTP consumption of elongation factor Tu during translation of heteropolymeric mRNAs. Proc. Natl. Acad. Sci. USA 92, 1945–1949 (1995).

    Article  CAS  Google Scholar 

  32. Milon, P. et al. Transient kinetics, fluorescence, and FRET in studies of initiation of translation in bacteria. Methods Enzymol. 430, 1–30 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank E. Deuerling (University of Konstanz, Germany) for the E. coli strain lacking ribosomal protein L23 and A. Bursy, F. Hummel, T. Wiles, S. Kappler and O. Geintzer for expert technical assistance. The work was supported by the Deutsche Forschungsgemeinschaft (grant WI 626/18-1 to W.W.).

Author information

Authors and Affiliations

  1. Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany

    Wolf Holtkamp, Sejeong Lee, Thomas Bornemann, Tamara Senyushkina, Marina V Rodnina & Wolfgang Wintermeyer

Authors
  1. Wolf Holtkamp
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sejeong Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thomas Bornemann
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tamara Senyushkina
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marina V Rodnina
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wolfgang Wintermeyer
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

W.H., T.B., M.V.R. and W.W. conceived the research and designed experiments. W.H. and S.L. prepared materials and conducted experiments. W.H., S.L., T.S. and M.V.R. analyzed the data. W.W. and M.V.R wrote the paper.

Corresponding author

Correspondence to Wolfgang Wintermeyer.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Note (PDF 1414 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Holtkamp, W., Lee, S., Bornemann, T. et al. Dynamic switch of the signal recognition particle from scanning to targeting. Nat Struct Mol Biol 19, 1332–1337 (2012). https://doi.org/10.1038/nsmb.2421

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2421

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing