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:

Structural basis for the control of translation initiation during stress

Nature Structural & Molecular Biology volume 11, pages 1054–1059 (2004)Cite this article

An Erratum to this article was published on 01 April 2007

This article has been updated

Abstract

During environmental stress, organisms limit protein synthesis by storing inactive ribosomes that are rapidly reactivated when conditions improve. Here we present structural and biochemical data showing that protein Y, an Escherichia coli stress protein, fills the tRNA- and mRNA-binding channel of the small ribosomal subunit to stabilize intact ribosomes. Protein Y inhibits translation initiation during cold shock but not at normal temperatures. Furthermore, protein Y competes with conserved translation initiation factors that, in bacteria, are required for ribosomal subunit dissociation. The mechanism used by protein Y to reduce translation initiation during stress and quickly release ribosomes for renewed translation initiation may therefore occur widely in nature.

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: Structural model of protein Y binding to the ribosome as determined by X-ray crystallography.
Figure 2: Details of the PY-binding site within the ribosome.
Figure 3: Chemical probing of the ribosome in the presence of PY.
Figure 4: Inhibition of P-site tRNA binding by PY.
Figure 5: Inhibition of translation initiation by PY.
Figure 6: Ribosomal subunit association and dissociation.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

Change history

  • 20 March 2007

    Revised PDB code

Notes

  1. *NOTE: In the version of this article initially published, the PDB codes are incorrect. The correct codes are 1VOQ, 1VOS, 1VOV, 1VOX, 1VOZ for the 30S and 1VOR, 1VOU, 1VOW, 1VOY and 1VP0 for the 50S. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Agafonov, D.E., Kolb, V.A. & Spirin, A.S. Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage. EMBO Rep. 2, 399–402 (2001).

    Article  CAS  Google Scholar 

  2. Maki, Y., Yoshida, H. & Wada, A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli . Genes Cells 5, 965–974 (2000).

    Article  CAS  Google Scholar 

  3. Ye, K., Serganov, A., Hu, W., Garber, M. & Patel, D.J. Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur. J. Biochem. 269, 5182–5191 (2002).

    Article  CAS  Google Scholar 

  4. Rak, A., Kalinin, A., Shcherbakov, D. & Bayer, P. Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli . Biochem. Biophys. Res. Commun. 299, 710–714 (2002).

    Article  CAS  Google Scholar 

  5. Agafonov, D.E., Kolb, V.A., Nazimov, I.V. & Spirin, A.S. A protein residing at the subunit interface of the bacterial ribosome. Proc. Natl. Acad. Sci. USA 96, 12345–12349 (1999).

    Article  CAS  Google Scholar 

  6. Agafonov, D.E. & Spirin, A.S. The ribosome-associated inhibitor A reduces translation errors. Biochem. Biophys. Res. Commun. 320, 354–358 (2004).

    Article  CAS  Google Scholar 

  7. VanBogelen, R.A. & Neidhardt, F.C. Ribosomes as sensors of heat and cold shock in Escherichia coli . Proc. Natl. Acad. Sci. USA 87, 5589–5593 (1990).

    Article  CAS  Google Scholar 

  8. Cashel, M., Gentry, D.R., Hernandez, V.J. & Vinella, D. The stringent response. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology Vol. 2 (eds. Neidhardt, F.C. et al.) 1458–1496 (ASM Press, Washington, DC, 1996).

    Google Scholar 

  9. Ashe, M.P., De Long, S.K. & Sachs, A.B. Glucose depletion rapidly inhibits translation initiation in yeast. Mol. Biol. Cell 11, 833–848 (2000).

    Article  CAS  Google Scholar 

  10. Vila-Sanjurjo, A. et al. X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli . Proc. Natl. Acad. Sci. USA 100, 8682–8687 (2003).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Maivali, U. & Remme, J. Definition of bases in 23S rRNA essential for ribosomal subunit association. RNA 10, 600–604 (2004).

    Article  CAS  Google Scholar 

  13. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. The path of messenger RNA through the ribosome. Cell 106, 233–241 (2001).

    Article  CAS  Google Scholar 

  14. Prince, J.B., Taylor, B.H., Thurlow, D.L., Ofengand, J. & Zimmermann, R.A. Covalent crosslinking of tRNA1Val to 16S RNA at the ribosomal P site: identification of crosslinked residues. Proc. Natl. Acad. Sci. USA 79, 5450–5454 (1982).

    Article  CAS  Google Scholar 

  15. 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 

  16. von Ahsen, U. & Noller, H.F. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 267, 234–237 (1995).

    Article  CAS  Google Scholar 

  17. Vila-Sanjurjo, A. & Dahlberg, A.E. Mutational analysis of the conserved bases C1402 and A1500 in the center of the decoding domain of Escherichia coli 16 S rRNA reveals an important tertiary interaction. J. Mol. Biol. 308, 457–463 (2001).

    Article  CAS  Google Scholar 

  18. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).

    Article  CAS  Google Scholar 

  19. Jacob, W.F., Santer, M. & Dahlberg, A.E. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc. Natl. Acad. Sci. USA 84, 4757–4761 (1987).

    Article  CAS  Google Scholar 

  20. Gualerzi, C.O., Giuliodori, A.M. & Pon, C.L. Transcriptional and post-transcriptional control of cold-shock genes. J. Mol. Biol. 331, 527–539 (2003).

    Article  CAS  Google Scholar 

  21. Brock, S., Szkaradkiewicz, K. & Sprinzl, M. Initiation factors of protein biosynthesis in bacteria and their structural relationship to elongation and termination factors. Mol. Microbiol. 29, 409–417 (1998).

    Article  CAS  Google Scholar 

  22. McCutcheon, J.P. et al. Location of translational initiation factor IF3 on the small ribosomal subunit. Proc. Natl. Acad. Sci. USA 96, 4301–4306 (1999).

    Article  CAS  Google Scholar 

  23. Dallas, A. & Noller, H.F. Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol. Cell 8, 855–864 (2001).

    Article  CAS  Google Scholar 

  24. Carter, A.P. et al. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291, 498–501 (2001).

    Article  CAS  Google Scholar 

  25. Giuliodori, A.M., Brandi, A., Gualerzi, C.O. & Pon, C.L. Preferential translation of cold-shock mRNAs during cold adaptation. RNA 10, 265–276 (2004).

    Article  CAS  Google Scholar 

  26. Thieringer, H.A., Jones, P.G. & Inouye, M. Cold shock and adaptation. Bioessays 20, 49–57 (1998).

    Article  CAS  Google Scholar 

  27. Uchida, T., Abe, M., Matsuo, K. & Yoneda, M. Amounts of free 70S ribosomes and ribosomal subunits found in Escherichia coli at various temperatures. Biochem. Biophys. Res. Commun. 41, 1048–1054 (1970).

    Article  CAS  Google Scholar 

  28. Broeze, R.J., Solomon, C.J. & Pope, D.H. Effects of low temperature on in vivo and in vitro protein synthesis in Escherichia coli and Pseudomonas fluorescens . J. Bacteriol. 134, 861–874 (1978).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Barbieri, M., Vittone, A. & Maraldi, N.M. Cell stress and ribosome crystallization. J. Submicrosc. Cytol. Pathol. 27, 199–207 (1995).

    CAS  PubMed  Google Scholar 

  30. Ranu, R.S., Levin, D.H., Delaunay, J., Ernst, V. & London, I.M. Regulation of protein synthesis in rabbit reticulocyte lysates: characteristics of inhibition of protein synthesis by a translational inhibitor from heme-deficient lysates and its relationship to the initiation factor which binds Met-tRNAf. Proc. Natl. Acad. Sci. USA 73, 2720–2724 (1976).

    Article  CAS  Google Scholar 

  31. Cooper, H.L., Berger, S.L. & Braverman, R. Free ribosomes in physiologically nondividing cells. Human peripheral lymphocytes. J. Biol. Chem. 251, 4891–4900 (1976).

    CAS  PubMed  Google Scholar 

  32. Kyrpides, N.C. & Woese, C.R. Universally conserved translation initiation factors. Proc. Natl. Acad. Sci. USA 95, 224–228 (1998).

    Article  CAS  Google Scholar 

  33. Lomakin, I.B., Kolupaeva, V.G., Marintchev, A., Wagner, G. & Pestova, T.V. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev. 17, 2786–2797 (2003).

    Article  CAS  Google Scholar 

  34. Johnson, C.H., Kruft, V. & Subramanian, A.R. Identification of a plastid-specific ribosomal protein in the 30S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J. Biol. Chem. 265, 12790–12795 (1990).

    CAS  PubMed  Google Scholar 

  35. Bubunenko, M.G. & Subramanian, A.R. Recognition of novel and divergent higher plant chloroplast ribosomal proteins by Escherichia coli ribosome during in vivo assembly. J. Biol. Chem. 269, 18223–18231 (1994).

    CAS  PubMed  Google Scholar 

  36. Tan, X., Varughese, M. & Widger, W.R. A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54. J. Biol. Chem. 269, 20905–20912 (1994).

    CAS  PubMed  Google Scholar 

  37. Otwinowski, Z. & Minor, W. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 307–326 (1997).

    Article  CAS  Google Scholar 

  38. Brünger, A.T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  Google Scholar 

  39. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  40. Kleywegt, G.J. & Read, R.J. Not your average density. Structure 5, 1557–1569 (1997).

    Article  CAS  Google Scholar 

  41. Yang, H. et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31, 3450–3460 (2003).

    Article  CAS  Google Scholar 

  42. Ramesh, V., Gite, S., Li, Y. & RajBhandary, U.L. Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition. Proc. Natl. Acad. Sci. USA 94, 13524–13529 (1997).

    Article  CAS  Google Scholar 

  43. Jelenc, P.C. & Kurland, C.G. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl. Acad. Sci. USA 76, 3174–3178 (1979).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Holton, G. Meigs and C. Ralston for help with data measurement at the Advanced Light Source. We thank S. Yang for the PY expression clone, D. Wilson for IF expression clones and K. Nierhaus for the tRNAPhe expression plasmid. We also thank J. Doudna, V. Ramakrishnan, M. O'Connor, M. Marletta and A. Dahlberg and his laboratory for helpful comments on the paper. A.V.-S. acknowledges F. Vila for balance and coherence. This work was funded by the US National Institutes of Health and by the Department of Energy.

Author information

Author notes

  1. Antón Vila-Sanjurjo and Barbara-S Schuwirth: These authors contributed equally to this work.

Authors and Affiliations

  1. Departments of Molecular and Cell Biology and Chemistry, University of California, Berkeley, 94720, California, USA

    Antón Vila-Sanjurjo, Barbara-S Schuwirth, Cathy W Hau & Jamie H D Cate

  2. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, 94720, California, USA

    Antón Vila-Sanjurjo, Barbara-S Schuwirth, Cathy W Hau & Jamie H D Cate

Authors
  1. Antón Vila-Sanjurjo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Barbara-S Schuwirth
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cathy W Hau
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jamie H D Cate
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jamie H D Cate.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vila-Sanjurjo, A., Schuwirth, BS., Hau, C. et al. Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol 11, 1054–1059 (2004). https://doi.org/10.1038/nsmb850

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb850

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