Abstract
Bacteria swim by means of long flagella extending from the cell surface. These are assembled from thousands of protein subunits translocated across the cell membrane by an export machinery at the base of each flagellum. Unfolded subunits1,2,3 then transit through a narrow channel at the core of the growing flagellum to the tip, where they crystallize into the nascent structure. As the flagellum lengthens outside the cell, the rate of flagellum growth does not change4. The mystery is how subunit transit is maintained at a constant rate without a discernible energy source in the channel of the external flagellum5. We present evidence for a simple physical mechanism for flagellum growth that harnesses the entropic force of the unfolded subunits themselves. We show that a subunit docked at the export machinery can be captured by a free subunit through head-to-tail linkage of juxtaposed amino (N)- and carboxy (C)-terminal helices. We propose that sequential rounds of linkage would generate a multisubunit chain that pulls successive subunits into and through the channel to the flagellum tip, and by isolating filaments growing on bacterial cells we reveal the predicted chain of head-to-tail linked subunits in the transit channel of flagella. Thermodynamic analysis confirms that links in the subunit chain can withstand the pulling force generated by rounds of subunit crystallization at the flagellum tip, and polymer theory predicts that as the N terminus of each unfolded subunit crystallizes, the entropic force at the subunit C terminus would increase, rapidly overcoming the threshold required to pull the next subunit from the export machinery. This pulling force would adjust automatically over the increasing length of the growing flagellum, maintaining a constant rate of subunit delivery to the tip.
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Acknowledgements
We thank P. Hinchliffe for help with analysis of atomic structures, K. Yonekura and K. Namba for providing information on filament structure, H. Berg and N. Greene for discussions, A. Crow for advice on ITC, and P. Dhillon for technical assistance. The work was supported by a Wellcome Trust Programme Grant (C.H. and G.M.F.).
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L.D.B.E., S.P., C.H. and G.M.F. designed the experiments; L.D.B.E. and S.P. performed experiments; L.D.B.E., C.H. and G.M.F. analysed the data; E.M.T. performed the thermodynamic and polymer theory analyses; L.D.B.E., E.M.T., C.H. and G.M.F. wrote the manuscript.
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Extended data figures and tables
Extended Data Figure 1 The bacterial flagellum.
The cell surface bacterial flagellum has three contiguous hollow substructures: the rod, hook and filament, which are assembled sequentially. The ‘drive-shaft’ rod (FliE, FlgB, FlgC, FlgF and FlgG), which together with a series of rings comprises the basal body, extends from the inner membrane (IM) to span the periplasm, peptidoglycan (PG) cell wall and outer membrane (OM). The cell surface hook (FlgE) is a flexible universal joint with a defined length of ∼55 nm that is controlled by the exported protein FliK2. The hook-filament junction proteins (FlgK and FlgL) connect the hook to the external flagellar filament (flagellin FliC). An export machinery at the base of the flagellum translocates subunits across the cytoplasmic membrane. Subunits then transit through the external flagellar central channel to the distal tip where they crystallize beneath cap foldases (FlgJ for rod, FlgD for hook and FliD for filament subunit assembly). During the early stages of flagellum assembly, rod and hook proteins are exported as a single class of early subunits (FliE, FlgB, FlgC, FlgF FlgG, FlgJ, FlgD, FlgE and FliK). Upon hook completion the export machinery switches subunit specificity to allow export of a single class of late filament subunits (FlgK, FlgL, FliC, FliD). Only proteins that remain in the mature structure are shown in the figure.
Extended Data Figure 2 Flagellar export gate FlhBC hydrophobic pocket is essential for subunit docking (in support of Fig. 1).
a, Isothermal titration calorimetry (ITC) of hook cap subunit FlgD binding to the C-terminal domain of the export machinery gate FlhB19 (FlhBC) reveals low-affinity binding (KD 39 μM), compatible with transient association20 and a 1:1 stoichiometry. b, Binding of FlgD subunit (input, middle panel) to purified wild-type FlhBC and its variants containing five-residue deletions (input, lower panel; for example, Δ278–282), assessed by affinity chromatography. Subunit binding (upper panel, immunoblot) was abolished by deletion of FlhBC residues 278–282, 283–287, 333–337, 338–342 or 343–347 identifying a single contiguous on FlhBC subunit-binding site containing a hydrophobic pocket. Glutathione S-transferase (GST) does not bind FlgD. c, Binding of FlgD hook and FlgG rod subunits (input, middle panel, immunoblot) to purified FlhBC wildtype and variants containing non-conservative point mutations within the hydrophobic pocket (input, lower panels, Coomassie stained; A286E, P287E, A341E and L344E). Binding was assessed by affinity chromatography (bound, upper panels immunoblot). d, Mapping subunit binding (b, c) on the FlhBC export gate structure (PDB 3B0Z)44 reveal a contiguous subunit docking surface (blue) containing the hydrophobic pocket. Mutations in the pocket (A286E, P287E, A341E and L344E; orange) abolish binding of FlgD subunit. All experiments were carried out at least three times and were biological replicates.
Extended Data Figure 3 A conserved recognition motif determines subunit docking at the flagellar export gate (in support of Fig. 1).
a, Identification of the subunit region that recognizes the export gate. FlhBC export gate binding (upper panels, immunoblot) by N-terminal (residues 1–100) subunit (FlgG, FlgD and FliK) regions, and FlgD subunit N-terminal peptides (residues 1–10, 1–50, 1–70) fused to SptP reporter (detected using anti-SptP sera). These data locate the gate-recognition region of FlgD to residues 10–50, and lead to the in vivo identification of the gate-recognition motif (e, below). The SptP reporter alone (−) did not bind FlhBC, nor did glutathione S-transferase (GST) alone bind the SptP reporter or subunit fusions (middle panels). Input samples are shown in the lower panels. b, Identification of an essential short conserved motif near the N terminus FlgD36–40 by assay of in vivo subunit export (exported) by cell cultures expressing wild-type FlgD hook cap subunit or recombinant five amino acid deletion (Δ) variants (cell). c, Alignment of S. typhimurium FlgD essential sequence motif 36–40 with homologous regions in FlgD subunits from other bacterial species. d, Conservation of the short motif comprising a phenylalanine followed by three residues and a hydrophobic residue (Fxxxϕ), revealed by alignment of S. typhimurium FlgD residues 36–40 with homologous N-terminal regions of all S. typhimurium rod and hook subunits. e, Subunits lacking the N-terminal conserved Fxxxϕ motif are severely attenuated for docking to the FlhBC export gate (these are termed gate-blind in Fig. 1). FlhBC binding assay of wild-type (+) subunits (FlgG, FlgD, FlgE and FliK) and their Fxxxϕ motif deletion (−) variants. FlhBC gate-bound subunits (upper panel; FlgD lanes) and subunit input fractions (lower panel) were immunoblotted with anti-Flag sera. f, Direct binding of the subunit gate-recognition motif to FlhBC, shown by the formation of covalent complexes using engineered ultraviolet-activated (+) site-specific crosslinking residues (FlgD V5X, L39X or L40X). g, Binding of FlgD subunit to autocleavage-defective FlhBC (N269A40) used in site-specific crosslinking assays (f) is comparable to wild-type FlhBC (upper panel; immunoblot, anti-FlgD sera). Input samples (middle and lower panels) of FlgD subunit (immunoblot, anti-FlgD sera) and FlhBC (Coomassie stain). All experiments were carried out at least three times and were biological replicates.
Extended Data Figure 4 Capture of hook cap subunit docked at the export gate by free hook subunits and identification of stable capture complexes (in support of Fig. 1).
a–d, Docked Flag-tagged FlgD hook cap subunit was challenged (as in Fig. 1a) by increasing concentrations of free His-tagged FlgE (a expanded from Fig. 1b), FliD (b), FlgD (c) or FliK (d) subunit, either wild-type or gate-blind (that is, unable to recognize the gate). e, Summary of capture (+) by challenge subunit of FlgD hook cap subunit docked at FlhBC (Fig. 1b, and Extended Data Fig. 4a–d). Capture assays establish that gate-docked FlgD can be captured by other hook subunits, but not by filament cap subunit that is only exported once the hook is complete45. These data could reflect the well-defined classing of subunits as either ‘early’ (subunits of the rod and hook) or ‘late’ (subunits of the filament, filament cap and hook-filament junction, which are only exported and assembled once the hook is complete). f, Subunit capture complexes released from the gate (generated in c and d, indicated by asterisks) were isolated using affinity chromatography confirming that captured FlgD is linked to wild-type challenge subunits (FlgD or FliK) and their gate-blind variants, supporting the evidence that docked subunits are captured (not displaced) from the export gate by free subunit (Fig. 1b, c). g, In vivo FlgE hook subunit export is attenuated by deletion of C-terminal helix involved in subunit capture from the gate (ΔCt; Fig. 1b) and/or the motif required for gate recognition (gate-blind) assessed in the S. typhimurium flgD null by collecting culture supernatants. All experiments were carried out at least three times and were biological replicates.
Extended Data Figure 5 Analysis of interactions between subunit terminal helices within the crystallized mature hook (in support of Fig. 1).
a, Subunits crystallized in a lattice as they would be in the flagellum, with the terminal helices that line the channel forming intra-subunit antiparallel coiled-coils and inter-subunit lateral and axial packing interactions. Distances between engineered cysteine residues (Extended Data Table 1) were assessed between intra, axial and lateral subunits within the lattice, indicated by the open circles and dashed lines. This analysis allows the identification of crosslink residue pairs within subunit terminal helices that would form in an alternative coiled-coil conformation (parallel; Fig. 1d), distinct from subunits crystallized in the hook (antiparallel). b, Electron cryomicroscopy of the flagellar hook12 (EMD 1647) carved to show four subunits within a lattice. Terminal helices are coloured as in a. c, Atomic model12 of four subunits, coloured as in a, assembled as they would in the flagellar hook (PDB 3A69), derived from high-resolution electron cryomicroscopy and the atomic resolution structure of the hook subunit24 (PDB 2BGZ). Subunit N-terminal helices and the C-terminal helix (light blue) of the upper central subunit are indicated by a dashed box. d, A magnification of c, showing N-terminal helices of four adjacent subunits (coloured as in a) and the C-terminal helix (light blue) of the upper central subunit (a). Distances (dashed lines) between specific selected engineered cysteine residues (yellow) are shown in Extended Data Table 1. e, Control crosslinking assay showing that FlgE-Ct without engineered cysteines, incubated with (+) or without (−) BMOE cross-linker (x-link), cannot form complexes with FlgE-Nt (no cysteine) or its mutated variants A6C, A14C, D18C, A25C or A40C. All experiments were carried out at least three times and were biological replicates.
Extended Data Figure 6 In vitro and in vivo head-to-tail linkage of flagellin subunits (in support of Fig. 2).
a, Isolation of flagellin linked (dimer) in vitro by site-specific cysteine–cysteine crosslinks. Flagellin (FliC) and its variants containing unique cysteines (S11C, L13C, L18C, R31C or K178C; Extended Data Table 1) within and adjacent to the N-terminal helix predicted to generate a coiled-coil were incubated, with (+) or without (−) BMOE cross-linker (x-link), with a FliC variant containing a unique cysteine (N489C) within the C-terminal helix (upper panel). Flagellin derivatives were engineered to lack either their C or N termini (FliC-Nt, FliC-Ct) to preclude self-interaction. Control crosslinking (lower panel) assay showing that FliC-Ct without engineered cysteines cannot form crosslinked complexes. b, Trapping of flagellin subunits linked head-to-tail in chains within flagella growing on S. typhimurium cells using in vivo site-specific cysteine–cysteine crosslinking. Cells expressing recombinant, export-competent full-length flagellin containing engineered cysteines (lanes from left to right: negative control L18C; L18C and Q488C predicted to trap chain; negative control Q488C alone; negative control wild type; negative control vector) were incubated with (+) or without (−) BMOE cross-linker (x-link). Flagellar filaments were then isolated, depolymerized and resolved (immunoblot, panel exposure times decrease from top to bottom) to reveal monomer (×1), dimer (×2) and higher order head-to-tail chains of flagellin. c, Depiction of the in vivo trapping of flagellin subunit chain in the transit channel of growing flagellar filaments. Panels show a series of magnifications of a flagellated S. typhimurium cell, flagellar filament containing flagellin subunit chain linked head-to-tail by N- and C-terminal helices (blue and red cylinders, respectively) and the flagellar transit channel containing the subunit–subunit link and figurative positions of engineered cysteine residues (yellow segment of cylinder). Engineered cysteine residues in C-terminal helices of assembled flagellin subunits that line the channel could form crosslinked dimers with subunits in transit. All experiments were carried out at least three times and were biological replicates.
Extended Data Figure 7 Generation of entropic force at the end of an unfolded polypeptide chain anchored to, and confined in, a narrow channel (in support of Supplementary Information section 3).
a, Depiction of the transit of an unfolded polypeptide chain (blue) anchored through its N terminus at the tip of a narrow channel (with a diameter of d and length of R). The pulling force (F, red arrow) at the C terminus of the polypeptide chain is generated by the total number (N) of free unfolded residues of length (a). b, Depiction of the increase in pulling force F(R,Na) as residues of the polypeptide chain crystallize at the tip of the channel, reducing the number of free residues within the channel, resulting in an increase in the ratio (R/Na) between channel length and number of free unfolded residues. This leads to an overstretched regime where the pulling force rapidly increases to reach the critical force (FM; dashed line) required to capture the awaiting subunit docked at the export machinery.
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Evans, L., Poulter, S., Terentjev, E. et al. A chain mechanism for flagellum growth. Nature 504, 287–290 (2013). https://doi.org/10.1038/nature12682
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DOI: https://doi.org/10.1038/nature12682
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