The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
25 06 2020
25 06 2020
Historique:
received:
21
10
2019
accepted:
29
05
2020
entrez:
27
6
2020
pubmed:
27
6
2020
medline:
29
8
2020
Statut:
epublish
Résumé
The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction.
Identifiants
pubmed: 32587243
doi: 10.1038/s41467-020-16981-4
pii: 10.1038/s41467-020-16981-4
pmc: PMC7316729
doi:
Substances chimiques
Bacterial Proteins
0
FlaD protein, Bacteria
147757-14-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
3210Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R009759/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R003491/1
Pays : United Kingdom
Références
Erhardt, M. in Current Topics in Microbiology and Immunology (eds Stadler, M. & Dersch, P) 185–205 (Springer, Cham, 2016).
Chaban, B., Hughes, H. V. & Beeby, M. The flagellum in bacterial pathogens: for motility and a whole lot more. Semin. Cell Dev. Biol. 46, 91–103 (2015).
doi: 10.1016/j.semcdb.2015.10.032
Rossez, Y., Wolfson, E. B., Holmes, A., Gally, D. L. & Holden, N. J. Bacterial flagella: twist and stick, or dodge across the kingdoms. PLoS Pathog. 11, https://doi.org/10.1371/journal.ppat.1004483 (2015).
Freitag, C. M., Strijbis, K. & van Putten, J. P. M. Host cell binding of the flagellar tip protein of Campylobacter jejuni. Cell. Microbiol. 19, https://doi.org/10.1111/cmi.12714 (2017).
Yonekura, K. et al. The bacterial flagellar cap as the rotary promoter of flagellin self-assembly. Science 290, 2148–2152 (2000).
doi: 10.1126/science.290.5499.2148
Maki-Yonekura, S., Yonekura, K. & Namba, K. Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum. Proc. Natl Acad. Sci. USA 100, 15528–15533 (2003).
doi: 10.1073/pnas.2534343100
Cho, S. Y. et al. Tetrameric structure of the flagellar cap protein FliD from Serratia marcescens. Biochem. Biophys. Res. Commun. 489, 63–69 (2017).
doi: 10.1016/j.bbrc.2017.05.093
Song, W. S., Cho, S. Y., Hong, H. J., Park, S. C. & Yoon, S. Self-oligomerizing structure of the flagellar cap protein FliD and its implication in filament assembly. J. Mol. Biol. 429, 847–857 (2017).
doi: 10.1016/j.jmb.2017.02.001
Postel, S. et al. Bacterial flagellar capping proteins adopt diverse oligomeric states. Elife 5, https://doi.org/10.7554/eLife.18857 (2016).
Cho, S. Y. et al. Structural analysis of the flagellar capping protein FliD from Helicobacter pylori. Biochem. Biophys. Res. Commun. 514, 98–104 (2019).
doi: 10.1016/j.bbrc.2019.04.065
Wang, F. et al. A structural model of flagellar filament switching across multiple bacterial species. Nat. Commun. 8, https://doi.org/10.1038/s41467-017-01075-5 (2017).
Maki-Yonekura, S., Yonekura, K. & Namba, K. Conformational change of flagellin for polymorphic supercoiling of the flagellar filament. Nat. Struct. Mol. Biol. 17, 417–422 (2010).
doi: 10.1038/nsmb.1774
Galkin, V. E. et al. Divergence of quaternary structures among bacterial flagellar filaments. Science 320, 382–385 (2008).
doi: 10.1126/science.1155307
Dasti, J. I., Tareen, A. M., Lugert, R., Zautner, A. E. & Groß, U. Campylobacter jejuni: a brief overview on pathogenicity-associated factors and disease-mediating mechanisms. Int. J. Med. Microbiol. 300, 205–211 (2010).
doi: 10.1016/j.ijmm.2009.07.002
Poly, F. & Guerry, P. Pathogenesis of Campylobacter infection. Curr. Opin. Gastrointerology 24, 27–31 (2008).
doi: 10.1097/MOG.0b013e3282f1dcb1
van Putten, J. P. M., van Alphen, L. B., Wösten, M. M. S. M. & de Zoete, M. R. Molecular mechanisms of Campylobacter infection Curr. Top. Microbiol. Immunol. 337, 197–229 (2009).
pubmed: 19812984
Yeh, H., Hiett, K. L., Line, J. E. & Seal, B. S. Characterization and antigenicity of recombinant Campylobacter jejuni flagellar capping protein FliD. 602–609. https://doi.org/10.1099/jmm.0.060095-0 (2014).
Chintoan-Uta, C., Cassady-Cain, R. L. & Stevens, M. P. Evaluation of flagellum-related proteins FliD and FspA as subunit vaccines against Campylobacter jejuni colonisation in chickens. Vaccine 34, 1739–1743 (2016).
doi: 10.1016/j.vaccine.2016.02.052
Ghasemi, A. et al. Immunization with recombinant FliD confers protection against Helicobacter pylori infection in mice. Mol. Immunol. 94, 176–182 (2018).
doi: 10.1016/j.molimm.2018.01.001
Imada, K. Bacterial flagellar axial structure and its construction. Biophys. Rev. 10, 559–570 (2018).
doi: 10.1007/s12551-017-0378-z
Matsunami, H., Barker, C. S., Yoon, Y. H., Wolf, M. & Samatey, F. A. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat. Commun. 7, https://doi.org/10.1038/ncomms13425 (2016).
Horvath, P., Kato, T., Miyata, T. & Namba, K. Structure of Salmonella Flagellar Hook Reveals Intermolecular Domain Interactions for the Universal Joint Function. MDPI Biomol. 9, https://doi.org/10.3390/biom9090462 (2019).
Kim, H. J., Yoo, W., Jin, K. S., Ryu, S. & Lee, H. H. The role of the FliD C-terminal domain in pentamer formation and interaction with FliT. Sci. Rep. 7, https://doi.org/10.1038/s41598-017-02664-6 (2017).
Kovács, N., Jankovics, H. & Vonderviszt, F. Deletion analysis of the flagellum-specific secretion signal in Salmonella flagellin. FEBS Lett. 592, 3074–3081 (2018).
doi: 10.1002/1873-3468.13200
Furukawa, Y. et al. Interactions between bacterial flagellar axial proteins in their monomeric state in solution. J. Mol. Biol. 318, 889–900 (2002).
doi: 10.1016/S0022-2836(02)00139-0
Vonderviszt, F. et al. Mechanism of self-association and filament capping by flagellar HAP2. J. Mol. Biol. 284, 1399–1416 (1998).
doi: 10.1006/jmbi.1998.2274
Maki, S., Vonderviszt, F., Furukawa, Y., Imada, K. & Namba, K. Plugging interactions of HAP2 pentamer into the distal end of flagellar filament revealed by electuon microscopy. J. Mol. Biol. 277, 771–777 (1998).
doi: 10.1006/jmbi.1998.1663
Zhang, K. et al. Analysis of a flagellar filament cap mutant reveals that HtrA serine protease degrades unfolded flagellin protein in the periplasm of Borrelia burgdorferi. Mol. Microbiol. 111, 1652–1670 (2019).
doi: 10.1111/mmi.14243
Blocker, A. J. et al. What’s the point of the type III secretion system needle? Proc. Natl Acad. Sci. USA 105, 6507–6513 (2008).
doi: 10.1073/pnas.0708344105
Motojima, F. How do chaperonins fold protein? Biophysics 11, 93–102 (2015).
doi: 10.2142/biophysics.11.93
Xing, Q. et al. Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system. Nat. Commun. https://doi.org/10.1038/s41467-018-04137-4 (2018).
Minamino, T., Imada, K. & Namba, K. Mechanisms of type III protein export for bacterial flagellar assembly. Mol. Biosyst. 4, 1105–1115 (2008).
doi: 10.1039/b808065h
Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).
doi: 10.1016/j.pep.2005.01.016
Grant, T., Rohou, A. & Grigorieff, N. CisTEM, user-friendly software for single-particle image processing. Elife 7, https://doi.org/10.7554/eLife.35383 (2018).
Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
doi: 10.1016/j.jsb.2015.08.008
Snijder, J. et al. Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids. J. Struct. Biol. 198, 38–42 (2017).
doi: 10.1016/j.jsb.2017.02.008
Scheres, S. H. W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
doi: 10.1016/j.jsb.2012.09.006
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
doi: 10.1038/nmeth.4193
Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D: Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
doi: 10.1038/nprot.2015.053
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D: Biol. Crystallogr. 66, 486–501 (2010).
doi: 10.1107/S0907444910007493
Frenz, B., Walls, A. C., Egelman, E. H., Veesler, D. & Di Maio, F. RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EMmaps. Nat. Methods 14, 797–800 (2017).
doi: 10.1038/nmeth.4340
Song, Y. et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735–1742 (2013).
doi: 10.1016/j.str.2013.08.005
Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, 320–324 (2014).
doi: 10.1093/nar/gku316
Zeng, H. et al. ComplexContact: a web server for inter-protein contact prediction using deep learning. Nucleic Acids Res. 46, W432–W437 (2018).
doi: 10.1093/nar/gky420