Structure of a bacterial type III secretion system in contact with a host membrane in situ
10.1038/ncomms10114
Crossref journal-article
Springer Science and Business Media LLC
Nature Communications (297)
Abstract

AbstractMany bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform–ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking ‘pump-action’ conformational changes that underpin effector injection.

Bibliography

Nans, A., Kudryashev, M., Saibil, H. R., & Hayward, R. D. (2015). Structure of a bacterial type III secretion system in contact with a host membrane in situ. Nature Communications, 6(1).

Authors 4
  1. Andrea Nans (first)
  2. Mikhail Kudryashev (additional)
  3. Helen R. Saibil (additional)
  4. Richard D. Hayward (additional)
References 55 Referenced 93
  1. Galán, J. E. & Wolf-Watz, H. Protein delivery into eukaryotic cells by type III secretion machines. Nature 444, 567–573 (2006). (10.1038/nature05272) / Nature by JE Galán (2006)
  2. Cornelis, G. R. The type III secretion injectisome. Nat. Rev. Microbiol. 4, 811–825 (2006). (10.1038/nrmicro1526) / Nat. Rev. Microbiol. by GR Cornelis (2006)
  3. Hodgkinson, J. L. et al. C12 symmetrized 3D reconstruction of the Shigella flexneri T3SS needle complex from negatively stained sample electron micrographs. Nat. Struct. Mol. Biol. 16, 477–485 (2009). (10.1038/nsmb.1599) / Nat. Struct. Mol. Biol. by JL Hodgkinson (2009)
  4. Schraidt, O. & Marlovits, T. C. Three-dimensional model of Salmonella’s needle complex and subnanometer resolution. Science 331, 1192–1195 (2011). (10.1126/science.1199358) / Science by O Schraidt (2011)
  5. Radics, J., Königsmaier, L. & Marlovits, T. C. Structure of a pathogenic type 3 secretion system in action. Nat. Struct. Mol. Biol. 1, 82–87 (2014). (10.1038/nsmb.2722) / Nat. Struct. Mol. Biol. by J Radics (2014)
  6. Mueller, C. A. et al. The V-antigen of Yersinia forms a distinct structure at the tip of injectisome needles. Science 310, 674–676 (2005). (10.1126/science.1118476) / Science by CA Mueller (2005)
  7. Yip, C. K. et al. Structural characterization of the molecular platform for type III secretion system assembly. Nature 435, 702–707 (2005). (10.1038/nature03554) / Nature by CK Yip (2005)
  8. Spreter, T. et al. A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system. Nat. Struct. Mol. Biol. 16, 468–476 (2009). (10.1038/nsmb.1603) / Nat. Struct. Mol. Biol. by T Spreter (2009)
  9. Bergeron, J. R. C. et al. A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. PLoS Pathog. 9, e1003307 (2013). (10.1371/journal.ppat.1003307) / PLoS Pathog. by JRC Bergeron (2013)
  10. Abrusci, P. et al. Architecture of the major component of the type III secretion system export apparatus. Nat. Struct. Mol. Biol. 20, 99–104 (2013). (10.1038/nsmb.2452) / Nat. Struct. Mol. Biol. by P Abrusci (2013)
  11. Loquet, A. et al. Atomic model of the type III secretion system needle. Nature 486, 276–279 (2012). (10.1038/nature11079) / Nature by A Loquet (2012)
  12. Hu, B. et al. Visualization of the type III secretion sorting platform of Shigella flexneri. Proc. Natl Acad. Sci. USA 112, 1047–1052 (2015). (10.1073/pnas.1411610112) / Proc. Natl Acad. Sci. USA by B Hu (2015)
  13. Akeda, Y. & Galán, J. E. Chaperone release and unfolding of substrates in type III secretion. Nature 437, 911–915 (2005). (10.1038/nature03992) / Nature by Y Akeda (2005)
  14. Cocchiaro, J. L. & Valdivia, R. H. New insights into Chlamydia intracellular survival mechanisms. Cell. Microbiol. 11, 1571–1578 (2009). (10.1111/j.1462-5822.2009.01364.x) / Cell. Microbiol. by JL Cocchiaro (2009)
  15. Abby, S. S. & Rocha, E. P. C. The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems. PLoS Genet. 8, e1002983 (2012). (10.1371/journal.pgen.1002983) / PLoS Genet. by SS Abby (2012)
  16. Kim, J. F. Revisiting the chlamydial type III protein secretion system: clues to the origin of type III protein secretion. Trends Genet. 17, 65–69 (2001). (10.1016/S0168-9525(00)02175-2) / Trends Genet. by JF Kim (2001)
  17. Betts-Hampikian, H. J. & Fields, K. A. The chlamydial type III secretion mechanism: revealing cracks in a tough nut. Front. Microbiol. 1, 114 (2010). (10.3389/fmicb.2010.00114) / Front. Microbiol. by HJ Betts-Hampikian (2010)
  18. Nans, A., Saibil, H. R. & Hayward, R. D. Pathogen-host reorganization during Chlamydia invasion revealed by cryo-electron tomography. Cell. Microbiol. 16, 1457–1472 (2014). (10.1111/cmi.12310) / Cell. Microbiol. by A Nans (2014)
  19. Dubrovsky, A., Sorrentino, S., Harapin, J., Sapra, K. T. & Medalia, O. Developments in cryo-electron tomography for in situ structural analysis. Arch. Biochem. Biophys. 581, 78–85 (2015). (10.1016/j.abb.2015.04.006) / Arch. Biochem. Biophys. by A Dubrovsky (2015)
  20. Kudryashev, M. et al. In situ structural analysis of the Yersinia enterocolitica injectisome. eLife 2, e00792 (2013). (10.7554/eLife.00792) / eLife by M Kudryashev (2013)
  21. Kawamoto, A. et al. Common and distinct structural features of Salmonella injectisome and flagellar basal body. Sci. Rep. 3, 3369 (2013). (10.1038/srep03369) / Sci. Rep. by A Kawamoto (2013)
  22. Tosi, T. et al. Structural similarity of secretins from type II and type III secretion systems. Structure 22, 1348–1355 (2014). (10.1016/j.str.2014.07.005) / Structure by T Tosi (2014)
  23. Marlovits, T. C. et al. Assembly of the inner rod determines needle length in the type III secretion injectisome. Nature 441, 637–640 (2006). (10.1038/nature04822) / Nature by TC Marlovits (2006)
  24. Liechti, G. W. et al. A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis. Nature 506, 507–510 (2014). (10.1038/nature12892) / Nature by GW Liechti (2014)
  25. Kosma, P. Chlamydial lipopolysaccharide. Biochim Biophys Acta 1455, 387–402 (1999). (10.1016/S0925-4439(99)00061-7) / Biochim Biophys Acta by P Kosma (1999)
  26. Rund, S., Lindner, B., Brade, H. & Holst, O. Structural analysis of the lipopolysaccharide from Chlamydia trachomatis serotype L2. J. Biol. Chem. 274, 16819–16824 (1999). (10.1074/jbc.274.24.16819) / J. Biol. Chem. by S Rund (1999)
  27. Journet, L., Agrain, C., Broz, P. & Cornelis, G. R. The needle length of bacterial injectisomes is determined by a molecular ruler. Science 302, 1757–1760 (2003). (10.1126/science.1091422) / Science by L Journet (2003)
  28. Kudryashev, M. et al. Yersinia entercolitica type III secretion injectisomes form regularly spaced clusters, which incorporate new machines upon activation. Mol. Microbiol. 95, 875–884 (2015). (10.1111/mmi.12908) / Mol. Microbiol. by M Kudryashev (2015)
  29. Kowal, J. et al. Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core. Structure 21, 2152–2161 (2013). (10.1016/j.str.2013.09.012) / Structure by J Kowal (2013)
  30. Fields, K. A., Fischer, E. R., Mead, D. J. & Hackstadt, T. Analysis of putative Chlamydia trachomatis chaperones Scc2 and Scc3 and their use in the identification of type III secretion substrates. J. Bacteriol. 187, 6466–6478 (2005). (10.1128/JB.187.18.6466-6478.2005) / J. Bacteriol. by KA Fields (2005)
  31. Spaeth, K. E., Chen, Y. S. & Valdivia, R. H. The Chlamydia type III secretion system C-ring engages a chaperone-effector protein complex. PLoS Pathog. 5, e1000579 (2009). (10.1371/journal.ppat.1000579) / PLoS Pathog. by KE Spaeth (2009)
  32. Chellas-Gery, B., Wolf, K., Tisoncik, J., Hackstadt, T. & Fields, K. A. Biochemical and localization analyses of putative type III secretion translocator protein CopB and CopB2 of Chlamydia trachomatis reveal significant distinctions. Infect. Immun. 79, 3036–3045 (2011). (10.1128/IAI.00159-11) / Infect. Immun. by B Chellas-Gery (2011)
  33. Ménard, R., Sansonetti, P. J. & Parsot, C. The secretion of the Shigella flexneri Ipa invasins is induced by the epithelial cell and controlled by IpaB and IpaD. EMBO J. 13, 5293–5302 (1994). (10.1002/j.1460-2075.1994.tb06863.x) / EMBO J. by R Ménard (1994)
  34. Zierler, M. K. & Galán, J. E. Contact with cultured epithelial cells stimulates secretion of Salmonella typhimurium invasion protein InvJ. Infect. Immun. 63, 4024–4028 (1995). (10.1128/iai.63.10.4024-4028.1995) / Infect. Immun. by MK Zierler (1995)
  35. Montagner, C., Arquint, C. & Cornelis, G. R. Translocators YopB and YoD from Yersinia enterocolitica form a multimeric integral membrane complex in eukaryotic cell membranes. J. Bacteriol. 193, 6923–6928 (2011). (10.1128/JB.05555-11) / J. Bacteriol. by C Montagner (2011)
  36. Deane, J. E. et al. Molecular model of a type III secretion system needle: Implications for host-cell sensing. Proc. Natl Acad. Sci. USA. 103, 12529–12533 (2006). (10.1073/pnas.0602689103) / Proc. Natl Acad. Sci. USA. by JE Deane (2006)
  37. Veenendaal, A. et al. The type III secretion system needle tip complex mediates host cell sensing and translocon insertion. Mol. Microbiol. 63, 1719–1730 (2007). (10.1111/j.1365-2958.2007.05620.x) / Mol. Microbiol. by A Veenendaal (2007)
  38. Harmon, D., Murphy, J., Davis, A. & Mecsas, J. A mutant with aberrant extracellular LcrV-YscF interactions fails to form pores and translocate Yop effector proteins but still retains the ability to trigger Yop secretion in response to cell contact. J. Bacteriol. 195, 2244–2254 (2013). (10.1128/JB.02011-12) / J. Bacteriol. by D Harmon (2013)
  39. Epier, C., Dickenson, N., Bullitt, E. & Picking, W. Ultrastructural analysis of IpaDa at the tip of the nascent MxiH type III secretion apparatus of Shigella flexneri. J. Mol. Biol. 420, 29–39 (2012). (10.1016/j.jmb.2012.03.025) / J. Mol. Biol. by C Epier (2012)
  40. Chatterjee, S. et al. The crystal structure of the Salmonella type III secretion system tip protein SipD in complex with deoxycholate and chenodeoxycholate. Protein Sci. 20, 75–86 (2011). (10.1002/pro.537) / Protein Sci. by S Chatterjee (2011)
  41. Lara-Tejero, M., Kato, J., Wagner, S., Liu, X. & Galán, J. E. A sorting platform determines the order of protein secretion in bacterial type III systems. Science 331, 1188–1191 (2011). (10.1126/science.1201476) / Science by M Lara-Tejero (2011)
  42. Jamison, W. P. & Hackstadt, T. Induction of type III secretion by cell-free Chlamydia trachomatis elementary bodies. Microb. Pathog. 45, 435–440 (2008). (10.1016/j.micpath.2008.10.002) / Microb. Pathog. by WP Jamison (2008)
  43. Diepold, A., Kudryashev, M., Delalez, N. J., Berry, R. M. & Armitage, J. P. Composition, formation, and regulation of the cytosolic c-ring, a dynamic component of the type III secretion injectisome. PLoS Biol. 13, e1002039 (2015). (10.1371/journal.pbio.1002039) / PLoS Biol. by A Diepold (2015)
  44. Chevance, F. F. V. & Hughes, K. T. Coordinating assembly of a bacterial macromolecular machine. Nat. Rev. Microbiol. 6, 455–465 (2008). (10.1038/nrmicro1887) / Nat. Rev. Microbiol. by FFV Chevance (2008)
  45. Wang, Y. et al. Development of a transformation system for Chlamydia trachomatis: restoration of glycogen biosynthesis by acquisition of a plasmid shuttle vector. PLoS Pathog. 7, e1002258 (2011). (10.1371/journal.ppat.1002258) / PLoS Pathog. by Y Wang (2011)
  46. Wickstrum, J., Sammons, L. R., Restivo, K. N. & Hefty, P. S. Conditional gene expression in Chlamydia trachomatis using the tet system. PLoS ONE 8, e76743 (2013). (10.1371/journal.pone.0076743) / PLoS ONE by J Wickstrum (2013)
  47. Scidmore, M. A. Cultivation and laboratory maintenance of Chlamydia trachomatis. Curr. Protoc. Microbiol Chapter 11, Unit 11A.1 (2005). (10.1002/9780471729259.mc11a01s00)
  48. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). (10.1016/j.jsb.2005.07.007) / J. Struct. Biol. by DN Mastronarde (2005)
  49. Kremer, J. R., Mastronarde, D. N. & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71–76 (1996). (10.1006/jsbi.1996.0013) / J. Struct. Biol. by JR Kremer (1996)
  50. Xiong, Q., Morphew, M. K., Schwartz, C. L., Hoenger, A. H. & Mastronarde, D. N. CTF determination and correction for low dose tomographic tilt series. J. Struct. Biol. 168, 378–387 (2009). (10.1016/j.jsb.2009.08.016) / J. Struct. Biol. by Q Xiong (2009)
  51. Frangakis, A. S. & Hegerl, R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J. Struct. Biol. 135, 239–250 (2001). (10.1006/jsbi.2001.4406) / J. Struct. Biol. by AS Frangakis (2001)
  52. Castaño-Díez, D., Kudryashev, M., Arheit, M. & Stahlberg, H. Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments. J. Struct. Biol. 178, 139–151 (2012). (10.1016/j.jsb.2011.12.017) / J. Struct. Biol. by D Castaño-Díez (2012)
  53. Martinez-Sanchez, A., Garcia, I. & Fernandez, J.–J. A differential structure approach to membrane-segmentation in electron tomography. J. Struct. Biol. 175, 372–383 (2011). (10.1016/j.jsb.2011.05.010) / J. Struct. Biol. by A Martinez-Sanchez (2011)
  54. Pruggnaller, S., Mayr, M. & Frangakis, A. S. A visualization and segmentation toolbox for electron microscopy. J. Struct. Biol. 164, 161–165 (2008). (10.1016/j.jsb.2008.05.003) / J. Struct. Biol. by S Pruggnaller (2008)
  55. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011). (10.1038/msb.2011.75) / Mol. Syst. Biol. by F Sievers (2011)
Dates
Type When
Created 9 years, 8 months ago (Dec. 11, 2015, 6:28 a.m.)
Deposited 2 years, 7 months ago (Jan. 5, 2023, 7:34 a.m.)
Indexed 4 weeks, 1 day ago (July 22, 2025, 6:40 a.m.)
Issued 9 years, 8 months ago (Dec. 11, 2015)
Published 9 years, 8 months ago (Dec. 11, 2015)
Published Online 9 years, 8 months ago (Dec. 11, 2015)
Funders 0

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@article{Nans_2015, title={Structure of a bacterial type III secretion system in contact with a host membrane in situ}, volume={6}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms10114}, DOI={10.1038/ncomms10114}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Nans, Andrea and Kudryashev, Mikhail and Saibil, Helen R. and Hayward, Richard D.}, year={2015}, month=dec }