Systems Microbiology
Monday Sept 11 - Ch 4 & Ch 8.13 (Purcell & Be
Structure/Function/Motility
• GENERAL ASPECTs of BEING SMALL
• CELL MEMBRANES AND CELL WALLS
WALLS
• FLAGELLA STRUCTURE/FUNCTION
• CHEMOTAXIS
Life’s History on Earth
Prokaryote
World
Multi-cell
Life
1
Man
First
Eukaryotes
0.01
First
Invertebrates
2
PO (atm)
0.1
0.001
0.0001
GREAT OXIDATION EVENT - 2.5 BILLION YEARS AG
0.00001
4.5
4
3.5
3
2.5
2
1.5
1
Time before Present (Ga)
Photographs of various forms of life removed due to copyright restrictions.
0.5
0
th
Clostr
idium
an
op
yn
us
Bacillus
m
acteriu
Heliob
ter
bac
o
r
Arth
S
AR
SB
fe
x
us
ric
ho
m
on
as
G
ia
rd
i
a
He
xa
m
ita
l
Va
Barns et al.,1996
n
o
zo
a
ph
or
rim
lito
ha
ep
c
En
sia
Dictyo
srobiu
m
Enta
moe
ba
Naegleria
Bab
e
Tr
it
um
ma
ar
so
ys
no
Ph
pa
Try
lena
Eug
EUCARYA
Pacific
ocean
e
in
rin
as
Zea
Achiya
ria
sta ra
o
C
hy
rp
m
Po
iu
c
e
am
r
Pa
no
ha
t
Me
m
illu
ir
sp
ar
m
KORARCHAEOTA
p
Co
Cr Hom
yp
to o
mo
n
27
P
pJ
pJP78
Aq
ui
Root
Bootstrap %
x
ra
e
of
us
cc s
o
u
c
ro rote
u
lf p
su rmo
CRENARCHAEOTA
e
D he filum
T mo
50
er
Th pSL
pJP 96
Environmental
pSL 17
sequences
pS pSL 4
L2
2
pS
L1
2
Thermal
spring
biu
ro
mic
rmo
The
m
a
us
m
og
r
t
e
o
Th
rm
e
Th
Me
tha
ha
noc
e
og
occ
m
lob
us
Su
us
van
lfo
nie
Th
llii
lo
erm
bu
op
s
las
ma
no
ha
et
M
Me
H
Arc
Plan
ctom
Fle
yces
xib
a ct
er
Fla
vo
ba
cte
riu
m
E.coli
Rhodo
e
lo
m
yd
ia
lor
ob
ium
Lep
tone
ma
Ch
EURYARCHAEOTO
al
Pyro
dies
iu
G
la
ARCHAEA
hii
ccus jamesc
Methanoco
s
ccu
oco
rm
um
us
The
teri
c
m
oba
er
han
th
Met
rium
cte
io
oba
ibr
Agr
fov
s ul
De
cus ter
coc
ac
ob
cho
ne
Sy
Ch
cyclus
BACTERIA
Figure by MIT OCW.
BACTERIA
E.coli
Rhodo
cyclus
Plan
ctom
Fle
yces
xib
act
er
Fla
vo
ba
cte
riu
m
α proteobacteria
cyanobacteria
rium
cte
io
oba
ibr
Agr
fov
sul
De
cus ter
coc
ac
cho
ne
Sy
Ch
G
la
e
lo
m
yd
ia
lor
ob
ium
L
epto
ob
Ch
nem
a
Clostr
idium
Bacillus
m
acteriu
Heliob
r
acte
ob
rthr
T
r
he
x
rmo
The
m
s
ga
mu
r
to
e
o
Th
m
biu
ro
mic
Aq
ui
fe
A
Root
Figure by MIT OCW.
ENDOSYMBIONT HYPOTHESIS
- Chloroplasts arose from a symbiotic partnership between an ancestral
eukaryote and a cyanobacterium
- Mitochondria arose from a symbiotic partnership between an ancestral
eukaryote and an “alpha proteobacterium”
Life on Earth Today: The
The
Foundation
Solar energy
energy
Photosynthesis
Plants
Phytoplankton
CO2
carbon
dioxide
+
H 2O
O
water
Chemical
energy or
heat
N,P,S,Fe…..
Respiration
Animals
Animals
Bacteria
Bacteria
C6H12O6 + O2
organic
carbon
oxygen
Systems Microbiology
Monday Sept 11 - Ch 4 & Ch 8.13 (Purcell & Be
Structure/Function/Motility
• GENERAL ASPECTs of BEING SMALL
• CELL MEMBRANES AND CELL WALLS
WALLS
• FLAGELLA STRUCTURE/FUNCTION
• CHEMOTAXIS
Images removed due to copyright restrictions.
See Figures 4-11, 4-13, and 4-10a in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.
11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
“Prokaryote”
Eukaryote
Diagrams of Prokaryotic structure vs. Eukaryotic structure removed due to copyright restrictions.
See Figures 2-1a and 2-1b in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.
11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
PROKARYOTES
ARCHAEA
Methanogens
Hyperthermophiles
BACTERIA
Proteobacteria
Extreme halophiles
EUKARYA
Gram-positive
bacteria
Slime molds
Mitochondrion
Animals
Eukaryotic
"Crown species"
Fungi
Plants
Cyanobacteria
Flagellates
Chloroplast
Giardia
Hyperthermophiles
Root of the tree
EUKARYOTES
Figure by MIT OCW.
Table summary of the major differential features among Bacteria, Archaea, and Eukarya removed due to copyright restrictions. See Table 11-3 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Courtesy of Norman R. Pace. Used with permission.
th
Clostr
idium
an
op
yn
us
Bacillus
m
acteriu
Heliob
ter
fe
x
Root
Bootstrap %
27
P
pJ
pJP78
Aq
ui
rmo
m
a
us
og
rm
t
e
o
Th
rm
e
Th
biu
ro
mic
Me
S
AR
SB
Tr
it
ric
ho
m
on
as
G
ia
rd
i
a
He
xa
m
ita
Barns et al.,1996
n
o
zo
a
ph
or
m
lri
Va
lito
ha
cep
En
um
ma
ar
so
ys
no
Ph
pa
Try
lena
Eug
sia
Dictyo
srobiu
m
Enta
moe
ba
Naegleria
us
Bab
e
Pacific
ocean
e
in
rin
EUCARYA
s
no
a
th
m
llu
i
pir
ar
m
p
Co
KORARCHAEOTA
Cr Hom
yp
to o
mo
na
s
Zea
Achiya
ria
sta ra
o
C
hy
rp
m
Po
iu
ec
m
ra
Pa
x
ra
e
of
s
cu s
c
co u
ro rote
u
lf p
su rmo
CRENARCHAEOTA
e
e
D h filum
T mo
50
er
Th pSL
pJP 96
Environmental
pSL 17
sequences
pSL
pS
4
L2
2
pS
L1
2
Thermal
spring
bac
ro
Arth
The
Me
tha
ha
noc
e
og
occ
m
lob
us
Su
u
van
s
lfo
nie
T
llii
lo
he
bu
rm
op
s
las
ma
et
M
Me
EURYARCHAEOTO
al
H
Arc
E.coli
Rhodo
e
lo
m
yd
ia
lor
ob
ium
Lep
tone
ma
Ch
Pyro
dies
iu
G
la
hii
ccus jamesc
Methanoco
s
ccu
oco
rm
m
us
The
eriu
t
c
m
oba
er
han
th
Met
no
ha
rium
cte
io
oba
ibr
Agr
fov
s ul
De
cus ter
coc
ac
ob
cho
ne
Sy
Ch
ARCHAEA
cyclus
Plan
ctom
Fle
yces
xib
a ct
er
Fla
vo
ba
cte
riu
m
BACTERIA
Figure by MIT OCW.
Diagrams of cell membranes removed due to copyright restrictions.
See Figures 4-15b and 4-16 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.
11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
PROKARYOTES
ARCHAEA
Methanogens
Hyperthermophiles
BACTERIA
Proteobacteria
Extreme halophiles
EUKARYA
Gram-positive
bacteria
Slime molds
Mitochondrion
Animals
Eukaryotic
"Crown species"
Fungi
Plants
Cyanobacteria
Flagellates
Chloroplast
Giardia
Hyperthermophiles
Root of the tree
EUKARYOTES
Figure by MIT OCW.
=
O _ Ester
_
_
_
H2C O C R
=
O
_
_
_
HC O C R
O
=
_
_
_
H2C O P OO_
Figure by MIT OCW.
_
Ether
_
_
_
H2C O C R
_
_
_
HC O C R
O
=
_
_
_
H2C O P OO_
Figure by MIT OCW.
Images of cell membranes removed due to copyright restrictions.
See Figures 4-19, 4-20, 4-22, 4-23, 4-36, and Table 4-2 in Madigan, Michael, and John Martinko.
Brock Biology of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Gram-Positive
Membrane
Peptidoglycan
Figure by MIT OCW.
Gram-Negative
Periplasm
Membrane
Peptidoglycan
Outer membrane
(lipopolysaccharide and protein)
Figure by MIT OCW.
Images of cell membranes and peptidoglycan removed due to copyright restrictions.
See Figures 4-27d, 4-29, 4-30, 4-35a, 4-31b, and 4-32 in Madigan, Michael, and John Martinko. Brock Biology
of Microorganisms. 11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN:0131443291.
Images of flagella and pili removed due to copyright restrictions.
See Figures 4-37, 4-54, and 4-38 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms.
11th ed. Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
http://www.rowland.harvard.edu/labs/bacteria/projects_filament.html, Howard Berg
Filaments in the bundle are usually normal, i.e., left-handed helices with pitch about 2.5 µm and diameter about 0.5 µm
with the motors turning counterclockwise. During the tumble, one or more motors switch to clockwise, and their filamen
leave the bundle and transform to semi-coiled, i.e., right handed helices with pitch about half of normal.
Courtesy of Howard C. Berg. Used with permission.
Purcell, Life @ Low R
Kinematic viscosity
a
h
n
r
inertial forces
viscous forces
Fluid density
anr
~
~ h
Fluid viscosity
anr
an
R= h =
V
cm2
= 10-2 sec for water
Figure by MIT OCW.
The ‘clamshell hypothesis’
Purcell, Life @ Low R
Reciprocal motion doesn’t work at low Reynolds number !
So, what does work ?
The corkscrew
Figures by MIT OCW.
Flexible oar
Purcell, Life @ Low R
Rman
=104
R=
ανρ
η
1m
Rgoldfish= 102
{
ν = 30 µ/sec
η = l centipaise
ν = 10−2 cm2/sec
R = 3x10-5
ο
coasting distance = 0.1 A
coasting time = 0.3 microsec.
{
Figure by MIT OCW.
Images of flagella removed due to copyright restrictions.
Figure by MIT OCW.
Flagellar motor
Motor is located in the membrane,
40 genes code for this protein
complex
Membrane part resemble to Fo
subunit of ATPase
S and M rings are separated from
membrane by intramembrane
proteins (mot A)
A rod connects fillament to a ring
Ring M carries 100 mot B proteins
Motion of protons through motA and
motB drives the rotation of rings and
associated rod and fillament
Rotation is driven by proton gradient
across the membrane not by ATP
hydrolyses
Diagrams of the flagellar motor
removed due to copyright restrictions .
H+
Rod
MS Ring
+
+ -+ -
+
+
+
+
+
+
-
-
-
-
+
+
+
+
-
-
-
-
+
+ -+
-
+
+ -+
Mot Protein
C Ring
+
+ -+ -
H+
+
+
-
-
-
H+
Figure by MIT OCW.
V. parahaemolyticus
100,000 rpm, 60um/sec
Sodium driven motor
Polar flagella motor senses
torque, induces laf genes !
Photographs of flagella removed due to copyright restrictions.
Ann Rev Microbiol 57: 77-100 (2003) R. Macnab, How Bacteira Assemble Flagella
Images of flagella removed due to copyright restrictions.
Diagram of flagellar assembly removed due to copyright restrictions.
See Figure 4-57 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed.
Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Flagellar assembly
Pre Type III Export
FlhA
FlhB
FliO
OM FliP
P
FliF
FliQ
CM
FliR
MS Ring
Export
FliH
Apparatus
FliI
FliJ
FlgJ
Sec-Mediated Export
Type III Export
Motor
Switch
Proximal Rod
Type III Export
OM
P
CM
FliK
P Ring
L Ring
Distal Rod
Full-Length Hook
Nascent
Filament
"Full-Length"
Filament
Figure by MIT OCW.
R. Macnab
Howard Berg
http://www.rowland.harvard.edu/labs/bacteria/projects_filament.html
Courtesy of Howard C. Berg. Used with permission.
Diagram of flagellar motion removed due to copyright restrictions.
See Figure 4-58 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed.
Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Tumble-flagella
pushed apart
(Clockwise rotation)
Bundled flagella
(Counter-clockwise
rotation)
Flagella bundled
(Counter-clockwise
rotation)
Figure by MIT OCW.
http://www.rowland.harvard.edu/labs/bacteria/projects_filament.html, Howard Berg
Filaments in the bundle are usually normal, i.e., left-handed helices with pitch about 2.5 µm and diameter about 0.5 µm
with the motors turning counterclockwise. During the tumble, one or more motors switch to clockwise, and their filamen
leave the bundle and transform to semi-coiled, i.e., right handed helices with pitch about half of normal.
Courtesy of Howard C. Berg. Used with permission.
50 µm
Figure by MIT OCW.
Purcell, Life @ Low R
ϑ
l
Figure by MIT OCW.
Diagram removed due to copyright restrictions.
See Figure 4-62 in Madigan, Michael, and John Martinko. Brock Biology of Microorganisms. 11th ed.
Upper Saddle River, NJ: Pearson Prentice Hall, 2006. ISBN: 0131443291.
Tumble
Run
No Attractant
Figure by MIT OCW.
a) Peritrichous Flagella
Helical
bundle
Movement
Counter-clockwise
rotation
Tumbling-random
reorientation
Clockwise rotation
b) Monotrichous Flagellum
Movement
Counter-clockwise
rotation
Clockwise rotation
Movement
(random reorientation)
Figure by MIT OCW.
Tumble
Run
Attractant
Attractant Present
Figure by MIT OCW.