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The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity

Nature Microbiology volume 4, pages 2357–2368 (2019)Cite this article

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Abstract

Bactofilins are small β-helical proteins that form cytoskeletal filaments in a range of bacteria. Bactofilins have diverse functions, from cell stalk formation in Caulobacter crescentus to chromosome segregation and motility in Myxococcus xanthus. However, the precise molecular architecture of bactofilin filaments has remained unclear. Here, sequence analysis and electron microscopy results reveal that, in addition to being widely distributed across bacteria and archaea, bactofilins are also present in a few eukaryotic lineages such as the Oomycetes. Electron cryomicroscopy analysis demonstrated that the sole bactofilin from Thermus thermophilus (TtBac) forms constitutive filaments that polymerize through end-to-end association of the β-helical domains. Using a nanobody, we determined the near-atomic filament structure, showing that the filaments are non-polar. A polymerization-impairing mutation enabled crystallization and structure determination, while reaffirming the lack of polarity and the strength of the β-stacking interface. To confirm the generality of the lack of polarity, we performed coevolutionary analysis on a large set of sequences. Finally, we determined that the widely conserved N-terminal disordered tail of TtBac is responsible for direct binding to lipid membranes, both on liposomes and in Escherichia coli cells. Membrane binding is probably a common feature of these widespread but only recently discovered filaments of the prokaryotic cytoskeleton.

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Fig. 1: Bactofilins are highly conserved and widespread across bacteria and archaea and also occur in some eukaryotic organisms.
Fig. 2: TtBac forms filaments that show a continuous β-stacking repeat of 4.7 Å.
Fig. 3: Cryo-EM structure of TtBac shows a head-to-head non-polar filament.
Fig. 4: A polymerization-impaired TtBac mutant crystallizes as non-polar filaments with reduced subunit length.
Fig. 5: Evolutionary sequence coupling analysis reveals the conserved non-polar architecture of bactofilin filaments.
Fig. 6: TtBac binds to lipid membranes through its N-terminal tail.

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Data availability

The data that support the findings of this study are available from the corresponding author, who will also provide all expression plasmids generated for this study on request. Atomic coordinates have been deposited in PDB with accession codes 6RIA and 6RIB. The cryo-EM volume has been deposited in EMDB with accession code EMD-4887.

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Acknowledgements

We thank H. S. Judelson (UC Riverside) for discussions regarding Oomycetes. We acknowledge Diamond Light Source for the cryo-EM facilities at eBIC. We thank M. Yu (MRC−LMB) for help with synchrotron data collection and the staff at beamline I03 (Diamond Light Source). This work was funded by the MRC (grant no. U105184326 to J.L.) and the Wellcome Trust (grant no. 202754/Z/16/Z to J.L.). J.W. and X.D. were also supported by the Boehringer Ingelheim Fonds.

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  1. These authors contributed equally: Xian Deng, Andres Gonzalez Llamazares.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology, Cambridge, UK

    Xian Deng, Andres Gonzalez Llamazares, James M. Wagstaff, Victoria L. Hale, Giuseppe Cannone, Stephen H. McLaughlin, Danguole Kureisaite-Ciziene & Jan Löwe

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Contributions

X.D., A.G.L. D.K.-C. and J.L. performed the protein purification experiments. X.D., A.G.L., G.C. and J.L. collected the cryo-EM data and processed the images. A.G.L. and J.L. performed the crystallization and crystallography. J.M.W. performed the phylogeny and coupling analyses. V.L.H. performed the cryo-ET experiments. S.H.M. and A.G.L. performed the SPR experiments and analyses. A.G.L., J.M.W. and J.L. wrote the manuscript.

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Correspondence to Jan Löwe.

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Supplementary Information

Supplementary Information

Supplementary Figs. 1−6, Tables 1−3, Supplementary Video legends, Dataset 2 legend and Supplementary References.

Reporting Summary

Supplementary Dataset 2

Eukaryotic bactofilins.

Supplementary Video 1

The cryo-EM density after helical reconstruction of a TtBac filament bound by NB4-mut2. Boundaries of the bactofilin monomers are clearly visible, as is their antiparallel arrangement in each protofilament. An image from this video is shown in Fig. 3f.

Supplementary Video 2

An overview of the TtBac cryo-EM structure, providing a better 3D impression of the assembly.

Supplementary Video 3

Cryo-ET of an E. coli cell with TtBac-WT overexpressed. Filament bundles are arranged all around the cell’s periphery, under the inner membrane, and are particularly obvious when the video goes through the upper and lower cellular envelope where the bactofilin bundles run at roughly 45° angles to the long cell axis. Images from the tomogram are shown in Fig. 6e (left).

Supplementary Video 4

The same as Supplementary Video 3, but ΔN-TtBac has been overexpressed. Because the filaments no longer bind to the inner membrane of the E. coli cells, a very large bactofilin bundle runs along the long cell axis, also inhibiting cell division at the septum site. An image from this tomogram is shown in Fig. 6e (right).

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Deng, X., Gonzalez Llamazares, A., Wagstaff, J.M. et al. The structure of bactofilin filaments reveals their mode of membrane binding and lack of polarity. Nat Microbiol 4, 2357–2368 (2019). https://doi.org/10.1038/s41564-019-0544-0

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