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Molecular Mechanisms of self-assembly and motion of the bacterial flagellum
Mexico-Japan Workshop on Pharmacobiology and NanobiologyUniversidad Nacional Autonoma de México (UNAM)
Mexico City, Mexico 2009.02.25-26
Keiichi Namba
Graduate School of Frontier BiosciencesOsaka University
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Protonic NanoMachine
Bacteria Swimming
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Protonic NanoMachine
Electron micrograph of Salmonella
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Protonic NanoMachine
Flagellar bundle rotation
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Protonic NanoMachine
Bacterial flagellum (Basal body-Hook-Filament)
By Nao Moriya
basal body
Hook-filament junction
hook
filament
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Protonic NanoMachine
Flagellar motor driven by the proton motive force
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Protonic NanoMachine
Filament
L ring
P ring
Hook
HAP2
S ring
C ring
HAP3HAP1
M ringFliGFliMFliN
Inner membrane
Outer membrane
Peptidoglycan layer
FliF
MotBMotA
Rod
Export apparatus
Structures and functions
ofthe bacterial flagellum
Cytoplasmic chaperones (FlgN,FliJ,FliS,FliT)
(FlhA,FlhB,FliH,FliI,FliO,FliP,FliQ,FliR)
Protein export system(ATPase driven)
Rotary motor(proton driven)
Universal joint Helical propeller
Assembly Promoter
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Protonic NanoMachine Lab
SPring-8 at Harima, Hyogo, Japan
Super Photon ring 8 GeV (giga electron volt)Highly brilliant X-ray with variable wavelength
by synchrotron radiation
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Protonic NanoMachine
Crystallography of flagllar proteins (update December 2007)
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Protonic NanoMachine Lab
Electron CryoMicroscope JEM3000SFF(300 kV FEG & specimen holder cooled at 4 K)
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Protonic NanoMachine
Electron cryomicroscopy of flagellar subcomplexes
Miyata & Kato, unpublished
Hook basal body Polyrod basal body
Fujii & Kato, unpublished
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Protonic NanoMachine
Filament
L ring
P ring
Hook
HAP2
S ring
C ring
HAP3HAP1
M ringFliGFliMFliN
Inner membrane
Outer membrane
Peptidoglycan layer
FliF
MotBMotA
Rod
Export apparatus
Structures and functions
ofthe bacterial flagellum
Cytoplasmic chaperones (FlgN,FliJ,FliS,FliT)
(FlhA,FlhB,FliH,FliI,FliO,FliP,FliQ,FliR)
Protein export system(ATPase driven)
Rotary motor(proton driven)
Universal joint Helical propeller
Assembly Promoter
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Protonic NanoMachine Lab
Structure of the filament as a helical propeller with switchable helical hand
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Protonic NanoMachine
Flagellar bundle rotation
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Protonic NanoMachine
Run and Tumble
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Protonic NanoMachine
Switching from left-handed to right-handed supercoil
by quick reversal of the motor rotation
Macnab & Ornston (1977) J. Mol. Biol.
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Protonic NanoMachine
A model of polymorphic supercoiling
Based on the proposal by Asakura (1970) and Calladine (1975)
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Protonic NanoMachine LabImage recorded by H. Hotani
Polymorphic transition - Normal to Curly 1 & 2
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Protonic NanoMachine
Repeat distance along the protofilament
L-type R-type
Yamashita et al. (1998) Nature Struct. Biol.
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Protonic NanoMachine Lab
Models of 10 supercoils with 2 straight filaments
#: the number of the R-type protofilaments
Left handed Right handed
2 3 4 51 6 9 10 117 80#
L R
Run
Tumble
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Protonic NanoMachine
Comparison of the two structures at 10 Å resolution
100 Å
Mimori-Kiyosue et al. (1996) P.N.A.S.
Subtle changes in the conformationstill not visibleat this resolution
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Protonic NanoMachine Lab
Disassembly into subunits for crystallization
D3
D3D2
D2D1
D1D0D0
D3
D2
D1
D0 D2
D3
D1
D0
○
○×
(1) (494)
SJW1103
F40
F27
(66)
(178) (422)
(450)
D1 D2 D1D0 D3 D0
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Protonic NanoMachine Lab
Crystal of the F41 fragment of flagellin
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Protonic NanoMachine
Cα backbone trace of F41
Samatey et al. (2001) Nature
D1D3 D2
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Protonic NanoMachine Lab
Crystal packing of F41 (a-c plane)
51.9 Å
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Protonic NanoMachine
A protofilament on EM map and the filament model
Samatey, Imada et al. (2001) Nature
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Protonic NanoMachine Lab
Crystal packing of F41 (a-c plane)
51.9 Å
52.7 Å
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Protonic NanoMachine Lab
Simulated extension of the protofilament
51.9 Å
52.7 Å
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Protonic NanoMachine Lab
Distribution and packing of hydrophobic side chains
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Protonic NanoMachine
Image of a single filament and its Fourier transform
Mimori et al. (1995) J. Mol. Biol.
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Protonic NanoMachine
High-resolution cryoEM map of the filament(Resolution: meridional, 4 Å; equatorial, 5 Å)
Average of 100 filament images (~ 41,000 molecules)with unbending and solvent flattening refinement
Yonekura & Maki-Yonekura et al. (2003) Nature
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Protonic NanoMachine
Complete atomic model of the flagellar filament
Yonekura & Maki-Yonekura et al. (2003)
Nature
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Protonic NanoMachine Lab
Structure of the hook for universal joint mechanism
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Protonic NanoMachine
The flagellar hook
Filament
L ring
P ring
Hook
HAP2
S ring
C ring
HAP3HAP1
M ringFliGFliMFliN
Inner membrane
Outer membrane
Peptidoglycan layer
FliF
MotBMotA
Rod
Export apparatus
(FliE,FlgB,FlgC,FlgF,FlgG)
hook
Functions as a universal joint, transmitting the motor torque to the helical propeller oriented in different directions.
Length: 55 nm (±6 nm)Number of subunits: ~130
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Protonic NanoMachine
Flagellar hook working as a universal joint
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Protonic NanoMachine
Run and Tumble
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Protonic NanoMachine
Samatey, Matsunami, Imada et al. (2004) Nature
Cα Backbone of FlgE-32
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Protonic NanoMachine
Bacterial flagellum (Basal body-Hook-Filament)
By Nao Moriya
basal body
Hook-filament junction
hook
filament
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Protonic NanoMachine
Universal joint motion of the flagellar hook
Basal body
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Protonic NanoMachine
Universal joint motion of the flagellar hook
Basal body
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Protonic NanoMachine
Simulated extension of a hook protofilament model
Molecular dynamic simulation of hook protofilament extension by Akio Kitao
Samatey, Matsunami, Imada et al. (2004) Nature
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Protonic NanoMachine
Universal joint motion of the flagellar hook
Basal body
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Protonic NanoMachine Lab
Self-assembly of the flagellum
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Protonic NanoMachine
The assembly process of the bacterial flagellum (update 2002)
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Protonic NanoMachine
Nature of lateral intersubnit interactions in the filamentand inner surface of the central channel
* D1-D1: hydrophilic* D0-D0: hydrophobic* Surface of the central channel: hydrophilic
(Inner diameter of the channel: 20 Å)
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Three caps for flagellar assembly
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Filament
L ring
P ring
Hook
HAP2
S ring
C ring
HAP3HAP1
M ringFliGFliMFliN
Inner membrane
Outer membrane
Peptidoglycan layer
FliF
MotBMotA
Rod
Export apparatus
Flagellar protein export at the base and self-assembly at the
distal end
Cytoplasmic chaperones (FlgN,FliJ,FliS,FliT)
(FlhA,FlhB,FliH,FliI,FliO,FliP,FliQ,FliR)
Assembly Promoter
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3D structure of the HAP2 pentamer cap
2D average of side-view images
Pentamer cap as one half of the HAP2 decamerMaki-Yonekura & Yonekura et al. (2003) P.N.A.S.
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Rotary mechanism of the flagellar cappromoting the self-assembly of flagellin
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Protonic NanoMachine
Single particle cryoEM image analysis of the basal body
Miyata & Kato unpublished
100 Å
C ring
M ringS ring
P ring
L ring
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Protonic NanoMachine
Structural information of important part still largely missing
Where? Where?
Where?
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Protonic NanoMachine
Lab members
April 5, 2007 at EXPO Park
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Protonic NanoMachine
Protonic NanoMachine Project, ERATO, JST (1997-2002)Dynamic NanoMachine Project, ICORP, JST (2002-2007)