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.

  • Review Article
  • Published:

The structural basis of protein targeting and translocation in bacteria

Abstract

In Gram-negative bacteria, two distinct targeting routes assist in the proper localization of secreted and membrane proteins. Signal recognition particle (SRP) mainly targets ribosome-bound nascent membrane proteins, whereas SecB facilitates the targeting of periplasmic and outer membrane proteins. These routes converge at the translocase, a protein-conducting pore in the membrane that consists of the SecYEG complex associated with the peripheral ATPase, SecA. Recent structural studies of the targeting and the translocating components provide insights into how substrates are recognized and suggest a mechanism by which proteins are transported through an aqueous pore in the cytoplasmic membrane.

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

Access options

Buy this article

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

Figure 1: Model for SRP-mediated targeting of ribosome-nascent chain complexes.
Figure 2: Crystal structures of SRP pathway components.
Figure 3: Model for SecB-mediated protein targeting.
Figure 4: Crystal structure of the H. Influenza SecB protein (1FX3)28.
Figure 5: Low resolution projection maps of the SecYEG structures48.

Similar content being viewed by others

References

  1. Herskovits, A.A., Bochkareva, E.S. & Bibi, E. New prospects in studying the bacterial signal recognition particle pathway. Mol. Microbiol. 38, 927–939 (2000).

    Article  CAS  Google Scholar 

  2. Fekkes, P. & Driessen, A.J.M. Protein targeting to the bacterial cytoplasmic membrane. Microbiol. Mol. Biol. Rev. 63, 161–173 (1999).

    CAS  PubMed  Google Scholar 

  3. Beck, K., Wu, L.F., Brunner, J. & Müller, M. Discrimination between SRP- and SecA/SecB-dependent substrates involves selective recognition of nascent chains by SRP and trigger factor. EMBO J. 19, 134–143 (2000).

    Article  CAS  Google Scholar 

  4. Valent, Q.A. et al. The Escherichia coli SRP and SecB targeting pathways converge at the translocon. EMBO J. 17, 2504–2512 (1998).

    Article  CAS  Google Scholar 

  5. Manting, E.H. & Driessen, A.J.M. Escherichia coli translocase: the unraveling of a molecular machine. Mol. Microbiol. 37, 226–238 (2000).

    Article  CAS  Google Scholar 

  6. Prinz, A., Behrens, C., Rapoport, T.A., Hartmann, E. & Kalies, K.U. Evolutionarily conserved binding of ribosomes to the translocation channel via the large ribosomal RNA. EMBO J. 19, 1900–1906 (2000).

    Article  CAS  Google Scholar 

  7. Scotti, P.A. et al. YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase. EMBO J. 19, 542–549 (2000).

    Article  CAS  Google Scholar 

  8. Duong, F. & Wickner, W. The SecDFyajC domain of preprotein translocase controls preprotein movement by regulating SecA membrane cycling. EMBO J. 16, 4871–4879 (1997).

    Article  CAS  Google Scholar 

  9. Hartmann, E. et al. Evolutionary conservation of components of the protein translocation complex. Nature 367, 654–657 (1994).

    Article  CAS  Google Scholar 

  10. Johnson, A.E. & van Waes, M.A. The translocon: a dynamic gateway at the ER membrane. Annu. Rev. Cell Dev. Biol. 15, 799–842 (1999).

    Article  Google Scholar 

  11. Hell, K., Neupert, W. & Stuart, R.A. Oxa1p acts as a general membrane insertion machinery for proteins encoded by mitochondrial DNA. EMBO J. 20, 1281–1288 (2001).

    Article  CAS  Google Scholar 

  12. Samuelson, J.C. et al. YidC mediates membrane protein insertion in bacteria. Nature 406, 637–641 (2000).

    Article  CAS  Google Scholar 

  13. Walter, P. & Johnson, A.E. Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu. Rev. Cell Biol. 10, 87–119 (1994).

    Article  CAS  Google Scholar 

  14. Powers, T. & Walter, P. Reciprocal stimulation of GTP hydrolysis by two directly interacting GTPases. Science 269, 1422–1424 (1995).

    Article  CAS  Google Scholar 

  15. 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 

  16. 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 

  17. Neumann-Haefelin, C., Schafer, U., Muller, M. & Koch, H.G. SRP-dependent co-translational targeting and SecA-dependent translocation analyzed as individual steps in the export of a bacterial protein. EMBO J. 19, 6419–6426 (2000).

    Article  CAS  Google Scholar 

  18. Freymann, D.M., Keenan, R.J., Stroud, R.M. & Walter, P. Structure of the conserved GTPase domain of the signal recognition particle. Nature 385, 361–364 (1997).

    Article  CAS  Google Scholar 

  19. Keenan, R.J., Freymann, D.M., Walter, P. & Stroud, R.M. Crystal structure of the signal sequence binding subunit of the signal recognition particle. Cell 94, 181–191 (1998).

    Article  CAS  Google Scholar 

  20. Freymann, D.M., Keenan, R.J., Stroud, R.M. & Walter, P. Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP. Nature. Struct. Biol. 6, 793–801 (1999).

    Article  CAS  Google Scholar 

  21. Batey, R.T., Rambo, R.P., Lucast, L., Rha, B. & Doudna, J.A. Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science 287, 1232–1239 (2000).

    Article  CAS  Google Scholar 

  22. Montoya, G., Svensson, C., Luirink, J. & Sinning, I. Crystal structure of the NG domain from the signal-recognition particle receptor FtsY. Nature 385, 365–368 (1997).

    Article  CAS  Google Scholar 

  23. Moser, C., Mol, O., Goody, R.S. & Sinning, I. The signal recognition particle receptor of Escherichia coli (FtsY) has a nucleotide exchange factor built into the GTPase domain. Proc. Natl. Acad. Sci. USA 94, 11339–11344 (1997).

    Article  CAS  Google Scholar 

  24. Kumamoto, C.A. & Francetiç, O. Highly selective binding of nascent polypeptides by an Escherichia coli chaperone protein in vivo. J. Bacteriol. 175, 2184–2188 (1993).

    Article  CAS  Google Scholar 

  25. Hartl, F.U., Lecker, S., Schiebel, E., Hendrick, J.P. & Wickner, W. The binding cascade of SecB to SecA to SecY/E mediates preprotein targeting to the E. coli plasma membrane. Cell 63, 269–279 (1990).

    Article  CAS  Google Scholar 

  26. Park, S., Liu, G., Topping, T.B., Cover, W.H. & Randall, L.L. Modulation of folding pathways of exported proteins by the leader sequence. Science 239, 1033–1035 (1988).

    Article  CAS  Google Scholar 

  27. Fekkes, P., van der Does, C. & Driessen, A.J.M. The molecular chaperone SecB is released from the carboxy-terminus of SecA during initiation of precursor protein translocation. EMBO J. 16, 6105–6113 (1997).

    Article  CAS  Google Scholar 

  28. Xu, Z., Knafels, J.D. & Yoshino, K. Crystal structure of the bacterial protein export chaperone SecB. Nature Struct. Biol. 7, 1172–1177 (2000).

    Article  CAS  Google Scholar 

  29. Muren, E.M., Suciu, D., Topping, T.B., Kumamoto, C.A. & Randall, L.L. Mutational alterations in the homotetrameric chaperone SecB that implicate the structure as dimer of dimers. J. Biol. Chem. 274, 19397–19402 (1999).

    Article  CAS  Google Scholar 

  30. Knoblauch, N.T. et al. Substrate Specificity of the SecB Chaperone. J. Biol. Chem. 274, 34219–34225 (1999).

    Article  CAS  Google Scholar 

  31. Randall, L.L., Topping, T.B., Suciu, D. & Hardy, S.J. Calorimetric analyses of the interaction between SecB and its ligands. Protein Sci. 7, 1195–1200 (1998).

    Article  CAS  Google Scholar 

  32. Hardy, S.J. & Randall, L.L. A kinetic partitioning model of selective binding of nonnative proteins by the bacterial chaperone SecB. Science 251, 439–443 (1991).

    Article  CAS  Google Scholar 

  33. Topping, T.B. & Randall, L.L. Determination of the binding frame within a physiological ligand for the chaperone SecB. Protein Sci. 3, 730–736 (1994).

    Article  CAS  Google Scholar 

  34. Fekkes, P. et al. Preprotein transfer to the Escherichia coli translocase requires the cooperative binding of SecB and the signal sequence to SecA. Mol. Microbiol. 29, 1179–1190 (1998).

    Article  CAS  Google Scholar 

  35. Kawasaki, S., Mizushima, S. & Tokuda, H. Membrane vesicles containing overproduced SecY and SecE exhibit high translocation ATPase activity and countermovement of protons in a SecA- and presecretory protein-dependent manner. J. Biol. Chem. 268, 8193–8198 (1993).

    CAS  PubMed  Google Scholar 

  36. Joly, J.C. & Wickner, W. The SecA and SecY subunits of translocase are the nearest neighbors of a translocating preprotein, shielding it from phospholipids. EMBO J. 12, 255–263 (1993).

    Article  CAS  Google Scholar 

  37. van Voorst, F., van der Does, C., Brunner, J., Driessen, A.J.M. & de Kruijff, B. Translocase-bound SecA is largely shielded from the phospholipid acyl chains. Biochemistry 37, 12261–12268 (1998).

    Article  CAS  Google Scholar 

  38. Schiebel, E., Driessen, A.J.M., Hartl, F.U. & Wickner, W. ΔμH+ and ATP function at different steps of the catalytic cycle of preprotein translocase. Cell 64, 927–939 (1991).

    Article  CAS  Google Scholar 

  39. van der Wolk, J.P., de Wit, J.G. & Driessen, A.J.M. The catalytic cycle of the Escherichia coli SecA ATPase comprises two distinct preprotein translocation events. EMBO J. 16, 7297–7304 (1997).

    Article  CAS  Google Scholar 

  40. Economou, A. & Wickner, W. SecA promotes preprotein translocation by undergoing ATP-driven cycles of membrane insertion and deinsertion. Cell 78, 835–843 (1994).

    Article  CAS  Google Scholar 

  41. Kaufmann, A., Manting, E.H., Veenendaal, A.K., Driessen, A.J.M. & van der Does, C. Cysteine-directed cross-linking demonstrates that helix 3 of SecE is close to helix 2 of SecY and helix 3 of a neighboring SecE. Biochemistry 38, 9115–9125 (1999).

    Article  CAS  Google Scholar 

  42. Hanein, D. et al. Oligomeric rings of the Sec61p complex induced by ligands required for protein translocation. Cell 87, 721–732 (1996).

    Article  CAS  Google Scholar 

  43. Beckmann, R. et al. Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex. Science 278, 2123–2126 (1997).

    Article  CAS  Google Scholar 

  44. Ménétret, J. et al. The structure of ribosome-channel complexes engaged in protein translocation. Mol. Cell 6, 1219–1232 (2000).

    Article  Google Scholar 

  45. Meyer, T.H. et al. The bacterial SecY/E translocation complex forms channel-like structures similar to those of the eukaryotic Sec61p complex. J. Mol. Biol. 285, 1789–1800 (1999).

    Article  CAS  Google Scholar 

  46. Hamman, B.D., Chen, J.C., Johnson, E.E. & Johnson, A.E. The aqueous pore through the translocon has a diameter of 40–60 Å during cotranslational protein translocation at the ER membrane. Cell 89, 535–544 (1997).

    Article  CAS  Google Scholar 

  47. Tani, K., Tokuda, H. & Mizushima, S. Translocation of ProOmpA possessing an intramolecular disulfide bridge into membrane vesicles of Escherichia coli. Effect of membrane energization. J. Biol. Chem. 265, 17341–17347 (1990).

    CAS  PubMed  Google Scholar 

  48. Manting, E.H., van der Does, C., Remigy, H., Engel, A. & Driessen, A.J.M. SecYEG assembles into a tetramer to form the active protein translocation channel. EMBO J. 19, 852–861 (2000).

    Article  CAS  Google Scholar 

  49. Karamanou, S. et al. A molecular switch in SecA protein couples ATP hydrolysis to protein translocation. Mol. Microbiol. 34, 1133–1145 (1999).

    Article  CAS  Google Scholar 

  50. Nakatogawa, H., Mori, H. & Ito, K. Two independent mechanisms down-regulate the intrinsic SecA ATPase activity. J. Biol. Chem. 275, 33209–33212 (2000).

    Article  CAS  Google Scholar 

  51. Eichler, J. & Wickner, W. Both an N-terminal 65-kDa domain and a C-terminal 30-kDa domain of SecA cycle into the membrane at SecYEG during translocation. Proc. Natl. Acad. Sci. USA 94, 5574–5581 (1997).

    Article  CAS  Google Scholar 

  52. Ramamurthy, V. & Oliver, D. Topology of the integral membrane form of Escherichia coli SecA protein reveals multiple periplasmically exposed regions and modulation by ATP binding. J. Biol. Chem. 272, 23239–23246 (1997).

    Article  CAS  Google Scholar 

  53. van der Does, C., Manting, E.H., Kaufmann, A., Lutz, M. & Driessen, A.J.M. Interaction between SecA and SecYEG in micellar solution and formation of the membrane-inserted state. Biochemistry 37, 201–210 (1998).

    Article  CAS  Google Scholar 

  54. Shilton, B. et al. Escherichia coli SecA shape and dimensions. FEBS Lett. 436, 277–282 (1998).

    Article  CAS  Google Scholar 

  55. Yahr, T.L. & Wickner, W.T. Evaluating the oligomeric state of SecYEG in preprotein translocase. EMBO J. 19, 4393–4401 (2000).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank A. Mark and N. Nouwen for careful reading of the manuscript, and the past and present members of the team who contributed to this work. This work was supported by the Earth and Life Sciences Foundation (Algemene Levenswetenschappen, ALW), the Netherlands Foundation for Chemical Research (Chemische Wetenschappen, CW), and the Netherlands Foundation for Scientific Research (Nederlandse Wetenschappelijk Onderzoek, NWO).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Arnold J.M. Driessen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Driessen, A., Manting, E. & van der Does, C. The structural basis of protein targeting and translocation in bacteria. Nat Struct Mol Biol 8, 492–498 (2001). https://doi.org/10.1038/88549

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/88549

This article is cited by

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