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Molecular structure of the intact bacterial flagellar basal body

Nature Microbiology volume 6, pages 712–721 (2021)Cite this article

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Abstract

The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids1,2,3. Here, we present structures of the intact Salmonella flagellar basal body4, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2–3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.

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Fig. 1: The flagellar OM bushing is a lipid anchored 26-mer.
Fig. 2: The structure of the in situ flagellar axial rod.
Fig. 3: Interactions of the rod and export gate with the OM and IM ring structures.
Fig. 4: The structure of the in situ hook cap complex (FlgD).

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Data availability

Cryo-EM volumes and atomic models have been deposited at the EMDB (accession codes: EMD-12183, EMD-12190, EMD-12192, EMD-12193, EMD-12195) and PDB (accession codes: 7BGL, 7BHQ, 7BIN, 7BJ2, 7BK0), respectively. Proteomics data were deposited in PRIDE as PXD025599. Raw data and related Python code are available in Supplementary Data 2.

Code availability

All code used for cryo-EM data analysis, structure determination and refinement are publicly available. Python code is available in Supplementary Data 2.

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Acknowledgements

We thank E. Johnson and A. Costin of the Central Oxford Structural Molecular Imaging Centre (COSMIC) for assistance with data collection; H. Elmlund (Monash) for access to SIMPLE code ahead of release; N. Moriarty, P. Emsley and G. Murshudov for help with modelling lipid ligands. We acknowledge the use of the University of St Andrews BSRC Mass Spectrometry facility, and the Advanced Proteomics Facility of the Department of Biochemistry, University of Oxford, including M. Fournier for data processing. The Central Oxford Structural Molecular Imaging Centre is supported by the Wellcome Trust (no. 201536), The EPA Cephalosporin Trust, The Wolfson Foundation and a Royal Society/Wolfson Foundation Laboratory Refurbishment Grant (no. WL160052). Research in S.M.L.’s laboratory is supported by the Wellcome Trust Investigator (no. 219477) and Collaborative awards (no. 209194) and an MRC Programme Grant (no. S021264). A.L.N. is a member of the CBS, which is part of the France-BioImaging (FBI) and the French Infrastructure for Integrated Structural Biology (FRISBI), two national infrastructures supported by the French National Research Agency (ANR-10-INBS-04-01 and ANR-10-INBS-05, respectively).

Author information

Author notes

  1. These authors contributed equally: Steven Johnson, Emily J. Furlong.

Authors and Affiliations

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

    Steven Johnson, Emily J. Furlong, Justin C. Deme, Joseph J. E. Caesar & Susan M. Lea

  2. Center for Structural Biology, CCR, NCI, Frederick, MD, USA

    Steven Johnson, Justin C. Deme & Susan M. Lea

  3. Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK

    Justin C. Deme, Joseph J. E. Caesar & Susan M. Lea

  4. Department of Physics, University of Oxford, Oxford, UK

    Ashley L. Nord & Richard M. Berry

  5. Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France

    Ashley L. Nord

  6. Department of Biology, University of Utah, Salt Lake City, UT, USA

    Fabienne F. V. Chevance & Kelly T. Hughes

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Contributions

S.J. and S.M.L. designed the project, interpreted the EM data and built atomic models. E.J.F. optimized the preparation of the basal body samples, prepared all of the samples and made all of the EM grids. J.C.D. screened EM grids and together with S.M.L. collected the EM data. J.J.E.C. assisted with EM data processing. A.L.N. and R.M.B. collected and interpreted data from the motor rotation experiments. F.F.V.C. and K.T.H. created the bacterial strain used for basal body preparation. S.J., S.M.L and E.J.F. contributed to writing the first draft of the manuscript and all of the authors commented on manuscript drafts.

Corresponding authors

Correspondence to Steven Johnson or Susan M. Lea.

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The authors declare no competing interests.

Additional information

Peer review information Nature Microbiology thanks Gert Bange, Marc Erhardt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Cryo-EM analyses of intact flagellar basal bodies.

a, Example micrograph of Salmonella enterica serovar Typhimurium basal bodies on a graphene oxide surface. Scale bar 200 Å. b, 2D class averages of basal bodies. Scale bar 100 Å. c, Simplified workflow to show key stages in generation of each volume.

Extended Data Fig. 2 Structure of the LP-ring.

a, Gold-standard Fourier shell correlation (FSC) curve of RELION-postprocessed LP-ring C26 map. Resolution at the gold-standard cut-off (FSC = 0.143) is indicated. Curves: red, phase-randomized; green, unmasked; blue, masked; black, corrected. b, Local resolution estimates (in Å, as calculated by RELION3.1 LocalRes. c, Representative modelled densities of the three protein chains. d, Representative modelled densities of the lipid moieties.

Extended Data Fig. 3 Rotation periodicity in flagellar motors.

a, Backscattering dark field setup. (M: mirror; L: lens; HWP: half wave plate; QWP: quarter wave plot; HeNe laser; fast CMOS camera). b, Schematic of the experimental assay: a gold nanoparticle of 100 nm is attached to the hook of a BFM on a surface-immobilised cell. c, Brightfield (left) and darkfield (right) image of a nanoparticle attached to the hook of a bacterial cell (scale bar is 1um). d-f, An example recording showing the 2D histogram of the position of the rotating nanoparticle, with 26-fold periodicity in rotation (d); the angular speed of the motor (median filtered, 20 ms window) (e); the kernel density distribution of the angular position of the motor (f). g, The average +/- S.D. (line and shading, respectively) of the weighted power spectrum of a histogram of the angular position. (27 motors recorded for 1–2 s, each from a different cell, where the sodium motive force ranged from 54–187 mV and speeds ranged from 2–300 Hz.). See Methods for details.

Extended Data Fig. 4 Structure of the intact flagellar rod.

a, Gold-standard Fourier shell correlation (FSC) curve of RELION-postprocessed rod C1 map. Resolution at the gold-standard cutoff (FSC = 0.143) is indicated. Curves: red, phase-randomized; green, unmasked; blue, masked; black, corrected. b, Local resolution estimates (in Å), as calculated by RELION3.1 LocalRes. c, Representative modelled protein densities. d, Interaction of FliE (green cartoon and surface) with FliP of the Export Gate (blue cartoon). e, Overlay of a full FliE subunit (FliE-b) with FliE-a, demonstrating the overlap with the position of the FliR N-terminus. f, Overlay of representative rod subunits demonstrates the conserved core and variation in inserted domains (subunits colored as in Fig. 2).

Extended Data Fig. 5 Analysis of the rod helical lattice.

a, Representation of the helical symmetry of the rod, with the different X-start helices highlighted. Protein subunits are represented as ellipses, colored as in Fig. 2. The lattice node shared by FliR and FliE-a is highlighted. b, Alternative representation of the lattice with ‘ghost’ additional protofilament to show how the structure closes.

Extended Data Fig. 6 Structure of the LP-rod bearing.

a, Slab through the LP-rod demonstrating the thin seal around the rod. Green boxes highlight the constriction point formed by residues 48–82 of FlgI. b, Electrostatic potential mapped onto the surface of the LP-ring (view from inside the ring) with the positively charged band at the seal point highlighted in a green box). c, Electrostatic potential mapped onto the surface of the rod. Electrostatics analysed using APBS within Pymol.

Extended Data Fig. 7 Structure of the P-ring in the absence of the L-ring.

a, Gold-standard Fourier shell correlation (FSC) curves of RELION-postprocessed P-ring C26 map. Resolution at the gold-standard cut-off (FSC = 0.143) is indicated. Curves: red, phase-randomized; green, unmasked; blue, masked; black, corrected. b, Volume (silver mesh) contoured at 0.018 electrons/Angstrom over one copy of FlgI (shown as ball-and-stick representation) c, Side by side views of the cut-away P-ring structure next to the intact basal body, aligned on the collar of the MS-ring/rod. The white dashed line highlights the centre of the P-ring assembly.

Extended Data Fig. 8 Structure of the flagellar hook cap assembly.

a, Gold-standard Fourier shell correlation (FSC) curve of RELION-postprocessed rod C1 cap map. Resolution at the gold-standard cutoff (FSC = 0.143) is indicated. Curves: red, phase-randomized; green, unmasked; blue, masked; black, corrected. b, Local resolution estimates (in Å), as calculated by RELION3.1 LocalRes. c, Representative modelled protein densities. d, Two-dimensional residue plot of FlgD showing co-variance between residue pairs, as calculated by Gremlin. Stronger co-variance is highlighted by darker colours. The N-terminal hairpin region is highlighted with a box.

Supplementary information

Supplementary Information

Supplementary Figures 1–3 and references, and the legend for Supplementary Video 1.

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Supplementary Video 1

Proposed motions involved in the FlgD-cap-catalysed assembly mechanism. The cap is shown as a surface, coloured as defined in Fig. 4c. The video (and Fig. 4f) shows a side view of sequential cap movements orientated as in Fig. 4e with the bacterial membranes below.

Supplementary Data 1

The proteomic identifications based on extraction from gel as described in the Methods.

Supplementary Data 2

Zip file containing a Python directory with full source data and the Python script used to analyse data and generate the plots shown in Fig. 1g, Extended Data Fig. 3 and Supplementary Figs. 2 and 3.

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Johnson, S., Furlong, E.J., Deme, J.C. et al. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol 6, 712–721 (2021). https://doi.org/10.1038/s41564-021-00895-y

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