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Structural basis of directional switching by the bacterial flagellum

Nature Microbiology volume 9, pages 1282–1292 (2024)Cite this article

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Abstract

The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2–5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.

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Fig. 1: Structure of the CCW rotating state of the S. Typhimurium flagellar C-ring.
Fig. 2: Structure of the CW rotating state of the S. Typhimurium flagellar C-ring and large domain rearrangements between the CCW and CW states.
Fig. 3: Both FliGN and FliGM domains are completed via inter-subunit domain swaps but FliGN inverts which subunit contributes the C-terminal portion of the fold in the CCW and CW states.
Fig. 4: Design, purification and cryo-EM structure of a stator complex bound to FliGC.
Fig. 5: Overlaying MotA5B2–FliG on the CCW and CW C-rings reveals the stator complex switches from the outside to inside the C-ring.
Fig. 6: Mechanism for switching based on structures for CCW and CW flagellar C-rings.

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Data availability

Cryo-EM volumes and atomic models have been deposited to the EMDB (accession codes EMD-42376, EMD-42387, EMD-42439, EMD-42451 and EMD-42139) and PDB (accession codes 8UMD, 8UMX, 8UOX, 8UPL and 8UCS). PDB entries 3AJC, 1LKV, 3USW and 3USY were used for structural superpositions. Source data are provided with this paper.

Code availability

All code used for cryo-EM data analysis, structure determination and refinement are publicly available.

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Acknowledgements

We thank E. Johnson and A. Costin (Central Oxford Structural Molecular Imaging Centre) and D. Shi (NCI) for assistance with data collection; H. Elmlund (NCI) for access to SIMPLE code ahead of release. This research was funded (in part) by the Intramural Research Program of the NIH (to S.M.L.). 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 was supported by Wellcome Trust Investigator (no. 219477) and Collaborative awards (no. 209194) and an MRC Programme grant (no. S021264).

Author information

Author notes

  1. Emily J. Furlong

    Present address: Division of Biomedical Science and Biochemistry, Australian National University, Canberra, Australian Capital Territory, Australia

  2. These authors contributed equally: Steven Johnson, Justin C. Deme.

Authors and Affiliations

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

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

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

    Emily J. Furlong & Joseph J. E. Caesar

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

    Joseph J. E. Caesar

  4. 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., J.C.D. 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 samples and made EM grids. J.C.D. prepared samples, made and screened EM grids and together with S.M.L. collected the EM data. J.C. assisted with EM data processing. F.F.V.C. and K.T.H. created the bacterial strain used for basal body preparation. S.J., S.M.L. and J.C.D. contributed to writing the first draft of the manuscript and all authors commented on manuscript drafts.

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Correspondence to Steven Johnson or Susan M. Lea.

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

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Extended data

Extended Data Fig. 1 Cryo-EM processing workflow, showing local and global map quality for the CCW C-ring structure.

a, Image processing workflow for the CCW C-ring. b, Gold-standard FSC curves used for global-resolution estimates within cryoSPARC. c, Local-resolution estimation of reconstructed map as determined within cryoSPARC.

Extended Data Fig. 2 Cryo-EM processing workflow, showing local and global map quality for the CW C-ring structure.

a, Image processing workflow for the CW C-ring. b, Gold-standard FSC curves used for global-resolution estimates within cryoSPARC. c, Local-resolution estimation of reconstructed map as determined within cryoSPARC.

Extended Data Fig. 3 Different Symmetries are apparent in 2D classes following particle classification in 3D.

2D class averages are shown for CCW and CW particles separated into different symmetries via 3D classification. An example of a side-view is shown above and a top-down view below. The subunit numbers in the top-down views can be counted to reveal a symmetry consistent with the 3D classification.

Extended Data Fig. 4 Protein domain boundaries within the context of the assembled C-ring subunit.

The C-ring subunit is shown in CCW and CW conformations with the protein chains colored FliF blue; FliG red; FliM green; FliN shades of yellow. Where termini are visible they are denoted as N or C-termini and where the view allows FliG and FliM subdomains are boxed and annotated. As shown in Fig. 3, the FliG N and M subdomains consist of residues donated from multiple C-ring subunits, hence these subdomains are shown in two boxes with the residues donated to the pro/pre-ceding subunit indicated as +/−1.

Extended Data Fig. 5 Fit of coordinates to CCW and CW cryoEM volumes.

a-e, show different views at different contour levesl of the CCW coordinates within the CCW volume.f-j, show the same for the CCW volume. a,b and f,g show the full subunits (CCW and CW respectively) at a lower (a,f) and higer (b,g) contour levels revealing the FliG domains at the top of the subunit are the most mobile regions. c,h depict the volume surrounding two of the three FliN domains, d,i the volume around FliG and e,j for two regions of FliM, all for CCW and CW respectively.

Extended Data Fig. 6 Domain swaps between C-ring subunits involving regions of FliG.

Two neighbouring C-ring subunits are shown in cartoon representation coloured pink (copy N) and either light blue (N + 1) or lavender (N-1). a,b,e, are from the CW assembly and c,d,e from the CCW. a-d, depict the domain swap to assemble the FliGM domain (dark red and dark blue to denote which subunit the sequences originate in). e-f depict the domain swap to assemble FliGN (coloured dark red and purple (e) or dark red and dark blue (f)). (g,h) The compound FliGN, FliGM and FliGC domains assembled via inter-subunit domain swaps share the same domain architecture in both the CCW (g – R.M.S.D. 2.3+/− 0.4 Å) and CW (h – R.M.S.D. 2.4+/−0.2 Å) states R.M.S.D. each domain onto all others, both states, 2.1+/− 0.6 Å. Two views of the overlaid domains in a cartoon representation are shown for each state with the domains coloured as shown in the key.

Extended Data Fig. 7 Complexity of Subunit Packing within the CCW and CW C-rings.

a, An unanticipated packing between a secondary structural element immediately following the FliMM domain leads to further inter-subunit packing interactions between FliM and FliN in addition to the previously proposed lock-washer interactions. This new element occurs in both states with subtly different contacts. b, A single subunit is colored red in the context of the C34 C-ring in both states to emphasise how the vertical subunits visible in previous low-resolution volumes are constructed from domains originated in multiple subunits. c, A subunit taken from a CW state (red ribbon) is incompatible with packing between subunits in the CCW states reinforcing the cooperativity in switching states that must exist. d, FliM Arginine 63 and 181 from the N and N + 1 subunits respectively, are proximal to each other at the subunit interface in the CW state, e, but are separated in the CCW state.

Extended Data Fig. 8 Structural Implications of the PAA CW-locking mutation.

a, Two subunits in the CCW states are shown colored light pink (N) and light blue (N + 1) with the FliG PAA sequence that, when deleted, locks the C-ring in the CW state highlighted in dark red and the FliG linker between FliGM and FliGC highlighted in dark blue. b, When the FliGM domains are used to overlay the CCW (light pink) and CW (silver) states the deletion of the PAA sequence (dark red in the CW state) leads to a pulling-up of that helix and reorientation of the FliGM-FliGC linker. c, overlaying the CCW (light pink) and CW (silver) by matching of the FliMM domain reveals how the FliGM helix containing the PAA sequence (dark red in the CCW state), is reoriented altering the side chains presented for interaction with the FliMM domain below. d-e, the linker between the FliGM and FliGC domains (green cartoon) is also in the inter-subunit interface and reorients becoming more helical in switching between CCW and CW states. d, shows full cartoon view of two neighbouring subunits in CCW (LHS) and CW (RHS) states with the PAA highlighted in red, the FliGM-FliGN linker in dark blue and the FliGM-FliGC linker in green. e, shows a closeup slab removing overlaying elements colored in the same way. f, The arrangement of the FliGC (residues 234–331) differs by a rotation of 180° between the CCW (light green) and CW (dark green) structures relative to FliGM (residues 198–233 shown at bottom of panels and used to generate overlays). g-h,Previous crystal structures of FliGC/FliGM have revealed a variety of different arrangements between the domains. Earlier crystal structures (PDB ids 3ajc, 1lkv, 3usw and 3usy (two chains independently overlaid)) were overlaid onto the CCW (panel g) and CW (panel h) FliGM-198–233 using matchmaker within ChimeraX. None of the earlier crystal structures place the C subdomain in either position seen within the C-ring states.

Extended Data Fig. 9 Cryo-EM processing workflow, showing local and global map quality for MotAB + FliGc.

a, Image processing workflow for MotAB + FliGc. b, Gold-standard FSC curves used for global-resolution estimates within cryoSPARC. c, Local-resolution estimation of reconstructed map as determined within cryoSPARC.

Extended Data Fig. 10 Structural alignment of C. sporogenes MotAB with FliG-bound MotAB.

C. sporogenes MotAB (PDB: 6YSF) superposed with FliG-bound MotAB structure presented in this study. MotAB shown in orange, FliG-bound MotAB shown blue. FliG and plug domains not modelled in 6YSF are transparent.

Supplementary information

Source data

Source Data Fig. 4

Source data for size-exclusion graph.

Source Data Fig. 4

Unprocessed gel.

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Johnson, S., Deme, J.C., Furlong, E.J. et al. Structural basis of directional switching by the bacterial flagellum. Nat Microbiol 9, 1282–1292 (2024). https://doi.org/10.1038/s41564-024-01630-z

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