The molecular control and evolution of bacterial shapecnls.lanl.gov/annual27/Speaker Talks/Weibel...
Transcript of The molecular control and evolution of bacterial shapecnls.lanl.gov/annual27/Speaker Talks/Weibel...
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Doug Weibel
The molecular control and evolution of bacterial shape
Dept. of BiochemistryUniversity of Wisconsin-Madison
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Overview
Introduction to bacteriaSpatial organization of intracellular components
Conclusion and outlook
Part iMolecular control of cell shape in bacteria
Part ii (brief)Evolution of bacterial cell shape
Part iii (brief)Shape vs hydrodynamics at low Re
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Overview
Introduction to bacteriaSpatial organization of intracellular components
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Spatial organization: three fundamentals
10 μm
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Spatial organization: three fundamentalsi. What is the organization of machinery in cells?
10 μm
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Spatial organization: three fundamentalsi. What is the organization of machinery in cells?ii. How is organization established (mol. level)?
10 μm
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Spatial organization: three fundamentalsi. What is the organization of machinery in cells?ii. How is organization established (mol. level)?iii. How is organization replicated?
10 μm
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Spatial organization: three fundamentalsi. What is the organization of machinery in cells?ii. How is organization established (mol. level)?iii. How is organization replicated?
Torsten Wittman, UCSF Nikon
10 μm
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Spatial organization: three fundamentalsi. What is the organization of machinery in cells?ii. How is organization established (mol. level)?iii. How is organization replicated?
Our understanding in eukaryotic cells is emerging
Torsten Wittman, UCSF Nikon
10 μm
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Spatial organization in bacteria
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Our understanding is just beginning to emerge
Spatial organization in bacteria
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Our understanding is just beginning to emerge
Spatial organization in bacteria
Bacteria are small; tools are still not available
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Our understanding is just beginning to emerge
Spatial organization in bacteria
Bacteria are small; tools are still not available
10 μm
Swiss 3T3 fibroblast
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Our understanding is just beginning to emerge
Spatial organization in bacteria
Bacteria are small; tools are still not available
10 μm
Swiss 3T3 fibroblast
Cell of E. coli
~1 μm
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Our understanding is just beginning to emerge
Spatial organization in bacteria
Bacteria are small; tools are still not available
10 μm
Swiss 3T3 fibroblast
Cell of E. coli
~1 μm
d = 0.61 λ/N.A.
NAmax (100x)=1.49
λmin=365 nm
dmax>150 nm
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Intracellular organization in bacteria
YFP-MreB chimera expressed in E. coli (Weibel)
Cell border
500 nm
GFP-FtsZ chimera expressed in E. coli (Beckwith)
GFP-Crescentin chimera expressed in C. crescentus (Jacobs-Wagner)
ParM chimera in vitro (Mullinsand Weibel)
5 μm 1 μm
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Intracellular organization in bacteria
YFP-MreB chimera expressed in E. coli (Weibel)
Cell border
500 nm
GFP-FtsZ chimera expressed in E. coli (Beckwith)
GFP-Crescentin chimera expressed in C. crescentus (Jacobs-Wagner)
ParM chimera in vitro (Mullinsand Weibel)
Actin homologs
5 μm 1 μm
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Intracellular organization in bacteria
YFP-MreB chimera expressed in E. coli (Weibel)
Cell border
500 nm
GFP-FtsZ chimera expressed in E. coli (Beckwith)
GFP-Crescentin chimera expressed in C. crescentus (Jacobs-Wagner)
ParM chimera in vitro (Mullinsand Weibel)
Actin homologs Tubulin homolog
5 μm 1 μm
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Intracellular organization in bacteria
YFP-MreB chimera expressed in E. coli (Weibel)
Cell border
500 nm
GFP-FtsZ chimera expressed in E. coli (Beckwith)
GFP-Crescentin chimera expressed in C. crescentus (Jacobs-Wagner)
ParM chimera in vitro (Mullinsand Weibel)
Actin homologs Tubulin homolog Intermediatefilament homolog
5 μm 1 μm
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Intracellular organization in bacteria
YFP-MreB chimera expressed in E. coli (Weibel)
Cell border
500 nm
GFP-FtsZ chimera expressed in E. coli (Beckwith)
GFP-Crescentin chimera expressed in C. crescentus (Jacobs-Wagner)
Bacteria ‘share’ the major classes of cytoskeletalproteins found in eukaryotes
ParM chimera in vitro (Mullinsand Weibel)
Actin homologs Tubulin homolog Intermediatefilament homolog
5 μm 1 μm
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Role of the bacterial cytoskeleton
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Role of the bacterial cytoskeleton
OrganizationPlays a role in cell shape
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Role of the bacterial cytoskeleton
OrganizationPlays a role in cell shape
DynamicsFunction?
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Role of the bacterial cytoskeleton
OrganizationPlays a role in cell shape
DynamicsFunction?
EvolutionUnknown?
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Role of the bacterial cytoskeleton
OrganizationPlays a role in cell shape
DynamicsFunction?
EvolutionUnknown?
We want to understand:The molecular basis for cell shapeThe evolution of bacterial cell shape
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Bacterial cell shape: an esoteric area?
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Bacterial cell shape: an esoteric area?
Fundamental biological question
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Bacterial cell shape: an esoteric area?
Fundamental biological question
Improves our systems level understanding of bacteria/microbes (recall: microbes account for ~50% of biomass on planet)
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Bacterial cell shape: an esoteric area?
Fundamental biological question
Improves our systems level understanding of bacteria/microbes (recall: microbes account for ~50% of biomass on planet)
Applications to pathogenesis and infectious diseases
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Overview
Part iMolecular control of cell shape in bacteria
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cocci; bacilli; spirillium
Bacterial cell shape: some examples
crescents
flat, square plates
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Copyright 2004 Pearson Education
Bacterial cell shape: structure of the cell wall
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D-Ala
L-Ala
D-Glu
meso-DAP
OO
OH
HOO
O
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C
HO2C NH2
NAG NAM
Bacterial cell shape: structure of the cell wall
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Copyright 2004 Pearson Education
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
D-Ala
L-Ala
D-Glu
meso-DAP
OO
OH
HOO
O
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C
HO2C NH2
NAG NAM
Bacterial cell shape: structure of the cell wall
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Copyright 2004 Pearson Education
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
D-Ala
L-Ala
D-Glu
meso-DAP
OO
OH
HOO
O
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C
HO2C NH2
NAG NAM
transglycosylases transglycosylases
Bacterial cell shape: structure of the cell wall
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Copyright 2004 Pearson Education
transpeptidasestranspeptidases
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
OO
OH
HOO
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C NH2
O
HO
D-Ala
L-Ala
D-Glu
meso-DAP
OO
OH
HOO
O
OH
HNO
H3C OHN
O CH3
O
ONH
H3C
H3C
HNO
CO2H
NHO
NH
CH3
O
HO2C
HO2C NH2
NAG NAM
transglycosylases transglycosylases
Bacterial cell shape: structure of the cell wall
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Copyright 2004 Pearson Education
Structure of peptidoglycan
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Structure of peptidoglycan
Mobashery, ND
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Copyright 2004 Pearson Education
Peptidoglycan (PG): Cross-linked polysaccharideSingle molecule (~100,000 kD)~20 nm thick (Gram-negative)Mechanical properties of cell
Structure of peptidoglycan
Mobashery, ND
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Mechanical properties of the PG
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Mechanical properties of the PGIsolate PG from cells (Triton X-100)Measure properties of intact PG with a scanning probe
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Mechanical properties of the PGIsolate PG from cells (Triton X-100)Measure properties of intact PG with a scanning probe
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Mechanical properties of the PGIsolate PG from cells (Triton X-100)Measure properties of intact PG with a scanning probe
T. Beveridge (1999) J. Bacteriology, 181, 6865
Properties of the PG: Perfectly elastic (no hysteresis)γpeptidoglycan: 2.5x107 N/m2
(γlatex: ~2.5x107 N/m2)
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Cell shape is controlled at the level of the PG
2. PG is synthesized in a specific orientation (sculpted into a specific shape during synthesis)
1. PG is reinforced with mechanical ‘struts’ (molded and held in place)
Two plausible mechanisms:
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Penicillin binding protein (PBP)
Does the orientation of the PG control shape?
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12 known PBPs in E. coli
Penicillin binding protein (PBP)
Does the orientation of the PG control shape?
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12 known PBPs in E. coli
Penicillin binding protein (PBP)
Does the orientation of the PG control shape?
PBPs play a key role in:Elongation of cell wall (PBP2)Division/septation (PBP3)Cell shape?
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12 known PBPs in E. coli
Penicillin binding protein (PBP)
Does the orientation of the PG control shape?
PBPs play a key role in:Elongation of cell wall (PBP2)Division/septation (PBP3)Cell shape?
PG with κlow
PG with κhigh
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Are PBPs moved/localized on a filament?
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PBP2 (synthesis of cylindrical walls) interacts with MreB
Are PBPs moved/localized on a filament?
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MreB: a homolog of actin that forms helical (?) filament(s) in rod-shaped cells
A GFP-MreB chimeraexpressed in B. subtilis(J. Errington et al.)
A mesoscale model; an elasticspring inserted in a flexible plastic tube (Weibel)
PBP2 (synthesis of cylindrical walls) interacts with MreB
Are PBPs moved/localized on a filament?
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MreB: a homolog of actin that forms helical (?) filament(s) in rod-shaped cells
A GFP-MreB chimeraexpressed in B. subtilis(J. Errington et al.)
A mesoscale model; an elasticspring inserted in a flexible plastic tube (Weibel)
PBP2 (synthesis of cylindrical walls) interacts with MreB
MreB may play a key role in controlling:Spatial organization within the cellCell shape
Are PBPs moved/localized on a filament?
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Method for dissecting role of proteins in cell shape
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We are systematically studying proteins (and protein interactions) that play a role in controlling cell shape
Method for dissecting role of proteins in cell shape
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We are systematically studying proteins (and protein interactions) that play a role in controlling cell shape
Method for dissecting role of proteins in cell shape
We want to understand how perturbations in protein levels and organization influence cell shape
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We are systematically studying proteins (and protein interactions) that play a role in controlling cell shape
Method for dissecting role of proteins in cell shape
To make this approach possible we have developed a technique for manipulating cell shape
We want to understand how perturbations in protein levels and organization influence cell shape
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hydrogel microchamber
cell growth release
Materials-based approach: (for example, rod-to-crescent)
S
N
CO2HH3C
NHH
O
NH2
O
Controlling cell shape
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hydrogel microchamber
cell growth release
Materials-based approach: (for example, rod-to-crescent)
S
N
CO2HH3C
NHH
O
NH2
O
Controlling cell shape
Steps:1. ‘Customize’ microchambers2. Seed cells3. Grow into filaments (antibiotic or Parab-FtsZ)4. Release by removing ‘ceiling’
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Filamentous cells of E. coli (filaments)
a cell of E. coli
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Filamentous cells of E. coli (filaments)
a cell of E. coli
(cephalexin)S
N
CO2HH3C
NHH
O
NH2
O
PBP3
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Filamentous cells of E. coli (filaments)
a cell of E. coli
a filament of E. coli
(cephalexin)S
N
CO2HH3C
NHH
O
NH2
O
PBP3
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Filamentous cells of E. coli (filaments)
de Pedro et al. (1997) J. Bacteriol., 179, 2823
Distribution of peptidoglycan from original cell (dark spots)
a cell of E. coli
a filament of E. coli
(cephalexin)S
N
CO2HH3C
NHH
O
NH2
O
PBP3
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transparency photomask1. expose (UV)
2. develop
3. cast hot agarose
4. cool
Fabricating molds for engineering cell shape
photoreactive polymeron Si wafer
micropatternedagarose
polymer patterned on Si wafer
coverslip
agarosecells
1. flip over
2. add cells
add transparentpolymer ‘ceiling’
polymer ceiling press ceilinginto contact
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Cells of E. coli in hydrogel containers are motile and metabolically active
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Cells of E. coli in hydrogel containers are motile and metabolically active
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Cells of E. coli in hydrogel containers are motile and metabolically active
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Cells of E. coli in hydrogel containers are motile and metabolically active
Hydrogel walls are ‘transparent’ to nutrients, ions, gas, metabolic waste
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8 μm
(di
amet
er o
f cha
mbe
r)
3 μm (width of channel)
growth over 1.5 hr; 37 ℃
Growth of cells in microchambers
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8 μm
(di
amet
er o
f cha
mbe
r)
3 μm (width of channel)
growth over 1.5 hr; 37 ℃
Growth of cells in microchambers
doubling timemold: 41 ± 4 min
doubling timesoln: ~40 min
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8 μm
(di
amet
er o
f cha
mbe
r)
3 μm (width of channel)
growth over 1.5 hr; 37 ℃
Cells retain all of the phenotypes we observe in liquid cultures
Growth of cells in microchambers
doubling timemold: 41 ± 4 min
doubling timesoln: ~40 min
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zigzags
Geometry of walls controls cell shape
sinusoids
circles
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zigzags
Geometry of walls controls cell shape
sinusoids
circles γmold >> γcell
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zigzags
Geometry of walls controls cell shape
sinusoids
circles
Cells appear to grow in an orientation that minimizesstress placed on the cell
γmold >> γcell
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Cells retain their shape after release
circles
Grow cells of E. coli (rods) in chambers
spirals/helices
Cells in liquid (with cephalexin)
Release
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Cells retain their shape after release
circles
Grow cells of E. coli (rods) in chambers
spirals/helices
Cells in liquid (with cephalexin)
Release
Cell shape has been manipulated by the application of mechanical constraints
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Dimensions of circular chambers: 8 μm diameter; 2.2 μm tall
Hysteresis accompanies release of cells
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Dimensions of circular chambers: 8 μm diameter; 2.2 μm tall
Hysteresis accompanies release of cells
After release
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Dimensions of circular chambers: 8 μm diameter; 2.2 μm tall
Hysteresis indicates strain on the cell wall
Hysteresis accompanies release of cells
After release
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Hysteresis and calculation of γcell
Serial: measurement of γcell
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Hysteresis and calculation of γcell
Serial: measurement of γcell
Calculate stress/strain curve using the ‘relaxation’ of shape after cell release
Parallel measurement of γcell
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t=0 after release t=30 min
20 μm
t=0 after release t=45 min
10 μm
Engineered cells retain their shape during growth in liquid
d=14 μm d=20 μm
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Washing out cephalexin causes cells to septate
Cells septate in the absence of cephalexin
Motile cells retain their shape
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Overview
Part ii (brief)Evolution of bacterial cell shape
Part iii (brief)Shape vs hydrodynamics at low Re
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Why do cells have defined shapes?
Evolution of bacterial shape
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Why do cells have defined shapes?
Evolution of bacterial shape
What is the evolutionary advantage of one shape over
another? cocci vs. bacilli vs. spirillium and so on...
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Why do cells have defined shapes?
Evolution of bacterial shape
What is the evolutionary advantage of one shape over
another? cocci vs. bacilli vs. spirillium and so on...
Do we understand what bacteria really look like in their
native habitats?
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Why do cells have defined shapes?
Evolution of bacterial shape
What is the evolutionary advantage of one shape over
another? cocci vs. bacilli vs. spirillium and so on...
Do we understand what bacteria really look like in their
native habitats?
Bacterial motility is one interesting case to consider
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E. coli motility requires the bundling of flagella
RunTumble
Protonic Nanomachine Projecthttp://www.npn.jst.go.jp/index.html
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Bacterial motility and shape
E. coli (wild type) vtrans~10-20 μm sec-1
Turner & Berg
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Crescents vtrans~3-4 μm sec-1
Bacterial motility and shape
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Crescents vtrans~3-4 μm sec-1
Bacterial motility and shape
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Spirals vtrans~0 μm sec-1
Bacterial motility and shape
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Spirals vtrans~0 μm sec-1
Bacterial motility and shape
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Extended spirals vtrans ~5 μm sec-1
Bacterial motility and shape
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Extended spirals vtrans ~5 μm sec-1
Bacterial motility and shape
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Hydrodynamics on motilityAre we observing hydrodynamic effects on the cell body?
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Hydrodynamics on motilityAre we observing hydrodynamic effects on the cell body?
Slender body theorum
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Hydrodynamics on motilityAre we observing hydrodynamic effects on the cell body?
Slender body theorum
translation
a
b
f = 4πηaln 2a 1
b 2_
a
b
translation
f = 8πηaln 2a 1
b 2+
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Hydrodynamics on motilityAre we observing hydrodynamic effects on the cell body?
Probably not
Slender body theorum
translation
a
b
f = 4πηaln 2a 1
b 2_
a
b
translation
f = 8πηaln 2a 1
b 2+
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Hydrodynamics on motility
Bundling
Are we observing hydrodynamic effects on the flagellum?
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Hydrodynamics on motility
Bundling
Are we observing hydrodynamic effects on the flagellum?
Probably
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Hydrodynamics on motility
Bundling
Are we observing hydrodynamic effects on the flagellum?
Probably
Why have multiple flagella if curvature prevents themfrom bundling?
Flagella are ‘expensive’ from an energetic standpoint
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Hydrodynamics on motility
Bundling
Are we observing hydrodynamic effects on the flagellum?
Probably
Why have multiple flagella if curvature prevents themfrom bundling?
Flagella are ‘expensive’ from an energetic standpoint
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Have motile cells evolved shapes that maximize the bundling of flagella?
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Have motile cells evolved shapes that maximize the bundling of flagella?
Vibrio have evolved into crescents. 21/24 species of Vibrio we have looked at have a crescent shape and a single, polar flagellum
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Have motile cells evolved shapes that maximize the bundling of flagella?
Vibrio have evolved into crescents. 21/24 species of Vibrio we have looked at have a crescent shape and a single, polar flagellum
E. coli and other multi-flagellated strains of motile bacteria are rod-shaped
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Conclusion
Relationship between intracellular organization and bacterial cell shape
Our approach is to develop new capabilities for manipulating and studying bacterial cells
New techniques for intracellular imaging
Theoretical models for studying the evolution of shape
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NIHFunding
JSPS
Matt CopelandHannah TusonCorinne LipscombBasu BhattacharyaJoe MolendaCharlie BurnsSean McMaster
George Whitesides (Harvard)
Collaborators
Shoji Takeuchi (Tokyo)
Acknowledgements
Group
Willow DiLuzio (Harvard)
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