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.

Conformational change of flagellin for polymorphic supercoiling of the flagellar filament

Abstract

The bacterial flagellar filament is a helical propeller rotated by the flagellar motor for bacterial locomotion. The filament is a supercoiled assembly of a single protein, flagellin, and is formed by 11 protofilaments. For bacterial taxis, the reversal of motor rotation switches the supercoil between left- and right-handed, both of which arise from combinations of two distinct conformations and packing interactions of the L-type and R-type protofilaments. Here we report an atomic model of the L-type straight filament by electron cryomicroscopy and helical image analysis. Comparison with the R-type structure shows interesting features: an orientation change of the outer core domains (D1) against the inner core domains (D0) showing almost invariant orientation and packing, a conformational switching within domain D1, and the conformational flexibility of domains D0 and D1 with their spoke-like connection for tight molecular packing.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Ribbon diagram of the Cα backbone of the filament models.
Figure 2: Comparison of the Cα backbones of L-type (blue) and R-type (red) flagellin in stereo.
Figure 3: Superposition of the L-type (blue) and R-type (red) filament structures showing the overall switching in the orientation of domains D1, D2 and D3 against the inner tube structure made of D0 domains, viewed in stereo.
Figure 4: Conformational changes that may be responsible for the switching.

Accession codes

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

References

  1. Berg, H.C. & Anderson, R.A. Bacteria swim by rotating their flagellar filaments. Nature 245, 380–382 (1973).

    CAS  Article  Google Scholar 

  2. Silverman, M. & Simon, M. Flagellar rotation and the mechanism of bacterial motility. Nature 249, 73–74 (1974).

    CAS  Article  Google Scholar 

  3. Kudo, S., Magariyama, Y. & Aizawa, S.-I. Abrupt changes in flagellar rotation observed by laser darkfield microscopy. Nature 346, 677–680 (1990).

    CAS  Article  Google Scholar 

  4. Ryu, W.S., Berry, R.M. & Berg, H.C. Torque-generating units of the flagellar motor of Escherichia coli have a high duty ratio. Nature 403, 444–447 (2000).

    CAS  Article  Google Scholar 

  5. O'Brien, E.J. & Bennett, P.M. Structure of straight flagella from a mutant Salmonella. J. Mol. Biol. 70, 133–152 (1972).

    CAS  Article  Google Scholar 

  6. Galkin, V.E. et al. Divergence of quaternary structures among bacterial flagellar filaments. Science 320, 382–385 (2008).

    CAS  Article  Google Scholar 

  7. Asakura, S. Polymerization of flagellin and polymorphism of flagella. Adv. Biophys. 1, 99–155 (1970).

    CAS  PubMed  Google Scholar 

  8. Larsen, S.H., Reader, R.W., Kort, E.N., Tso, W.W. & Adler, J. Change in direction of flagellar rotation is the basis of the chemotactic response in Escherichia coli. Nature 249, 74–77 (1974).

    CAS  Article  Google Scholar 

  9. Macnab, R.M. & Ornston, M.K. Normal-to-curly flagellar transitions and their role in bacterial tumbling. Stabilization of an alternative quaternary structure by mechanical force. J. Mol. Biol. 112, 1–30 (1977).

    CAS  Article  Google Scholar 

  10. Turner, L., Ryu, W.S. & Berg, H.C. Real-time imaging of fluorescent flagellar filaments. J. Bacteriol. 182, 2793–2801 (2000).

    CAS  Article  Google Scholar 

  11. Kamiya, R. & Asakura, S. Helical transformations of Salmonella flagella in vitro. J. Mol. Biol. 106, 167–186 (1976).

    CAS  Article  Google Scholar 

  12. Kamiya, R. & Asakura, S. Flagellar transformations at alkaline pH. J. Mol. Biol. 108, 513–518 (1977).

    Article  Google Scholar 

  13. Kamiya, R., Asakura, S., Wakabayashi, K. & Namba, K. Transition of bacterial flagella from helical to straight forms with different subunit arrangements. J. Mol. Biol. 131, 725–742 (1979).

    CAS  Article  Google Scholar 

  14. Calladine, C.R. Construction of bacterial flagella. Nature 225, 121–124 (1975).

    Article  Google Scholar 

  15. Calladine, C.R. Design requirements for the construction of bacterial flagella. J. Theor. Biol. 57, 469–489 (1976).

    CAS  Article  Google Scholar 

  16. Calladine, C.R. Change of waveform in bacterial flagella: the role of mechanics at the molecular level. J. Mol. Biol. 118, 457–479 (1978).

    CAS  Article  Google Scholar 

  17. Hyman, H.C. & Trachtenberg, S. Point mutations that lock Salmonella typhimurium flagellar filaments in the straight right-handed and left-handed forms and their relation to filament superhelicity. J. Mol. Biol. 220, 79–88 (1991).

    CAS  Article  Google Scholar 

  18. Kanto, S., Okino, H., Aizawa, S.-I. & Yamaguchi, S. Amino acids responsible for flagellar shape are distributed in terminal regions of flagellin. J. Mol. Biol. 219, 471–480 (1991).

    CAS  Article  Google Scholar 

  19. Kamiya, R., Asakura, S. & Yamaguchi, S. Formation of helical filaments by copolymerization of two types of 'straight' flagellins. Nature 286, 628–630 (1980).

    CAS  Article  Google Scholar 

  20. Mimori, Y. et al. The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J. Mol. Biol. 249, 69–87 (1995).

    CAS  Article  Google Scholar 

  21. Morgan, D.G., Owen, C., Melanson, L.A. & DeRosier, D.J. Structure of bacterial flagellar filaments at 11 Å resolution: packing of the α-helices. J. Mol. Biol. 249, 88–110 (1995).

    CAS  Article  Google Scholar 

  22. Mimori-Kiyosue, Y., Vonderviszt, F., Yamashita, I., Fujiyoshi, Y. & Namba, K. Direct interaction of flagellin termini essential for polymorphic ability of flagellar filament. Proc. Natl. Acad. Sci. USA 93, 15108–15113 (1996).

    CAS  Article  Google Scholar 

  23. Mimori-Kiyosue, Y., Vonderviszt, F. & Namba, K. Locations of terminal segments of flagellin in the filament structure and their roles in polymorphism and polymerization. J. Mol. Biol. 270, 222–237 (1997).

    CAS  Article  Google Scholar 

  24. Vonderviszt, F., Aizawa, S.-I. & Namba, K. Role of the disordered terminal regions of flagellin in filament formation and stability. J. Mol. Biol. 221, 1461–1474 (1991).

    CAS  Article  Google Scholar 

  25. Yamashita, I. et al. Structure and switching of bacterial flagellar filament studied by X-ray fiber diffraction. Nat. Struct. Biol. 5, 125–132 (1998).

    CAS  Article  Google Scholar 

  26. Hasegawa, K., Yamashita, I. & Namba, K. Quasi- and nonequivalence in the structure of bacterial flagellar filament. Biophys. J. 74, 569–575 (1998).

    CAS  Article  Google Scholar 

  27. Yonekura, K., Maki-Yonekura, S. & Namba, K. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643–650 (2003).

    CAS  Article  Google Scholar 

  28. Samatey, F.A. et al. Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410, 331–337 (2001).

    CAS  Article  Google Scholar 

  29. Kitao, A. et al. Switch interactions control energy frustration and multiple flagellar filament structures. Proc. Natl. Acad. Sci. USA 103, 4894–4899 (2006).

    CAS  Article  Google Scholar 

  30. Namba, K. & Vonderviszt, F. Molecular architecture of bacterial flagellum. Q. Rev. Biophys. 30, 1–65 (1997).

    CAS  Article  Google Scholar 

  31. Yonekura, K., Maki-Yonekura, S. & Namba, K. Building the atomic model for the bacterial flagellar filament by electron cryomicroscopy and image analysis. Structure 13, 407–412 (2005).

    CAS  Article  Google Scholar 

  32. Yonekura, K., Toyoshima, C., Maki-Yonekura, S. & Namba, K. GUI programs for processing individual images in early stages of helical image reconstruction—for high-resolution structure analysis. J. Struct. Biol. 144, 184–194 (2003).

    Article  Google Scholar 

  33. Yonekura, K. & Toyoshima, C. Structure determination of tubular crystals of membrane proteins. IV. Distortion correction and its combined application with real-space averaging and solvent flattening. Ultramicroscopy 107, 1141–1158 (2007).

    CAS  Article  Google Scholar 

  34. Yonekura, K. & Toyoshima, C. Structure determination of tubular crystals of membrane proteins. III. Solvent flattening. Ultramicroscopy 84, 29–45 (2000).

    CAS  Article  Google Scholar 

  35. Wakabayashi, T., Huxley, H.E., Amos, L.A. & Klug, A. Three-dimensional image reconstruction of actin-tropomyosin complex and actin-tropomyosin-troponin T-troponin I complex. J. Mol. Biol. 93, 477–497 (1975).

    CAS  Article  Google Scholar 

  36. Yonekura, K. & Toyoshima, C. Structure determination of tubular crystals of membrane proteins. II. Averaging of tubular crystals of different helical classes. Ultramicroscopy 84, 15–28 (2000).

    CAS  Article  Google Scholar 

  37. Jones, T.A., Zhou, J.Y., Cowan, S.W. & Kjeldgaard, M. 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 

  38. Wang, H. & Stubbs, G. Molecular dynamics in refinement against fiber diffraction data. Acta Crystallogr. A 49, 504–513 (1993).

    CAS  Article  Google Scholar 

  39. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemistry of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).

    CAS  Article  Google Scholar 

  40. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

  41. Merritt, E.A. & Bacon, D.J. Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505–524 (1997).

    CAS  Article  Google Scholar 

  42. Pettersen, E.F. et al. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank C. Toyoshima for part of the helical image reconstruction programs, D.A. Agard and J.W. Sedat for support to S.M.-Y. and K.Y. and F. Oosawa, S. Asakura and D.L.D. Caspar for continuous support and encouragement. This work was partly supported by funds from the W.M. Keck Advanced Microscopy Laboratory at the University of California, San Francisco, to K.Y. and by Grants-in-Aid for Scientific Research (16087207) 'National Project on Protein Structural and Functional Analyses' from the Ministry of Education, Science and Culture of Japan to K.N.

Author information

Authors and Affiliations

Authors

Contributions

S.M.-Y. prepared filament samples, collected electron cryomicroscopy images, analyzed images and carried out model building; K.Y. developed programs for graphical user interface, spline fitting and superimposition of the molecular models of the L- and R-type filaments; K.Y. also supervised all the computational analysis; S.M.-Y., K.Y. and K.N. wrote the paper.

Corresponding authors

Correspondence to Koji Yonekura or Keiichi Namba.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1 and 2, Supplementary Tables 1–3 (PDF 1614 kb)

Supplementary Movie 1

Transition between the L-type and R-type straight filaments in stereo (MOV 763 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Maki-Yonekura, S., Yonekura, K. & Namba, K. Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. Nat Struct Mol Biol 17, 417–422 (2010). https://doi.org/10.1038/nsmb.1774

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1774

Further reading

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