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Structural Study of the Bacterial Flagellar Basal Body by Electron Cryomicroscopy and Image Analysis

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The Bacterial Flagellum

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1593))

Abstract

The bacterial flagellum is a large assembly of about 30 different proteins and is divided into three parts: filament, hook, and basal body. The machineries for its crucial functions, such as torque generation, rotational switch regulation, protein export, and assembly initiation, are all located around the basal body. Although high-resolution structures of the filament and hook have already been revealed, the structure of the basal body remains elusive. Recently, the purification protocol for the MS ring, which is the core ring of the basal body, has been improved for the structural study of the MS ring by electron cryomicroscopy (cryoEM) and single particle image analysis. The structure of intact basal body has also been revealed in situ at a resolution of a few nanometers by electron cryotomography (ECT) of minicells. Here, we describe the methods for the MS ring purification, Salmonella minicell culture, and cryoEM/ECT data collection and image analysis.

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References

  1. Berg HC (2003) The rotary motor of bacterial flagella. Annu Rev Biochem 72:19–54

    Article  CAS  PubMed  Google Scholar 

  2. Ueno T, Oosawa K, Aizawa SI (1992) M ring, S ting and proximal rod of the flagellar basal body of Salmonella typhimurium are composed of subunits of a single protein FliF. J Mol Biol 227:672–677

    Article  CAS  PubMed  Google Scholar 

  3. Berg HC (2000) Constraints on models for the flagellar rotary motor. Philos Trans R Soc London B Biol Sci 335:491–502

    Article  Google Scholar 

  4. González-Pedrajo B, Minamino T, Kihara M et al (2006) Interactions between C ring proteins and export apparatus components: a possible mechanism for facilitating type III protein export. Mol Microbiol 60:984–998

    Article  PubMed  Google Scholar 

  5. Zhou J, Lloyd SA, Blair DF (1998) Electro-static interactions between rotor and stator in the bacterial flagellar motor. Proc Natl Acad Sci U S A 95:6436–6441

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Francis NR, Irikura VM, Yamaguchi S et al (1992) Localization of the Salmonella typhimurium flagellar switch protein FliG to the cytoplasmic M-ring face of the basal body. Proc Natl Acad Sci U S A 89:6304–6308

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Jones CJ, Macnab RM, Okino H et al (1990) Stoichiometric analysis of the flagellar hook-(basal-body) complex of Salmonella typhimurium. J Mol Biol 212:377–387

    Article  CAS  PubMed  Google Scholar 

  8. Suzuki H, Yonekura K, Namba K (2004) Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis. J Mol Biol 337:105–113

    Article  CAS  PubMed  Google Scholar 

  9. Thomas DR, Francis NR, Xu C et al (2006) The three-dimensional structure of the flagellar rotor from a clockwise-locked mutant of Salmonella enterica serovar typhimurium. J Bacteriol 188:7039–7048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Gao Y, Cao E, Julius D et al (2016) TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action. Nature 534:347–351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Taylor NM, Prokhorov NS, Guerrero-Ferreira RC et al (2016) Structure of the T4 baseplate and its function in triggering sheath contraction. Nature 533:346–352

    Article  CAS  PubMed  Google Scholar 

  12. Frauenfeld J, Löving R, Armache JP et al (2016) A saposin-lipoprotein nanoparticle system for membrane protein. Nat Methods 13:345–351

    Article  PubMed  PubMed Central  Google Scholar 

  13. Liao M, Cao E, Julius D et al (2013) Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature 504:107–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hauer F, Gerle C, Fischer N et al (2015) GraDeR: membrane protein complex preparation for single-particle cryo-EM. Structure 23:1769–1775

    Article  CAS  PubMed  Google Scholar 

  15. Kawamoto A, Morimoto VY, Miyata T et al (2013) Common and distinct structural features of Salmonella injectisome and flagellar basal body. Sci Rep 3:3369

    Article  PubMed  PubMed Central  Google Scholar 

  16. Yamaguchi S, Fujita H, Ishihara A et al (1986) Subdivision of flagellar gens of Salmonella typhimurium into regions responsible for assembly, rotation and switching. J Bacteriol 166:187–193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Li X, Mooney P, Zheng S et al (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Mindell JA, Grigorieff N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347. doi:10.1016/S1047-8477(03)00069-8

    Article  PubMed  Google Scholar 

  19. Scheres SH (2012) RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol 180:519–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-EM density maps. Nat Methods 11:63–65

    Article  CAS  PubMed  Google Scholar 

  21. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    Article  CAS  PubMed  Google Scholar 

  22. Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The research study described in this chapter was supported by JSPS KAKENHI Grant Number JP25000013 to K.N.

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Correspondence to Keiichi Namba .

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Kawamoto, A., Namba, K. (2017). Structural Study of the Bacterial Flagellar Basal Body by Electron Cryomicroscopy and Image Analysis. In: Minamino, T., Namba, K. (eds) The Bacterial Flagellum. Methods in Molecular Biology, vol 1593. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6927-2_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6927-2_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6926-5

  • Online ISBN: 978-1-4939-6927-2

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