1. Zarkani, A. A. et al. Salmonella heterogeneously expresses flagellin during colonization of plants. Microorganisms 8, 815 (2020).
2. Haiko, J. & Westerlund-Wikström, B. The role of the bacterial flagellum in adhesion and virulence. Biology (Basel). 2, 1242–1267 (2013).
3. 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, e1004483 (2015).
4. Berg, H. C. The rotary motor of bacterial flagella. Annu. Rev. Biochem. 72, 19–54 (2003).
5. Magariyama, Y. et al. Very fast flagellar rotation. Nature 371, 752 (1994).
6. Macnab, R. M. & Ornston, M. K. Normal-to-curly flagellar transitions and their role in bacterial tumbling. Stabilization of an alternative quaternary structure by mechanical force. J. Mol. Biol. 112, 1–30 (1977).
7. DeRosier, D. J. The turn of the screw: The bacterial flagellar motor. Cell 93, 17–20 (1998).
8. Minamino, T., Terahara, N., Kojima, S. & Namba, K. Autonomous control mechanism of stator assembly in the bacterial flagellar motor in response to changes in the environment. Mol. Microbiol. 109, 723–734 (2018).
9. Fujii, T. et al. Identical folds used for distinct mechanical functions of the bacterial flagellar rod and hook. Nat. Commun. 8, 14276 (2017).
10. Saijo-Hamano, Y., Matsunami, H., Namba, K. & Imada, K. Architecture of the bacterial flagellar distal rod and hook of Salmonella. Biomolecules 9, 260 (2019).
11. Minamino, T. & Namba, K. Self-assembly and type III protein export of the bacterial flagellum. J. Mol. Biol. Biotechnol. 7, 5–17 (2004).
12. Nakamura, S. & Minamino, T. Flagella-driven motility of bacteria. Biomolecules 9, 279 (2019).
13. Darnton, N. C. & Berg, H. C. Force-extension measurements on bacterial flagella: Triggering polymorphic transformations. Biophys. J. 92, 2230–2236 (2007).
14. Asakura, S. Polymerization of flagellin and polymorphism of flagella. Adv. Biophys. 1, 99–155 (1970).
15. Stocker, B. A. D. Measurements of rate of mutation of flagellar antigenic phase in Salmonella typhimurium. J. Hyg. (Lond). 47, 398–413 (1949).
16. Andrewes, F. W. Studies in group agglutination. II.—The absorption of agglutinin in the diphasic salmonellas. J. Pathol. Bacteriol. 28, 345–359 (1925).
17. Silverman, M., Zieg, J., Hilmen, M. & Simon, M. Phase variation in Salmonella: Genetic analysis of a recombinational switch. PNAS. 76, 391–395 (1979).
18. Zieg, J., Silverman, M., Hilmen, M. & Simon, M. Recombinational switch for gene expression. Science. 196, 170–172 (1977).
19. Zieg, J. & Simon, M. Analysis of the nucleotide sequence of an invertible controlling element. PNAS. 77, 4196–4200 (1980).
20. Bonifield, H. R. & Hughes, K. T. Flagellar phase variation in Salmonella enterica is mediated by a posttranscriptional control mechanism. J. Bacteriol. 185, 3567–3574 (2003).
21. Aldridge, P. D. et al. Regulatory protein that inhibits both synthesis and use of the target protein controls flagellar phase variation in Salmonella enterica. PNAS. 103, 11340–11345 (2006).
22. Aldridge, P., Gnerer, J., Karlinsey, J. E. & Hughes, K. T. Transcriptional and translational control of the Salmonella fliC gene. J. Bacteriol. 188, 4487–4496 (2006).
23. Yamamoto, S. & Kutsukake, K. FljA-mediated posttranscriptional control of phase 1 flagellin expression in flagellar phase variation of Salmonella enterica serovar typhimurium. J. Bacteriol. 188, 958–967 (2006).
24. Horstmann, J. A. et al. Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion. Nat. Commun. 11, 2013 (2020).
25. Ikeda, J. S. et al. Flagellar phase variation of Salmonella enterica serovar typhimurium contributes to virulence in the murine typhoid infection model but does not influence Salmonella induced enteropathogenesis. Infect. Immun. 69, 3021–3030 (2001).
26. Horstmann, J. A. et al. Flagellin phase-dependent swimming on epithelial cell surfaces contributes to productive Salmonella gut colonisation. Cell. Microbiol. 19, e12739 (2017).
27. Samatey, F. A. et al. Structure of the bacterial flagellar protofilament and implications for a switch for supercoiling. Nature 410, 331–337 (2001).
28. Yonekura, K., Maki-Yonekura, S. & Namba, K. Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature 424, 643–650 (2003).
29. 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).
30. Mimori-Kiyosue, Y., Yamashita, I., Fujiyoshi, Y., Yamaguchi, S. & Namba, K. Role of the outermost subdomain of Salmonella flagellin in the filament structure revealed by electron cryomicroscopy. J. Mol. Biol. 284, 521–530 (1998).
31. Yamaguchi, S., Fujita, H., Sugata, K., Taira, T. & Iino, T. Genetic analysis of H2, the structural gene for phase-2 flagellin in Salmonella. J. Gen. Microbiol. 130, 255–265 (1984).
32. Yamaguchi, T. et al. Structural and functional comparison of Salmonella flagellar filaments composed of FljB and FliC. Biomolecules 10, 246 (2020).
33. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. PNAS. 97, 6640–6645 (2000).
34. Hara, N., Namba, K. & Minamino, T. Genetic characterization of conserved charged residues in the bacterial flagellar type III export protein FlhA. PLoS One 6, e22417 (2011).
35. Toma, S. Structure of the Flagellar Filament of Salmonella FljB and Its Difference from the FliC Filament. Dr. thesis (2015).
36. Dubochet, J. et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129– 228 (1988).
37. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
38. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. elife 7, e42166 (2018).
39. Webb, B. & Sali, A. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinforma. 54, 5.6.1-5.6.37. (2016).
40. Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
41. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
42. Afonine, P. V et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. Sect. D Struct. Biol. 74, 531–544 (2018).
43. Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
44. Mimori, Y. et al. The structure of the R-type straight flagellar filament of Salmonella at 9 Å resolution by electron cryomicroscopy. J. Mol. Biol. 249, 69–87 (1995).
45. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: Recent developments in Phenix. Acta Crystallogr. Sect. D Struct. Biol. 75, 861–877 (2019).
46. Vonderviszt, F., Aizawa, S.-I. & Namba, K. Role of the disordered terminal regions of flagellin in filament formation and stability. J. Mol. Biol. 221, 1461–1474 (1991).
47. Flemming, H. C. et al. Biofilms: An emergent form of bacterial life. Nat. Rev. Microbiol. 14, 563–575 (2016).
48. Houry, A. et al. Bacterial swimmers that infiltrate and take over the biofilm matrix. PNAS. 109, 13088–13093 (2012).
49. Kubori, T. et al. Purification and characterization of the flagellar hook-basal body complex of Bacillus subtilis. Mol. Microbiol. 24, 399–410 (1997).
50. Akiba, T., Yoshimura, H. & Namba, K. Monolayer crystallization of flagellar L-P rings by sequential addition and depletion of lipid. Science 252, 1544–1546 (1991).
51. Aizawa, S.-I., Dean, G. E., Jones, C. J., Macnab, R. M. & Yamaguchi, S. Purification and Characterization of the Flagellar Hook-Basal Body Complex of Salmonella typhimurium. J. Bacteriol. 161, 836–849 (1985).
52. Kaplan, M. et al. In situ imaging of the bacterial flagellar motor disassembly and assembly processes. EMBO J. 38, e100957 (2019).
53. Zhu, S. et al. In situ structures of polar and lateral flagella revealed by cryo-electron tomography. J. Bacteriol. 201, e00117-19 (2019).
54. Ferreira, J. L. et al. γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures. PLoS Biol. 17, e3000165 (2019).
55. Zhu, S. & Gao, B. Bacterial Flagella Loss under Starvation. Trends Microbiol. vol. 28 785–788 (2020).
56. Kaplan, M. et al. Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient. PNAS. 117, 8941–8947 (2020).
57. Kubori, T., Shimamoto, N., Yamaguchi, S., Namba, K. & Aizawa, S.-I. Morphological pathway of flagellar assembly in Salmonella typhimurium. J. Mol. Biol. 226, 433–446 (1992).
58. Nambu, T., Minamino, T., Macnab, R. M. & Kutsukake, K. Peptidoglycan-hydrolyzing activity of the FlgJ protein, essential for flagellar rod formation in Salmonella typhimurium. J. Bacteriol. 181, 1555–1561 (1999).
59. Cohen, E. J. & Hughes, K. T. Rod-to-hook transition for extracellular flagellum assembly is catalyzed by the L-ring-dependent rod scaffold removal. J. Bacteriol. 196, 2387–2395 (2014).
60. Rapoport, T. A. Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes. Nature 450, 663–669 (2007).
61. Homma, M., Komeda, Y., Iino, T. & Macnab, R. M. The flaFIX gene product of Salmonella typhimurium is a flagellar basal body component with a signal peptide for export. J. Bacteriol. 169, 1493–1498 (1987).
62. Jones, C. J., Homma, M. & Macnab, R. M. L-, P-, and M-ring proteins of the flagellar basal body of Salmonella typhimurium: Gene sequences and deduced protein sequences. J. Bacteriol. 171, 3890–3900 (1989).
63. Nambu, T. & Kutsukake, K. The Salmonella FlgA protein, a putative periplasmic chaperone essential for flagellar P ring formation. Microbiology 146, 1171–1178 (2000).
64. Matsunami, H., Yoon, Y. H., Meshcheryakov, V. A., Namba, K. & Samatey, F. A. Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Sci. Rep. 6, 27399 (2016).
65. Hizukuri, Y., Yakushi, T., Kawagishi, I. & Homma, M. Role of the Intramolecular Disulfide Bond in FlgI, the Flagellar P-Ring Component of Escherichia coli. J. Bacteriol. 188, 4190–4197 (2006).
66. Chevance, F. F. V. et al. The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. Genes Dev. 21, 2326–2335 (2007).
67. Hizukuri, Y., Kojima, S., Yakushi, T., Kawagishi, I. & Homma, M. Systematic Cys mutagenesis of FlgI, the flagellar P-ring component of Escherichia coli. Microbiology 154, 810–817 (2008).
68. Okuda, S. & Tokuda, H. Lipoprotein sorting in bacteria. Annu. Rev. Microbiol. 65, 239–259 (2011).
69. Schoenhals, G. J. & Macnab, R. M. Physiological and biochemical analyses of FlgH, a lipoprotein forming the outer membrane L ring of the flagellar basal body of Salmonella typhimurium. J. Bacteriol. 178, 4200–4207 (1996).
70. Jones, C. J., Macnab, R. M., Okino, H. & Aizawa, S.-I. Stoichiometric analysis of the flagellar hook-(basal-body) complex of Salmonella typhimurium. J. Mol. Biol. 212, 377–387 (1990).
71. Sosinsky, G. E. et al. Mass determination and estimation of subunit stoichiometry of the bacterial hook-basal body flagellar complex of Salmonella typhimurium by scanning transmission electron microscopy. PNAS. 89, 4801–4805 (1992).
72. Tan, J. et al. Structural basis of assembly and torque transmission of the bacterial flagellar motor. Cell 184, 2665-2679.e19 (2021).
73. Hiraoka, K. D. et al. Straight and rigid flagellar hook made by insertion of the FlgG specific sequence into FlgE. Sci. Rep. 7, 46723 (2017).
74. Johnson, S. et al. Molecular structure of the intact bacterial flagellar basal body. Nat. Microbiol. 6, 712–721 (2021).
75. Minamino, T., Kinoshita, M. & Namba, K. Fuel of the bacterial Flagellar type III protein export apparatus. Methods Mol. Biol. 1593, 3–16 (2017).
76. Kawamoto, A. et al. Common and distinct structural features of Salmonella injectisome and flagellar basal body. Sci. Rep. 3, 3369 (2013).
77. Karlinsey, J. E., Pease, A. J., Winkler, M. E., Bailey, J. L. & Hughes, K. T. The flk gene of Salmonella typhimurium couples flagellar P-and L-ring assembly to flagellar morphogenesis. J. Bacteriol. 179, 2389–2400 (1997).
78. Yamaguchi, T. et al. Structure of the molecular bushing of the bacterial flagellar motor. Nat. Commun. 12, 4469 (2021).
79. Redmon, J., Divvala, S., Girshick, R. & Farhadi, A. You only look once: Unified, real-time object detection. Proc. IEEE Conf. Comput. Vis. Pattern Recognit. 779–788 https://doi.org/10.1109/CVPR.2016.91 (2016)..
80. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
81. Rubinstein, J. L. & Brubaker, M. A. Alignment of cryo-EM movies of individual particles by optimization of image translations. J. Struct. Biol. 192, 188–195 (2015).
82. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 2017 143 14, 290–296 (2017).
83. Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999).
84. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome. PNAS. 98, 10037–10041 (2001).
85. Dolinsky, T. J., Nielsen, J. E., McCammon, J. A. & Baker, N. A. PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32, W665-667 (2004).
86. Johnson, S. et al. Molecular structure of the intact bacterial flagellar basal body. Nat. Microbiol. 6, 712–721 (2021).
87. Diepold, A. & Armitage, J. P. Type III secretion systems: The bacterial flagellum and the injectisome. Philos Trans R Soc L. B Biol Sci 370, 20150020 (2015).
88. Hu, J. et al. Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin. Nat. Commun. 9, 3840 (2018).
89. Yan, Z., Yin, M., Xu, D., Zhu, Y. & Li, X. Structural insights into the secretin translocation channel in the type II secretion system. Nat. Struct. Mol. Biol. 24, 177–183 (2017).
90. Weaver, S. J. et al. CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae. Nat. Commun. 11, 5080 (2020).
91. Kojima, S. et al. Insights into the stator assembly of the Vibrio flagellar motor from the crystal structure of MotY. PNAS. 105, 7696–7701 (2008).
92. Kawabata, T. MATRAS: A program for protein 3D structure comparison. Nucleic Acids Res. 31, 3367–3369 (2003).
93. Minamino, T. & Macnab, R. M. Components of the Salmonella flagellar export apparatus and classification of export substrates. J. Bacteriol. 181, 1388–1394 (1999).
94. Sowa, Y. et al. Direct observation of steps in rotation of the bacterial flagellar motor. Nature 437, 916–919 (2005).
95. Nakamura, S., Kami-ike, N., Yokota, J.-I. P., Minamino, T. & Namba, K. Evidence for symmetry in the elementary process of bidirectional torque generation by the bacterial flagellar motor. PNAS. 107, 17616–17620 (2010).
96. Thomas, D. R., Morgan, D. G. & DeRosier, D. J. Rotational symmetry of the C ring and a mechanism for the flagellar rotary motor. PNAS. 96, 10134–10139 (1999).
97. Suzuki, H., Yonekura, K. & Namba, K. Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single-particle image analysis. J. Mol. Biol. 337, 105– 113 (2004).
98. Johnson, S. et al. Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation. Nat. Microbiol. 5, 966–975 (2020).
99. Kawamoto, A. et al. Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries. Nat. Commun. 12, 4223 (2021).
100. Suzuki, T., Iino, T., Horiguchi, T. & Yamaguchi, S. Incomplete flagellar structures in nonflagellate mutants of Salmonella typhimurium. J. Bacteriol. 133, 904–915 (1978).