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.

  • Letter
  • Published:

The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device

Nature volume 501, pages 547–550 (2013)Cite this article

Subjects

Abstract

The ABC toxin complexes produced by certain bacteria are of interest owing to their potent insecticidal activity1,2 and potential role in human disease3. These complexes comprise at least three proteins (A, B and C), which must assemble to be fully toxic4. The carboxy-terminal region of the C protein is the main cytotoxic component5, and is poorly conserved between different toxin complexes. A general model of action has been proposed, in which the toxin complex binds to the cell surface via the A protein, is endocytosed, and subsequently forms a pH-triggered channel, allowing the translocation of C into the cytoplasm, where it can cause cytoskeletal disruption in both insect and mammalian cells5. Toxin complexes have been visualized using single-particle electron microscopy6,7, but no high-resolution structures of the components are available, and the role of the B protein in the mechanism of toxicity remains unknown. Here we report the three-dimensional structure of the complex formed between the B and C proteins, determined to 2.5 Å by X-ray crystallography. These proteins assemble to form an unprecedented, large hollow structure that encapsulates and sequesters the cytotoxic, C-terminal region of the C protein like the shell of an egg. The shell is decorated on one end by a β-propeller domain, which mediates attachment of the B–C heterodimer to the A protein in the native complex. The structure reveals how C auto-proteolyses when folded in complex with B. The C protein is the first example, to our knowledge, of a structure that contains rearrangement hotspot (RHS) repeats8, and illustrates a marked structural architecture that is probably conserved across both this widely distributed bacterial protein family and the related eukaryotic tyrosine-aspartate (YD)-repeat-containing protein family, which includes the teneurins9. The structure provides the first clues about the function of these protein repeat families, and suggests a generic mechanism for protein encapsulation and delivery.

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: Structure of the B–CNTR complex.
Figure 2: Auto-proteolysis of the C protein.
Figure 3: RHS repeat structure.
Figure 4: Position of the B–CNTR complex in the complete Yen-Tc particle.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

Data deposits

The atomic coordinates of the B–CNTR complex and the Chi2 chitinase have been deposited in the Protein Data Bank (http://www.pdb.org) under the accession codes 4IGL and 4DWS, respectively.

References

  1. Bowen, D. et al. Insecticidal toxins from the bacterium Photorhabdus luminescens. Science 280, 2129–2132 (1998)

    Article  CAS  ADS  PubMed  Google Scholar 

  2. ffrench-Constant, R. H. & Waterfield, N. R. Ground control for insect pests. Nature Biotechnol. 24, 660–661 (2006)

    Article  CAS  Google Scholar 

  3. Pinheiro, V. B. & Ellar, D. J. Expression and insecticidal activity of Yersinia pseudotuberculosis and Photorhabdus luminescens toxin complex proteins. Cell. Microbiol. 9, 2372–2380 (2007)

    Article  CAS  PubMed  Google Scholar 

  4. Waterfield, N., Hares, M., Yang, G., Dowling, A. & ffrench-Constant, R. Potentiation and cellular phenotypes of the insecticidal toxin complexes of Photorhabdus bacteria. Cell. Microbiol. 7, 373–382 (2005)

    Article  CAS  PubMed  Google Scholar 

  5. Lang, A. E. et al. Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering. Science 327, 1139–1142 (2010)

    Article  CAS  ADS  PubMed  Google Scholar 

  6. Landsberg, M. J. et al. 3D structure of the Yersinia entomophaga toxin complex and implications for insecticidal activity. Proc. Natl Acad. Sci. USA 108, 20544–20549 (2011)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  7. Gatsogiannis, C. et al. A syringe-like injection mechanism in Photorhabdus luminescens toxins. Nature 495, 520–523 (2013)

    Article  CAS  ADS  PubMed  Google Scholar 

  8. Hill, C. W., Sandt, C. H. & Vlazny, D. A. Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein. Mol. Microbiol. 12, 865–871 (1994)

    Article  CAS  PubMed  Google Scholar 

  9. Minet, A. D., Rubin, B. P., Tucker, R. P., Baumgartner, S. & Chiquet-Ehrismann, R. Teneurin-1, a vertebrate homologue of the Drosophila pair-rule gene ten-m, is a neuronal protein with a novel type of heparin-binding domain. J. Cell Sci. 112, 2019–2032 (1999)

    CAS  PubMed  Google Scholar 

  10. Hurst, M. R. H. et al. The main virulence determinant of Yersinia entomophaga MH96 is a broad-host-range toxin complex active against insects. J. Bacteriol. 193, 1966–1980 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Zhang, D., de Souza, R. F., Anantharaman, V., Iyer, L. M. & Aravind, L. Polymorphic toxin systems: comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol. Direct 7, 18 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Buetow, L., Flatau, G., Chiu, K., Boquet, P. & Ghosh, P. Structure of the Rho-activating domain of Escherichia coli cytotoxic necrotizing factor 1. Nature Struct. Biol. 8, 584–588 (2001)

    Article  CAS  PubMed  Google Scholar 

  13. Iyer, L. M., Zhang, D., Rogozin, I. B. & Aravind, L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acids Res. 39, 9473–9497 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Jackson, A. P., Thomas, G. H., Parkhill, J. & Thomson, N. R. Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement. BMC Genomics 10, 584 (2009)

    Article  PubMed  PubMed Central  Google Scholar 

  15. Wang, Y. D., Zhao, S. & Hill, C. W. Rhs elements comprise three subfamilies which diverged prior to acquisition by Escherichia coli. J. Bacteriol. 180, 4102–4110 (1998)

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Mosca, T. J., Hong, W., Dani, V. S., Favaloro, V. & Luo, L. Trans-synaptic Teneurin signalling in neuromuscular synapse organization and target choice. Nature 484, 237–241 (2012)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  17. Hong, W., Mosca, T. J. & Luo, L. Teneurins instruct synaptic partner matching in an olfactory map. Nature 484, 201–207 (2012)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  18. Feng, K. et al. All four members of the Ten-m/Odz family of transmembrane proteins form dimers. J. Biol. Chem. 277, 26128–26135 (2002)

    Article  CAS  PubMed  Google Scholar 

  19. Chand, D. et al. C-terminal processing of the teneurin proteins: Independent actions of a teneurin C-terminal associated peptide in hippocampal cells. Mol. Cell. Neurosci. 52, 38–50 (2013)

    Article  CAS  PubMed  Google Scholar 

  20. Tucker, R. P. & Chiquet-Ehrismann, R. Teneurins: a conserved family of transmembrane proteins involved in intercellular signaling during development. Dev. Biol. 290, 237–245 (2006)

    Article  CAS  PubMed  Google Scholar 

  21. Busby, J. N. et al. Structural analysis of Chi1 chitinase from Yen-Tc: the multisubunit insecticidal ABC toxin complex of Yersinia entomophaga. J. Mol. Biol. 415, 359–371 (2012)

    Article  CAS  PubMed  Google Scholar 

  22. Xu, Z., Horwich, A. L. & Sigler, P. B. The crystal structure of the asymmetric GroEL–GroES–(ADP)7 chaperonin complex. Nature 388, 741–750 (1997)

    Article  CAS  ADS  PubMed  Google Scholar 

  23. McPhillips, T. M. et al. Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J. Synchrotron Radiat. 9, 401–406 (2002)

    Article  CAS  PubMed  Google Scholar 

  24. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. The. CCP4 suite. Programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  26. Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Crystallogr. D 61, 449–457 (2005)

    Article  PubMed  Google Scholar 

  27. Panjikar, S., Parthasarathy, V., Lamzin, V. S., Weiss, M. S. & Tucker, P. A. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination. Acta Crystallogr. D 65, 1089–1097 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  30. Orthaber, D., Bergmann, A. & Glatter, O. SAXS experiments on absolute scale with Kratky systems using water as a secondary standard. J. Appl. Crystallogr. 33, 218–225 (2000)

    Article  CAS  Google Scholar 

  31. Franke, D. & Svergun, D. I. DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering. J. Appl. Crystallogr. 42, 342–346 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Volkov, V. V. & Svergun, D. I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36, 860–864 (2003)

    Article  CAS  Google Scholar 

  33. Svergun, D. I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76, 2879–2886 (1999)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  34. Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768–773 (1995)

    Article  CAS  Google Scholar 

  35. Scheres, S. H. W., Nuñez-Ramirez, R., Sorzano, C. O. S., Carazo, J. M. & Marabini, R. Image processing for electron microscopy single-particle analysis using Xmipp. Nature Protocols 3, 977–990 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We are grateful to M. Sullivan, R. Kingston, T. Baker and many other members of the Structural Biology section at the University of Auckland for discussions, to V. Arcus for initial enthusiasm, and to B. Hankamer for provision of laboratory space at the University of Queensland and for mentorship. This work was supported by the New Zealand Foundation for Research, Science and Technology contract C10X0804, awarded to M.R.H.H. We would like to thank all beamline staff at the MX1, MX2 and SAXS/WAXS beamlines at the Australian Synchrotron for their support, and to the New Zealand Synchrotron Group Ltd for synchrotron access arrangements.

Author information

Authors and Affiliations

  1. AgResearch Structural Biology Laboratory, School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand,

    Jason N. Busby & J. Shaun Lott

  2. Australian Synchrotron, 800 Blackburn Road, Clayton, 3168, Victoria, Australia

    Santosh Panjikar

  3. Department of Biochemistry and Molecular Biology, Monash University, 3800, Victoria, Australia

    Santosh Panjikar

  4. Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, Queensland, Australia

    Michael J. Landsberg

  5. Innovative Farming Systems, AgResearch, Lincoln Research Centre, Christchurch 8140, New Zealand,

    Mark R. H. Hurst

Authors
  1. Jason N. Busby
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Santosh Panjikar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael J. Landsberg
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mark R. H. Hurst
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Shaun Lott
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.N.B. cloned constructs, expressed, purified and crystallized proteins, collected and processed X-ray crystallography and SAXS data, and refined and analysed the protein structure; S.P. determined the protein structure; M.J.L. processed, refined and analysed negative-stain electron microscopy data; M.R.H.H. and J.S.L. designed the study; J.N.B. and J.S.L. wrote the paper and all authors discussed the results and contributed to the manuscript.

Corresponding authors

Correspondence to Mark R. H. Hurst or J. Shaun Lott.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-5, Supplementary Figures 1-12 and additional references. (PDF 5176 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Busby, J., Panjikar, S., Landsberg, M. et al. The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device. Nature 501, 547–550 (2013). https://doi.org/10.1038/nature12465

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature12465

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

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