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Biogenesis and structure of a type VI secretion baseplate

Nature Microbiology volume 3, pages 1404–1416 (2018)Cite this article

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Abstract

To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates.

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Fig. 1: Composition of the T6SS wedges complex.
Fig. 2: Cryo-EM density map of the TssKFGE wedge complex.
Fig. 3: Structure of the TssKFGE complex.
Fig. 4: Structural model of the EAEC T6SS baseplate.
Fig. 5: Comparison between the T4 bacteriophage and T6SS baseplates.
Fig. 6: Schematic representation of the T6SS assembly pathway.

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Data availability

The cryo-EM structures of the full complex TssKFG, TssK and TssFGE have been deposited in the Electron Microscopy Data Bank under ID codes EMD-0008, EMD-0010 and EMD-0009. The TssKFG, TssK and TssFGE models have been deposited in the PDB under ID codes PDB 6GIY, 6GJ3 and 6GJ1. Raw cryo-EM data are available on request.

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Acknowledgements

We thank members of the E.C. and R.F. research groups, and J. Sturgis for helpful discussions and support, M. Weigt and C. Feinauer for useful discussion on evolutionary covariance, T. Huynh and G. Canet for assistance with the computer clusters at the Institut Pasteur and Institut Européen de Chimie et Biologie (IECB), respectively, A. Kosta (Plateforme de microscopie, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France) for providing access to the IMM EM facility and for checking the quality of samples by negative stain EM, A. Bezault for support at the cryo-EM facility at IECB and T. Doan and L. Espinosa for their helpful support with the fluorescence microscopy device and analysis. We thank M. Nilges (Institut Pasteur) for access to the computer cluster of the ERC project 'BayCellS'. This work was supported by the CNRS, the Aix-Marseille Université, the Institut Pasteur and the INSERM, and by grants from the Agence Nationale de la Recherche (grants no. ANR-14-CE14-0006 and ANR-17-CE11-0039 to E.C., and no. ANR-11-EQPX-008 to J.C.R.). Work of Y.C. was supported by an 'Ecole Doctorale' PhD fellowship from the 'Fondation pour la Recherche Médicale' (grant no. FRM-ECO20160736014). R.F. and C.R. were supported by IDEX Bordeaux through a 'chaire d’excellence' to R.F. We acknowledge the European Synchrotron Radiation Facility for provision of beamtime on CM01 and thank G. Effantin and E. Kandiah for assistance. F.A. thanks the French Institute of Bioinformatics (IFB; grant no. ANR-11-INBS-0013) for financial support.

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  1. These authors contributed equally: Yassine Cherrak, Chiara Rapisarda.

Authors and Affiliations

  1. Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, UMR7255, Aix-Marseille Université – CNRS, Marseille, France

    Yassine Cherrak, Eric Cascales & Eric Durand

  2. Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France

    Chiara Rapisarda & Rémi Fronzes

  3. CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Paris, France

    Chiara Rapisarda & Rémi Fronzes

  4. Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756, Paris, France

    Riccardo Pellarin, Guillaume Bouvier, Benjamin Bardiaux & Fabrice Allain

  5. USR 2000, CNRS, Institut Pasteur, Paris, France

    Christian Malosse, Martial Rey & Julia Chamot-Rooke

  6. Mass Spectrometry for Biology Unit, Institut Pasteur, Paris, France

    Christian Malosse, Martial Rey & Julia Chamot-Rooke

  7. Laboratoire d’Ingénierie des Systèmes Macromoléculaires , Institut de Microbiologie de la Méditerranée, UMR7255, INSERM, Marseille, France

    Eric Durand

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Contributions

E.D., R.F. and E.C. designed the research, assembled results and wrote the paper with input from all authors. E.D. and Y.C. performed the biochemical experiments and the initial negative stain EM observations. C.R. performed the sample preparation for cryo-EM, de novo reconstruction and structure refinement. C.R. and R.F. analysed the cryo-EM data and the final structure. C.M. and M.R. performed the mass spectrometry experiments. Y.C. performed all in vivo experiments. R.P. and G.B. carried out the method development and structural modelling. B.B. and F.A. carried out the structural modelling. J.C.R. performed the design and analysis of the mass spectrometry experiments.

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Cherrak, Y., Rapisarda, C., Pellarin, R. et al. Biogenesis and structure of a type VI secretion baseplate. Nat Microbiol 3, 1404–1416 (2018). https://doi.org/10.1038/s41564-018-0260-1

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