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Port Meadow flooded, February 2021

Professor Richard Berry D. Phil.

Professor of Biological Physics

Research theme

  • Biological physics

Sub department

  • Condensed Matter Physics

Research groups

  • Oxford Molecular Motors
Richard.Berry@physics.ox.ac.uk
Telephone: 01865 (2)72288,01865 (2)71723
Clarendon Laboratory, room 273B
  • About
  • Links
  • Publications

Molecular structure of the intact bacterial flagellar basal body

Nature Microbiology Springer Nature 6:6 (2021) 712-721

Authors:

Steven Johnson, Emily J Furlong, Justin C Deme, Ashley L Nord, Joseph JE Caesar, Fabienne FV Chevance, Richard M Berry, Kelly T Hughes, Susan M Lea
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The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility

The EMBO journal EMBO Press 40:6 (2021) e104683

Authors:

Oshri Afanzar, Diana Di Paolo, Miriam Eisenstein, Kohava Levi, Anne Plochowietz, Achillefs N Kapanidis, Richard Michael Berry, Michael Eisenbach

Abstract:

Regulatory switches are wide spread in many biological systems. Uniquely among them, the switch of the bacterial flagellar motor is not an on/off switch but rather controls the motor's direction of rotation in response to binding of the signaling protein CheY. Despite its extensive study, the molecular mechanism underlying this switch has remained largely unclear. Here, we resolved the functions of each of the three CheY-binding sites at the switch in E. coli, as well as their different dependencies on phosphorylation and acetylation of CheY. Based on this, we propose that CheY motor switching activity is potentiated upon binding to the first site. Binding of potentiated CheY to the second site produces unstable switching and at the same time enables CheY binding to the third site, an event that stabilizes the switched state. Thereby, this mechanism exemplifies a unique combination of tight motor regulation with inherent switching flexibility.
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Motile ghosts of the halophilic archaeon, Haloferax volcanii

Proceedings of the National Academy of Sciences National Academy of Sciences 117:43 (2020) 26766-26772

Authors:

Yoshiaki Kinosita, Nagisa Mikami, Zhengqun Li, Frank Braun, Tessa EF Quax, Chris van der Does, Robert Ishmukhametov, Sonja-Verena Albers, Richard M Berry

Abstract:

Archaea swim using the archaellum (archaeal flagellum), a reversible rotary motor consisting of a torque-generating motor and a helical filament, which acts as a propeller. Unlike the bacterial flagellar motor (BFM), ATP (adenosine-5′-triphosphate) hydrolysis probably drives both motor rotation and filamentous assembly in the archaellum. However, direct evidence is still lacking due to the lack of a versatile model system. Here, we present a membrane-permeabilized ghost system that enables the manipulation of intracellular contents, analogous to the triton model in eukaryotic flagella and gliding Mycoplasma. We observed high nucleotide selectivity for ATP driving motor rotation, negative cooperativity in ATP hydrolysis, and the energetic requirement for at least 12 ATP molecules to be hydrolyzed per revolution of the motor. The response regulator CheY increased motor switching from counterclockwise (CCW) to clockwise (CW) rotation. Finally, we constructed the torque–speed curve at various [ATP]s and discuss rotary models in which the archaellum has characteristics of both the BFM and F1-ATPase. Because archaea share similar cell division and chemotaxis machinery with other domains of life, our ghost model will be an important tool for the exploration of the universality, diversity, and evolution of biomolecular machinery.
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Distinct chemotactic behavior in the original Escherichia coli K-12 depending on forward-and-backward swimming, not on run-tumble movements

Scientific Reports Springer Nature 10:1 (2020) 15887

Authors:

Yoshiaki Kinosita, Tsubasa Ishida, Myu Yoshida, Rie Ito, Yusuke V Morimoto, Kazuki Goto, Richard M Berry, Takayuki Nishizaka, Yoshiyuki Sowa
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Assembly and Dynamics of the Bacterial Flagellum.

Annual review of microbiology 74 (2020) 181-200

Authors:

Judith P Armitage, Richard M Berry

Abstract:

The bacterial flagellar motor is the most complex structure in the bacterial cell, driving the ion-driven rotation of the helical flagellum. The ordered expression of the regulon and the assembly of the series of interacting protein rings, spanning the inner and outer membranes to form the ∼45-50-nm protein complex, have made investigation of the structure and mechanism a major challenge since its recognition as a rotating nanomachine about 40 years ago. Painstaking molecular genetics, biochemistry, and electron microscopy revealed a tiny electric motor spinning in the bacterial membrane. Over the last decade, new single-molecule and in vivo biophysical methods have allowed investigation of the stability of this and other large protein complexes, working in their natural environment inside live cells. This has revealed that in the bacterial flagellar motor, protein molecules in both the rotor and stator exchange with freely circulating pools of spares on a timescale of minutes, even while motors are continuously rotating. This constant exchange has allowed the evolution of modified components allowing bacteria to keep swimming as the viscosity or the ion composition of the outside environment changes.
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