Faculty Profiles - KOJIMA, Seiji

Papers - KOJIMA, Seiji

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Structural analysis of S-ring composed of FliFG fusion proteins in marine Vibrio polar flagellar motor. International journal

Norihiro Takekawa, Tatsuro Nishikino, Jun-Ichi Kishikawa, Mika Hirose, Miki Kinoshita, Seiji Kojima, Tohru Minamino, Takayuki Uchihashi, Takayuki Kato, Katsumi Imada, Michio Homma

mBio Vol. 15 ( 10 ) page： e0126124 2024.9

Language：English Publishing type：Research paper (scientific journal)

The marine bacterium Vibrio alginolyticus possesses a polar flagellum driven by a sodium ion flow. The main components of the flagellar motor are the stator and rotor. The C-ring and MS-ring, which are composed of FliG and FliF, respectively, are parts of the rotor. Here, we purified an MS-ring composed of FliF-FliG fusion proteins and solved the near-atomic resolution structure of the S-ring-the upper part of the MS-ring-using cryo-electron microscopy. This is the first report of an S-ring structure from Vibrio, whereas, previously, only those from Salmonella have been reported. The Vibrio S-ring structure reveals novel features compared with that of Salmonella, such as tilt angle differences of the RBM3 domain and the β-collar region, which contribute to the vertical arrangement of the upper part of the β-collar region despite the diversity in the RBM3 domain angles. Additionally, there is a decrease of the inter-subunit interaction between RBM3 domains, which influences the efficiency of the MS-ring formation in different bacterial species. Furthermore, although the inner-surface electrostatic properties of Vibrio and Salmonella S-rings are altered, the residues potentially interacting with other flagellar components, such as FliE and FlgB, are well structurally conserved in the Vibrio S-ring. These comparisons clarified the conserved and non-conserved structural features of the MS-ring across different species.IMPORTANCEUnderstanding the structure and function of the flagellar motor in bacterial species is essential for uncovering the mechanisms underlying bacterial motility and pathogenesis. Our study revealed the structure of the Vibrio S-ring, a part of its polar flagellar motor, and highlighted its unique features compared with the well-studied Salmonella S-ring. The observed differences in the inter-subunit interactions and in the tilt angles between the Vibrio and Salmonella S-rings highlighted the species-specific variations and the mechanism for the optimization of MS-ring formation in the flagellar assembly. By concentrating on the region where the S-ring and the rod proteins interact, we uncovered conserved residues essential for the interaction. Our research contributes to the advancement of bacterial flagellar biology.

DOI： 10.1128/mbio.01261-24

PubMed

Regulatory Role of a Hydrophobic Core in the FliG C-Terminal Domain in the Rotary Direction of a Flagellar Motor.

Nishikino T, Hatano A, Kojima S, Homma M

Biomolecules Vol. 15 ( 2 ) 2025.2

Structural insight into sodium ion pathway in the bacterial flagellar stator from marine Vibrio.

Nishikino T, Takekawa N, Kishikawa JI, Hirose M, Kojima S, Homma M, Kato T, Imada K

Proceedings of the National Academy of Sciences of the United States of America Vol. 122 ( 1 ) page： e2415713122 2025.1

Structure, function, and biophysics of bacterial motility and the flagellar motor-IUPAB2024 session commentary.

Baker MAB, Kojima S

Biophysical reviews Vol. 16 ( 5 ) page： 537 - 538 2024.10

Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2.

Uesaka K, Inaba K, Nishioka N, Kojima S, Homma M, Ihara K

PeerJ Vol. 12 page： e17126 2024

Interaction of FlhF, SRP-like GTPase with FliF, MS ring component assembling the initial structure of flagella in marine Vibrio.

Fukushima Y, Homma M, Kojima S

Journal of biochemistry Vol. 174 ( 2 ) page： 125 - 130 2023.7

Purification of the Na(+)-Driven PomAB Stator Complex and Its Analysis Using ATR-FTIR Spectroscopy.

Kojima S, Homma M, Kandori H

Methods in molecular biology (Clifton, N.J.) Vol. 2646 page： 95 - 107 2023

1. Function and structure of FlaK, a master regulator of the polar flagellar genes in marine Vibrio. Reviewed

Homma M, Kobayakawa T, Hao Y, Nishikino T, Kojima S

Journal of Bacteriology Vol. 204 ( 11 ) page： e0032022 2022.11

Roles of the second messenger c-di-GMP in bacteria: Focusing on the topics of flagellar regulation and Vibrio spp.

Homma M, Kojima S

Genes to cells : devoted to molecular & cellular mechanisms Vol. 27 ( 3 ) page： 157 - 172 2022.3

The Periplasmic Domain of the Ion-Conducting Stator of Bacterial Flagella Regulates Force Generation.

Homma M, Kojima S

Frontiers in microbiology Vol. 13 page： 869187 2022

Editorial: Flagellar Motors and Force Sensing in Bacteria.

Baker MAB, Kojima S, Nord AL, Partridge JD

Frontiers in microbiology Vol. 13 page： 833011 2022

Solution structure analysis of the periplasmic region of bacterial flagellar motor stators by small angle X-ray scattering

Liew C. W., Hynson R. M., Ganuelas L. A., Shah-Mohammadi N., Duff A. P., Kojima S., Homma M., Lee L. K.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS Vol. 495 ( 2 ) page： 1614 - 1619 2018.1

Probing the mechanism of bacterial flagella assembly by real-time fluorescent imaging

Zhuang X. -Y., Zhao Z., Homma M., Kojima S., Bai F., Lo C. -J.

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Vol. 46 page： S297 - S297 2017.7

Sodium-Driven Energy Conversion for Flagellar Rotation of the Earliest Divergent Hyperthermophilic Bacterium

Takekawa Norihiko, Nishiyama Masayoshi, Kaneseki Tsuyoshi, Kanai Tamotsu, Atomi Haruyuki, Kojima Seij, Homma Michio

BIOPHYSICAL JOURNAL Vol. 110 ( 3 ) page： 468A - 468A 2016.2

Pressure-Speed Relationship of the Sodium-Driven Flagellar Motor of Vibrio Alginolyticus

Nishiyama Masayoshi, Shimoda Yoshiki, Kimura Yoshifumi, Terazima Masahide, Homma Michio, Kojima Seiji

BIOPHYSICAL JOURNAL Vol. 106 ( 2 ) page： 578A - 578A 2014.1

Structure and function of the peptidoglycan-binding (PGB) domain of bacterial flagellar motor component MotB using systematic mutagenesis and chimeric protein with Pal

Hizukuri, Y; Morton, JF; Yakushi, T; Kojima, S; Homma, M

GENES & GENETIC SYSTEMS Vol. 83 ( 6 ) page： 488 - 488 2008.12

The polar flagellar motor of Vibrio cholerae is driven by an Na+ motive force

Kojima S, Yamamoto K, Kawagishi I, Homma M

JOURNAL OF BACTERIOLOGY Vol. 181 ( 6 ) page： 1927 - 1930 1999.3

Structural insight into sodium ion pathway in the bacterial flagellar stator from marine<i>Vibrio</i>

Tatsuro Nishikino, Norihiro Takekawa, Jun-ichi Kishikawa, Mika Hirose, Seiji Kojima, Michio Homma, Takayuki Kato, Katsumi Imada

2024.7

Publisher：Cold Spring Harbor Laboratory

Abstract

Many bacteria swim in liquid or swarm on surface using the flagellum rotated by a motor driven by specific ion flow. The motor consists of the rotor and stator, and the stator converts the energy of ion flow to mechanical rotation. However, the ion pathway and the mechanism of stator rotation coupled with specific ion flow are still obscure. Here, we determined the structures of the Na<sup>+</sup>-driven stator ofVibrio, namely PomAB, in the presence and absence of sodium ions and the structure with its specific inhibitor, phenamil, by cryo-electron microscopy. The structures and following functional analysis revealed the sodium ion pathway, the mechanism of ion selectivity, and the inhibition mechanism by phenamil. We propose a model of sodium ion flow coupled with the stator rotation based on the structures. This work provides insights into the molecular mechanisms of ion specificity and conversion of the electrochemical potential into mechanical functions.

DOI： 10.1101/2024.07.15.603494

Roles of linker region flanked by transmembrane and peptidoglycan binding region of PomB in energy conversion of the Vibrio flagellar motor. International journal

Yusuke Miyamura, Tatsuro Nishikino, Hiroaki Koiwa, Michio Homma, Seiji Kojima

Genes to cells : devoted to molecular & cellular mechanisms Vol. 29 ( 4 ) page： 282 - 289 2024.2

Language：English Publishing type：Research paper (scientific journal)

The flagellar components of Vibrio spp., PomA and PomB, form a complex that transduces sodium ion and contributes to rotate flagella. The transmembrane protein PomB is attached to the basal body T-ring by its periplasmic region and has a plug segment following the transmembrane helix to prevent ion flux. Previously we showed that PomB deleted from E41 to R120 (Δ41-120) was functionally comparable to the full-length PomB. In this study, three deletions after the plug region, PomB (Δ61-120), PomB (Δ61-140), and PomB (Δ71-150), were generated. PomB (Δ61-120) conferred motility, whereas the other two mutants showed almost no motility in soft agar plate; however, we observed some swimming cells with speed comparable for the wild-type cells. When the two PomB mutants were introduced into a wild-type strain, the swimming ability was not affected by the mutant PomBs. Then, we purified the mutant PomAB complexes to confirm the stator formation. When plug mutations were introduced into the PomB mutants, the reduced motility by the deletion was rescued, suggesting that the stator was activated. Our results indicate that the deletions prevent the stator activation and the linker and plug regions, from E41 to S150, are not essential for the motor function of PomB but are important for its regulation.

DOI： 10.1111/gtc.13102

PubMed

Changes in the hydrophobic network of the FliGMC domain induce rotational switching of the flagellar motor. International journal

Tatsuro Nishikino, Atsushi Hijikata, Seiji Kojima, Tsuyoshi Shirai, Masatsune Kainosho, Michio Homma, Yohei Miyanoiri

iScience Vol. 26 ( 8 ) page： 107320 - 107320 2023.8

Language：English Publishing type：Research paper (scientific journal)

The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliGMC, and the switch-defective FliGMC-G215A, using nuclear magnetic resonance (NMR) and molecular dynamics simulations. NMR analysis revealed multiple conformations of FliGMC, and the exchange process between these conformations was suppressed by the G215A residue substitution. Furthermore, changes in the intradomain orientation of FliG were induced by changes in hydrophobic interaction networks throughout FliG. Our finding applies to FliG in a ring complex in the flagellar basal body, and clarifies the switching mechanism of the flagellar motor.

DOI： 10.1016/j.isci.2023.107320

PubMed

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Papers - KOJIMA, Seiji