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Type 9 secretion system structures reveal a new protein transport mechanism

Nature volume 564, pages 77–82 (2018)Cite this article

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Abstract

The type 9 secretion system (T9SS) is the protein export pathway of bacteria of the Gram-negative Fibrobacteres–Chlorobi–Bacteroidetes superphylum and is an essential determinant of pathogenicity in severe periodontal disease. The central element of the T9SS is a so-far uncharacterized protein-conducting translocon located in the bacterial outer membrane. Here, using cryo-electron microscopy, we provide structural evidence that the translocon is the T9SS protein SprA. SprA forms an extremely large (36-strand) single polypeptide transmembrane β-barrel. The barrel pore is capped on the extracellular end, but has a lateral opening to the external membrane surface. Structures of SprA bound to different components of the T9SS show that partner proteins control access to the lateral opening and to the periplasmic end of the pore. Our results identify a protein transporter with a distinctive architecture that uses an alternating access mechanism in which the two ends of the protein-conducting channel are open at different times.

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Fig. 1: Characterization of SprA.
Fig. 2: Structural features of SprA extracellular domains.
Fig. 3: Structural analysis of the SprA translocon complexes.
Fig. 4: Biological consequences of removing SprA partner proteins.

Data availability

The cryo-EM volumes have been deposited in the Electron Microscopy Data Bank under accession codes EMD-0133 and EMD-0134, and the coordinates have been deposited in the Protein Data Bank under accession numbers 6h3i and 6h3j. Source Data for Figs. 1d and 4a, b are available with the online version of the paper.

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Acknowledgements

We thank M. McBride and Y. Zhu for providing reagents for the genetic manipulation of F. johnsoniae; A. Shrivastava and H. Berg for advice on measuring gliding motility; L. Lavis for supplying the Janelia Fluor 646 HaloTag ligand; S. Hickman for advice on fluorescence imaging; and O. Meacock and K. Foster for providing additional imaging facilities. We acknowledge the use of Central Oxford Structural Microscopy and Imaging Centre (COSMIC), the Oxford Micron Advanced Imaging Facility, and the Oxford Advanced Proteomics Facility. This work was supported by Wellcome Trust Investigator Awards 107929/Z/15/Z and 100298/Z/12/Z. COSMIC was supported by a Wellcome Trust Collaborative Award 201536/Z/16/Z, the Wolfson Foundation, a Royal Society Wolfson Refurbishment Grant, the John Fell Fund, and the EPA and Cephalosporin Trusts.

Reviewer information

Nature thanks M. McBride and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Author notes

  1. These authors contributed equally: Frédéric Lauber, Justin C. Deme

Authors and Affiliations

  1. Department of Biochemistry, University of Oxford, Oxford, UK

    Frédéric Lauber & Ben C. Berks

  2. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK

    Justin C. Deme & Susan M. Lea

  3. The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK

    Justin C. Deme & Susan M. Lea

Authors
  1. Frédéric Lauber
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Contributions

F.L. carried out all genetic and biochemical work. J.C.D. collected EM data. J.C.D. and S.M.L. determined the structure. B.C.B. conceived the project. All authors interpreted data and wrote the manuscript.

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Correspondence to Susan M. Lea or Ben C. Berks.

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Extended data figures and tables

Extended Data Fig. 1 Phenotypic analysis of strains expressing HaloTag and Twin-Strep SprA fusion proteins.

a, b, Immunoblot analysis of HaloTag-SprA (a) and Twin-Strep-SprA (b) expression in whole-cell lysates. Similar data were obtained for three biological repeats. c, Immunoblot detection of levels of the T9SS-dependent chitinase ChiA in culture supernatants. Similar data were obtained for three biological repeats. d, T9SS-dependent spreading (gliding) morphology of colonies on agar. Scale bar, 5 mm. Similar data were obtained for three biological repeats. e, Peptide mass spectrometry of the three highest molecular mass bands in Fig. 1d. Intensity values are normalized to the most abundant SprA peptide detected for each band. Peptide numbering is from the N terminus of the native SprA precursor sequence. For immunoblot source data, see Supplementary Fig. 1.

Extended Data Fig. 2 Experimental quality and resolution estimation of SprA complexes.

a, Representative micrograph of SprA complexes. b, Selected reference-free 2D class averages. c, Gold-standard FSC curves of the final map calculated using a soft-edged mask. d, Local resolution estimates of the final maps. e, Representative density for SprA in the PorV complex (left) and Plug complex (right).

Extended Data Fig. 3 Structural analysis of the SprA complex components.

a, Structural alignment of SprA-bound proteins against the homology models used in initial sequence docking. b, Access routes to the SprA pore viewed from the periplasm (top) or towards the lateral opening (bottom). In the PorV complex two loops involved in coordinating PorV occlude the lateral opening. The step domain is poorly ordered in the Plug complex. For clarity, PorV, Plug, and PPI are not shown. c, The PorV barrel is tilted relative to the SprA barrel. Aromatic residues on the surface of PorV are shown in green spacefill.

Extended Data Fig. 4 Phenotypes of SprA partner deletion strains.

a, Immunoblot analysis of Twin-Strep–SprA levels in whole-cell lysates. Similar data were obtained for three biological repeats. For immunoblot source data, see Supplementary Fig. 1. b, Quantification by liquid chromatography–mass spectrometry of T9SS substrates detected in cell culture supernatants according to CTD type. A detection threshold of more than 1% of the protein abundance in the sprA+ parental strain was applied. c, d, Heat map representations of secreted T9SS substrates from b with type A CTDs (c) or type B CTDs (d). Protein intensities for each protein are normalized to the level detected in the sprA+ parental strain. e, Measurement of vancomycin inhibition zones in a disc diffusion assay. The mean radius of inhibition (red bar) was measured from the disc edge. Error bars represent s.d. (n = 4 for ΔporV and Δplug; n = 5 for other strains) and statistical significance is shown above each measurement set from a one-way ANOVA with post-hoc Dunnett’s test using sprA+ as control group (NS, not significant; ****P < 0.0001). Other comparisons (bracketed) use two-tailed unpaired t-tests; *P = 0.0134, ****P < 0.0001). A control for the DMSO solvent used to dissolve the vancomycin is shown. a–e, All sprA+ strains express the Twin-Strep–SprA fusion protein.

Extended Data Fig. 5 Single-particle cryo-EM image processing workflow for the SprA complexes.

Cryo-EM data sets for SprA complexes in LMNG, in the presence or absence of fluorinated detergents, were combined following 2D classification and subjected to 3D classification against a low-resolution model generated from the fluorinated octyl-maltoside data set. Particle images corresponding to the PorV complex or the Plug complex were then independently refined. A soft mask, generated from these maps, was then used to perform masked refinement against the same particle images, resulting in global map resolutions of 3.5 Å for the PorV complex and 3.7 Å for the Plug complex.

Extended Data Table 1 Cryo-EM data collection, refinement and validation statistics
Full size table
Extended Data Table 2 Bacterial strains and plasmids used in this study
Full size table

Supplementary information

Supplementary Information

This file contains Supplementary Figure 1, which contains the uncropped gel and immunoblot images and Supplementary Table 1, a list of oligonucleotides used in this study

Reporting Summary

Video 1

Movement of F. johnsoniae cells on glass. F. johnsoniae cells are imaged in real time at 25 °C in tunnel slides containing Motility Medium. The wild-type strain and twinstrep-sprA, halotag-sprA, plug, and ppi mutants display rapid gliding motility. Few sprA or porV cells attach to glass and those that do display limited (sprA) or normal (porV) motility, in agreement with published studies. Scale bar: 5μm. For each strain a representative result is shown. The experiments were each repeated on three independent biological samples with similar results.

Video 2

Live cell fluorescence imaging of HaloTag-SprA. F. johnsoniae cells are imaged in HiLo mode in real time at 25 °C in either tunnel slides containing PY2 medium (for mobile cells) or on agar pads containing PY2 medium (for stationary cells). Scale bar: 5μm Representative results are shown. The experiments were repeated on two independent biological samples with similar results.

Video 3

Architecture of the PorV complex. SprA, blue; PorV, grey; PPI, pink.

Video 4

Architecture of the Plug complex. SprA, blue; Plug, orange; PPI, pink.

Video 5

Changes in SprA conformation between the PorV and Plug complexes. The structures are initially viewed from the periplasmic side of SprA and then from the extracellular side. SprA in chainbows; PorV, Plug, PPI, grey.

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Lauber, F., Deme, J.C., Lea, S.M. et al. Type 9 secretion system structures reveal a new protein transport mechanism. Nature 564, 77–82 (2018). https://doi.org/10.1038/s41586-018-0693-y

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