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Interplay between trigger factor and other protein biogenesis factors on the ribosome

Nature Communications volume 5, Article number: 4180 (2014) | Download Citation

Abstract

Nascent proteins emerging from translating ribosomes in bacteria are screened by a number of ribosome-associated protein biogenesis factors, among them the chaperone trigger factor (TF), the signal recognition particle (SRP) that targets ribosomes synthesizing membrane proteins to the membrane and the modifying enzymes, peptide deformylase (PDF) and methionine aminopeptidase (MAP). Here, we examine the interplay between these factors both kinetically and at equilibrium. TF rapidly scans the ribosomes until it is stabilized on ribosomes presenting TF-specific nascent chains. SRP binding to those complexes is strongly impaired. Thus, TF in effect prevents SRP binding to the majority of ribosomes, except those presenting SRP-specific signal sequences, explaining how the small amount of SRP in the cell can be effective in membrane targeting. PDF and MAP do not interfere with TF or SRP binding to translating ribosomes, indicating that nascent-chain processing can take place before or in parallel with TF or SRP binding.

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References

  1. 1.

    , & Cotranslational processing mechanisms: towards a dynamic 3D model. Trends Biochem. Sci. 34, 417–426 (2009).

  2. 2.

    & Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295, 1852–1858 (2002).

  3. 3.

    et al. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431, 590–596 (2004).

  4. 4.

    , , , & Molecular chaperone functions in protein folding and proteostasis. Annu. Rev. Biochem. 82, 323–355 (2013).

  5. 5.

    , , , & Versatility of trigger factor interactions with ribosome-nascent chain complexes. J. Biol. Chem. 285, 27911–27923 (2010).

  6. 6.

    et al. Binding specificity of Escherichia coli trigger factor. Proc. Natl Acad. Sci. USA 98, 14244–14249 (2001).

  7. 7.

    , & Structure and function of the molecular chaperone trigger factor. Biochim. Biophys. Acta. 1803, 650–661 (2010).

  8. 8.

    & Ribosome-associated chaperones as key players in proteostasis. Trends Biochem. Sci. 37, 274–283 (2012).

  9. 9.

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

  10. 10.

    , , & Biogenesis of inner membrane proteins in Escherichia coli. Annu. Rev. Microbiol. 59, 329–355 (2005).

  11. 11.

    , & Protein targeting by the signal recognition particle. Biol. Chem. 390, 775–782 (2009).

  12. 12.

    , , & Signal sequence-independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel. Nat. Struct. Mol. Biol. 15, 494–499 (2008).

  13. 13.

    et al. Dynamic switch of the signal recognition particle from scanning to targeting. Nat. Struct. Mol. Biol. 19, 1332–1337 (2012).

  14. 14.

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

  15. 15.

    et al. Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. Proc. Natl Acad. Sci. USA 102, 12017–12022 (2005).

  16. 16.

    et al. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J. 27, 1622–1632 (2008).

  17. 17.

    , , , & The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome. RNA 9, 566–573 (2003).

  18. 18.

    et al. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427, 808–814 (2004).

  19. 19.

    et al. Trigger factor binds to ribosome-signal-recognition particle (SRP) complexes and is excluded by binding of the SRP receptor. Proc. Natl Acad. Sci. USA 101, 7902–7906 (2004).

  20. 20.

    et al. Interplay of signal recognition particle and trigger factor at L23 near the nascent chain exit site on the Escherichia coli ribosome. J. Cell Biol. 161, 679–684 (2003).

  21. 21.

    , , , & Interaction of trigger factor with the ribosome. J. Mol. Biol. 326, 585–592 (2003).

  22. 22.

    et al. Real-time observation of trigger factor function on translating ribosomes. Nature 444, 455–460 (2006).

  23. 23.

    et al. Dynamics of trigger factor interaction with translating ribosomes. J. Biol. Chem. 283, 4124–4132 (2008).

  24. 24.

    et al. A peptide deformylase-ribosome complex reveals mechanism of nascent chain processing. Nature 452, 108–111 (2008).

  25. 25.

    , & In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179–186 (1986).

  26. 26.

    , & Methionine or not methionine at the beginning of a protein. Bioessays 3, 27–31 (1985).

  27. 27.

    et al. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147, 1295–1308 (2011).

  28. 28.

    et al. Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding. Nat. Struct. Mol. Biol. 20, 843–850 (2013).

  29. 29.

    , , & The ‘trigger factor cycle’ includes ribosomes, presecretory proteins, and the plasma membrane. Cell 54, 1013–1018 (1988).

  30. 30.

    , , , & ProOmpA is stabilized for membrane translocation by either purified E. coli trigger factor or canine signal recognition particle. Cell 54, 1003–1011 (1988).

  31. 31.

    , , & Trigger factor binding to ribosomes with nascent peptide chains of varying lengths and sequences. J. Biol. Chem. 281, 28033–28038 (2006).

  32. 32.

    et al. Three-state equilibrium of Escherichia coli trigger factor. Biol. Chem. 383, 1611–1619 (2002).

  33. 33.

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

  34. 34.

    & High-throughput screening of peptide deformylase inhibitors. Methods Mol. Med. 142, 117–130 (2008).

  35. 35.

    , , & The anti-angiogenic agent fumagillin covalently modifies a conserved active-site histidine in the Escherichia coli methionine aminopeptidase. Proc. Natl Acad. Sci. USA 95, 12153–12157 (1998).

  36. 36.

    et al. Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding. Mol. Cell. 48, 63–74 (2012).

  37. 37.

    , & Control of peptide deformylase activity by metal cations. J. Mol. Biol. 280, 515–523 (1998).

  38. 38.

    , , & Divalent metal binding properties of the methionyl aminopeptidase from Escherichia coli. Biochemistry 39, 3817–3826 (2000).

  39. 39.

    et al. Thiostrepton inhibits the turnover but not the GTPase of elongation factor G on the ribosome. Proc. Natl Acad. Sci. USA 96, 9586–9590 (1999).

  40. 40.

    , , , & Chain dynamics of nascent polypeptides emerging from the ribosome. ACS Chem. Biol. 3, 555–566 (2008).

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Acknowledgements

We thank Marina Rodnina for helpful discussions and critical reading of the manuscript. We thank Elke Deuerling for providing us with the construct for SUMO-tagged trigger factor and acknowledge the expert technical assistance of Anna Bursy, Franziska Hummel, Sandra Kappler and Tanja Wiles.

Author information

Affiliations

  1. Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany

    • Thomas Bornemann
    • , Wolf Holtkamp
    •  & Wolfgang Wintermeyer

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Contributions

T.B., W.H. and W.W. designed experiments; T.B. and W.H. carried out the experiments and analysed the data. W.W. and T.B. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Wolfgang Wintermeyer.

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DOI

https://doi.org/10.1038/ncomms5180

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