Berg)

Systems MicrobiologyMonday Sept 11 - Ch 4 & Ch 8.13 (Purcell &

Structure/Function/Motility •• GENERALGENERAL ASPECTsASPECTs of BEING SMALLof BEING SMALL

•• CELL MEMBRANES AND CELLCELL WALLSMEMBRANES AND CELL WALLS

•• FLAGELLA STRUCTURE/FUNCTIONFLAGELLA STRUCTURE/FUNCTION

•• CHEMOTAXISCHEMOTAXIS

FirstEukaryotes

LifeLife’’s History on Earths History on EarthProkaryote

World

1

0.1

0.01

0.001

0.0001

0.00001

Time before Present (Ga)

P O2 (a

tm)

4.5 4 3.5 3 2.5 2 1.5 1 0.5 0

Multi-cell Life

Man

First Invertebrates

GREAT OXIDATION EVENT - 2.5 BILLION YEARS AGO

Photographs of various forms of life removed due to copyright restrictions.

BACTERIA ARCHAEA

EUCARYA

EURYARCHAEOTO

CRENARCHAEOTA

KORARCHAEOTA

Methan

ospiril

lum

Halofera

x

Ther

mop

lasm

a

Arc

haeo

glob

us

Met

hano

cocc

us v

anni

ellii

Euglena

Meth

anoco

ccus jam

eschii

Thermococcus

Methanobacterium

Methanothermus

Methanopynus

Flavo

bact

eriu

m

Plan

ctom

yces

Rhod

ocyc

lus

E.c

oli

Agrobacterium

Synechococcus

ChlamydiaChlorobiumLeptonema

ClostridiumBacillus

Heliobacterium

Arthrobacter

Thermomicrobium

Therm

us

Ther

mot

oga

Aquifex

Coprinus

Flex

ibac

ter

Desulfovibrio

Gloeobacter

HomoCryptomonas

ZeaAchiya

Costaria

Porphyra

Para

mec

ium

Bab

esia

Dic

tyos

robiu

mEnta

moe

baN

aegle

ria Trypanosom

a

Physarum EncephalitozoonValrim

orpha

Hexamita

Giardia

pJP 27

pJP7

8

marine SBARS

Pacificocean

Thermal spring

Environmentalsequences

pSL 12

pSL 4pSL 22

pSL 17

pSL 50

pJP 96Therm

ofilum

Ther

mopro

teus

Desulf

uroc

occu

s

Sulfo

lobu

s

Pyro

dies

ium

Root

Barns et al.,1996

Bootstrap %

Tritrichomonas

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”

BACTERIA

Flavo

bacte

rium

Plan

ctom

yces

Rhod

ocyc

lus

E.co

li

Agrobacterium

Synechococcus

ChlamydiaChlorobiumLeptonema

ClostridiumBacillus

Heliobacterium

Arthrobacter

Thermomicrobium

Thermus

Ther

motog

a

Aquifex

Flex

ibac

ter

Desulfovibrio

Gloeobacter

Root

α proteobacteria

cyanobacteria

Figure by MIT OCW.

Life on Earth Today: TheLife on Earth Today: TheSolar energySolar energy

COCO22 ++ HH22OOcarbon watercarbon waterdioxidedioxide

ChemicalChemicalenergy orenergy or

heatheat

FoundationFoundationPhotosynthesisPhotosynthesisPlantsPlantsPhytoplanktonPhytoplankton

CC66HH1212OO66 ++ OO22organic oxygenorganic oxygencarboncarbon

N,P,S,FeN,P,S,Fe……..

RespirationRespirationAnimalsAnimalsBacteriaBacteria

Berg)

Systems MicrobiologyMonday Sept 11 - Ch 4 & Ch 8.13 (Purcell &

Structure/Function/Motility •• GENERALGENERAL ASPECTsASPECTs of BEING SMALLof BEING SMALL

•• CELL MEMBRANES AND CELLCELL WALLSMEMBRANES AND CELL WALLS

•• FLAGELLA STRUCTURE/FUNCTIONFLAGELLA STRUCTURE/FUNCTION

•• CHEMOTAXISCHEMOTAXIS

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.

Hyperthermophiles

Giardia

Root of the tree

Flagellates

Eukaryotic"Crown species"

Plants

Fungi

AnimalsSlime molds

Hyperthermophiles Extreme halophiles

Methanogens

Chloroplast

Cyanobacteria

ProteobacteriaMitochondrion

Gram-positivebacteria

BACTERIA

PROKARYOTES

EUKARYA

EUKARYOTES

ARCHAEA

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.

BACTERIA ARCHAEA

EUCARYA

EURYARCHAEOTO

CRENARCHAEOTA

KORARCHAEOTA

Methan

ospiril

lum

Halofera

x

Ther

mop

lasm

a

Arc

haeo

glob

us

Met

hano

cocc

us v

anni

ellii

Euglena

Meth

anoco

ccus jam

eschii

Thermococcus

Methanobacterium

Methanothermus

Methanopynus

Flavo

bact

eriu

m

Plan

ctom

yces

Rhod

ocyc

lus

E.c

oli

Agrobacterium

Synechococcus

ChlamydiaChlorobiumLeptonema

ClostridiumBacillus

Heliobacterium

Arthrobacter

Thermomicrobium

Therm

us

Ther

mot

oga

Aquifex

Coprinus

Flex

ibac

ter

Desulfovibrio

Gloeobacter

HomoCryptomonas

ZeaAchiya

Costaria

Porphyra

Para

mec

ium

Bab

esia

Dic

tyos

robiu

mEnta

moe

baN

aegle

ria Trypanosom

a

Physarum EncephalitozoonValrim

orpha

Hexamita

Giardia

pJP 27

pJP7

8

marine SBARS

Pacificocean

Thermal spring

Environmentalsequences

pSL 12

pSL 4pSL 22

pSL 17

pSL 50

pJP 96Therm

ofilum

Ther

mopro

teus

Desulf

uroc

occu

s

Sulfo

lobu

s

Pyro

dies

ium

Root

Barns et al.,1996

Bootstrap %

Tritrichomonas

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.

Hyperthermophiles

Giardia

Root of the tree

Flagellates

Eukaryotic"Crown species"

Plants

Fungi

AnimalsSlime molds

Hyperthermophiles Extreme halophiles

Methanogens

Chloroplast

Cyanobacteria

ProteobacteriaMitochondrion

Gram-positivebacteria

BACTERIA

PROKARYOTES

EUKARYA

EUKARYOTES

ARCHAEA

Figure by MIT OCW.

H2C _ O _ C _ R

H2C _ O _ P _ O-

HC _ O _ C _ R

=O

=O

=O

_ Ester

_

O-Figure by MIT OCW.

H2C _ O _ C _ R

H2C _ O _ P _ O-

HC _ O _ C _ R

=O_

_

O-

Ether

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.

Peptidoglycan

Membrane

Gram-Positive

Figure by MIT OCW.

Peptidoglycan

Gram-Negative

Periplasm

Outer membrane (lipopolysaccharide and protein)

Membrane

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.

µm, 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 with the motors turning counterclockwise. During the tumble, one or more motors switch to clockwise, and their filaments 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

a

η

η

ρν

inertial forcesviscous forces ~~ aνρ

ηaνρ aν

V

Fluid viscosity

Fluid density

=

= 10-2 cm2sec for water

R =

Figure by MIT OCW.

Kinematic viscosity

The ‘clamshell hypothesis’ Purcell, Life @ Low R

Reciprocal motion doesn’t work at low Reynolds number !

So, what does work ?

The corkscrew Flexible oar

Figures by MIT OCW.

Purcell, Life @ Low R

Rman=104

Rgoldfish= 102

µν = 30 µ/sec

η = l centipaise ν = 10−2 cm2/secR = 3x10-5

coasting distance = 0.1 Acoasting time = 0.3 microsec.{ {

R =ανρ

η

ο

1

Figure by MIT OCW.

Images of flagella removed due to copyright restrictions.

Figure by MIT OCW.

FlagellarFlagellar motormotorMotor 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 .

+++- - -

++ +

+++ +

++-

-- -

--

---

+++- - -

++ +

+++ +

++-

-- -

--

---

Rod

MS Ring

C Ring

Mot Protein

H+

H+H+

Figure by MIT OCW.

V. parahaemolyticus

100,000 rpm, 60um/secSodium driven motor Polar flagella motor sensestorque, 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

R. Macnab

Motor Switch

Proximal Rod Distal Rod

FliF

FlhAFlhBFliOFliPFliQFliRFliHFliIFliJFlgJ

FliK

OM

CMP

OM

CMP

MS Ring Export Apparatus

Sec-Mediated Export

P Ring L Ring Full-Length Hook Nascent Filament

"Full-Length"Filament

Pre Type III ExportType III Export

Type III Export

Figure by MIT OCW.

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.

Bundled flagella(Counter-clockwise rotation)

Flagella bundled(Counter-clockwise rotation)

Tumble-flagella pushed apart (Clockwise rotation)

Figure by MIT OCW.

µm, 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 with the motors turning counterclockwise. During the tumble, one or more motors switch to clockwise, and their filaments 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

lϑ

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.

Run

Tumble

No Attractant Figure by MIT OCW.

Movement

Movement Movement(random reorientation)

Counter-clockwiserotation

Counter-clockwiserotation

Helical bundle

Tumbling-random reorientation Clockwise rotation

Clockwise rotation

a) Peritrichous Flagella

b) Monotrichous Flagellum

Figure by MIT OCW.

Run

Tumble

Attractant

Attractant Present

Figure by MIT OCW.