Archaea

Domain Prokarya/Archaea

Kingdom Archaea

Discovery of Archaea

• Prior to 1977 they were considered bacteria

• 1977 Carl Woese and George Fox proposed a new domain/kingdom

• 1990 16S rRNA and 18S rRNA sequences justify separation

• 2003 genome sequence analysis justifies kingdom/domain status

Shifting Kingdoms2 3 5 6 8

Bacteria Bacteria Bacteria Bacteria Bacteria

Archaebacteria Archaebacteria Archaebacteria Archaebacteria Archaebacteria

Archezoans Archezoans Archezoans Archezoans Archezoans

Euglenoids Euglenoids Euglenoids Euglenoids Euglenoids

Chrysophytes Chrysophytes Chrysophytes Chrysophytes Chrysophytes

Green Algae Green Algae Green Algae Green Algae Green Algae

Brown Algae Brown Algae Brown Algae Brown Algae Brown Algae

Red algae Red algae Red algae Red algae Red algae

Slime Molds Slime Molds Slime Molds Slime Molds Slime Molds

True Fungi True Fungi True Fungi True Fungi True Fungi

Bryophytes Bryophytes Bryophytes Bryophytes Bryophytes

Tracheophytes Tracheophytes Tracheophytes Tracheophytes Tracheophytes

Protozoans Protozoans Protozoans Protozoans Protozoans

Myxozoans Myxozoans Myxozoans Myxozoans Myxozoans

Multicellular Animals

Multicellular Animals

Multicellular Animals

Multicellular Animals

Multicellular Animals

Lumpers SplittersPlantae Monera Archaea

How Many Kingdoms?

Mul

ticell

ular

Animals

Myx

ozoa

ns

Proto

zoan

s

Trache

ophy

tes

Bryop

hytes

True F

ungi

Slime M

olds

Red al

gae

Brown A

lgae

Green A

lgae

Chrys

ophy

tes

Euglen

oids

Archez

oans

Archae

bacte

ria

Bacter

ia

Original Cell

Extant

Extinct

Long Time with

Prokaryotes only

8

5

3

2

1

The prokaryotes are a? Grade!

Archaea• Ancient origin, but appreciated more recently• Somewhat more advanced than Bacteria

• Extremophiles-90°C pH2 25M anaerobic -4°C Antarctica!– Methanogens– Halophytes– Sulfur metabolism

• DNA binding proteins (but not histones)

• Unicellular, colonial, filamentous• Bacillus, coccus, spirillum, plate-like, etc.• Size: 0.1 to 15 µm diam. x 200 µm long

Archaea Cladogram

Pyrod

ictiu

m

Thermop

roteu

s

Haloc

occu

s

Thermof

ilum

Archae

oglo

bus

Desulfu

roco

ccus

Sulfolo

bus

Pyroc

occu

s

Meth

anoc

occu

s

Meth

anob

acter

ium

Thermop

lasm

a

Halof

erox

Haloa

rcula

Original Cell

ExtantGenera

to Bacteria

IgneococcalesPleu

roph

illus

Thermoc

occu

s

Ferro

glob

us

Pyrob

aculu

m

Sulfolo-hales

ThermoprotealesArchaeoglobales

Thermo-coccales

ThermoplasmalesHalobacteriales Methanogenales

EuarchaeotaCrenarchaeota

to Eukarya

ThermophilicAcidophilic

Autotrophic (CO2)Sulfur + H2 -> H2S + H+

-O2 Heterotrophic (CH2O)Sulfur+CH2O->CO2+H2S

+O2 Heterotrophic (TCAR)Sulfur + O2 -> H2SO4

HalophilicChemoheterotroph resp O2

ChemoautotrophLight->bacteriorhodopsin->ATP

Methanogens-anaerobesCO2+H2->F420 fluorescent ->CH4

Ruminant gut flora

Marshes, landfills

S+org->H2S+CO2 Hydrothermal ventsMethanogenR lactate->H2+CO2

Autotroph H2+SO4-2->H2S

Prokaryotic Growth• Cells are generally very small• Cells may double in size but only before binary

fission• Growth mostly in terms of cell number or colony

size, etc.• Doubling time in cell numbers may be 20 minutes

in ideal conditions• Could quickly take over the earth if conditions

could remain ideal• Very competitive in ideal environments• Ultimate survivors - 3.5 billion years!

Cell Structure: Boundary

Gram PositiveMethanobacterium

Gram NegativeThermoproteus

Thermoplasmacell membrane bilayer phosphoglycerohydrocarbon, etc. sulfo- or glyco-glycerohydrocarbon (ether link not ester link) transport proteins

cell wall-glycan (no muramic acid)

thin surface layer glycoprotein

cytosol

regulates input/output

prevents burstingturgor pressure

releases dye

Homeostasis - metabolism

Chemoautotroph acetyl-CoA or reverse TCA to fix CO2 Photoautotroph Calvin Cycle (Methanococcus, Pyrococcus)Chemoheterotroph citric acid cycle, fermentation Sulfur transporters used to drive ATP synthesis

Nutrition Mode Energy Source Carbon Source

Photoautotroph Light CO2

Chemoautotroph Inorganic chem CO2

Photoheterotroph Light Organic chem

Chemoheterotroph Organic chem Organic chem

Facultative and Obligate Anaerobes and Aerobes

How do Archaea tolerate the heat?• Proteins stabilized by more ionic bridges between amino acid r-groups

and more-hydrophobic core amino acids

• Heat shock protein (chaperonins) refold denatured proteins…Pyrococcus 121°C for 1 hour!

• DNA depurination reduced by presence of 2,3-diphosphoglycerate.

• DNA supercoiling by reverse gyrase reduces denaturation

• Sac7d in Sulfobolus is a minor groove protein increases the melting temperature by 40°C

• Histone-like proteins help stabilize DNA as well

• Heat-resistant di-bi-phytanyl diether lipid membranes (monolayer) prevent delamination of membrane

Cell Membrane Structure

O O

O O

R

R

O O

O O

R

R

Composed of diglyceridesR group may be phosphate, sulfate, or sugarLong chain branched hydrocarbon (not fatty acid) Hydrocarbons may be C20 or C40

If C20, the membrane is a bilayer:

If C40, the membrane is a monolayer

In some species, the membrane is a mixture of both C20 and C40 diglycerides forming a mixed mono-/bi-layer