2. ARCHAEA
by:Abbas Morovvati

3. Contents
History
Morphology, Genetics,
Comparison of Archaean, Bacterial and
Eukaryotic cells
Habitat
Scientific classification
Chaperones
Archaea in the biotechnology

4. History of archaean
microbiology
• Prior to 1977 the archaea were considered to be just
another group of bacteria when there were only two
kingdoms
• . In 1977 Carl Woese and George Fox proposed that
archaea are different enough to have their own kingdom
• In 1990 16S rRNA and 18S rRNA sequences for the
archaea were found different enough from the other
bacteria to justify this
• By 2003, the genome sequence analysis results
confirmed that archaea are really quite different from
bacteria
• The word archaea (comes from Greek αρχαία), "ancient
ones
• Archaea, Eukaryota and Bacteria are the fundamental
classifications in what is called the three-domain system

5. Phylogeny
Three Domains of Life
Prokaryota

6. Morphology
• 0.1 μm to over 15 μm in diameter
• occur in various shapes
• coccus, , rod-shape, spiral,, or plate-like
• one or more flagella attached to them, or
may lack flagella altogether

7. Cell Wall
• pseudopeptidoglycan, which is a peptide
cross-linked (beta 1,3 polysaccharide
(NAGlucosamine and
NATalosaminuronic acid).

8. Cell Membranes
• Archael lipids = branched chain hydrocarbons linked to
glycerol
• molecules by ether linkages
 Archaeal lipids are based upon the isoprenoid
 Glycerol diether(glycerol +C20 hydrocarbons ) bilayered
Membranes
 Glycerol tetraether(glycerol +C40 hydrocarbons )
monolayer Membranes
 mixture of di-&tetra-mon/bi layered
membranes

12. archaea cells come in three basic forms of
the cell boundary.
• Mycoplasma-like :
Thermoplasma cells lack a cell wall.
They have a cell membrane bilayer, but it is
made of phosphoglycohydrocarbons
live isotonic environments rather than in,
say, freshwater environments.

13. • Gram positive like:
• they retain the blue
dye-iodine complex inside the
thick cell wall after the Gram staining process
• There is no muramic acid here...so no murein
• wall material is a glycan...not a peptidoglycan
• archaea to live in a hypotonic environment

14. • Gram negative like:
• Thermoproteus surface layer
of glycan wall which may include
glycoproteins
• So the purple dye-iodine complex inside
the cell rinses right out with the alcohol
rinse.

15. Genetics
• no nucleus
• have one circular chromosome
• 30% of their genome may be contained in
plasmids
• evidenced by different GC content from
the main chromosome.
• Many archaeal tRNA and rRNA genes
harbor unique archaeal introns which are
neither like eukaryotic introns

16. Archaeal Flagella
• Distribution of flagellation throughout
the Domain Archaea
+ Halobacterium
- Halococcus Methanoplanus +
- Natronococcus Methanospirillum +
+ Archaeoglobus Methanosarcina -
- Methanobacterium
+ Methanothermus
+ Thermoproteus Thermofilum - Thermoplasma +
+ Pyrobaculum Methanococcus +
+ Sulfolobus
Pyrococcus +
+ Desulfurococcus Methanopyrus +
Pyrodictium+
EUCARYA
BACTERIA

17. Structure flagella
• composed of 3 parts; the filament, hook
and anchoring structure.
• Filament
thinner than the bacterial flagella filament
but thicker than bacterial pili

18. Genetics flagella
• only one operon has been shown to be
involved in archaeal flagellation. The
complete operon looks like:
FlaB1 FlaB2 FlaB3 FlaC FlaD FlaE FlaF FlaG FlaH FlaI FlaJ
Homology to Membrane protein
Flagellins Unknown function nucleotide FlaK
binding proteins
of the type IV Signal peptidase
pilus family

19. Comparison of Archaean,
Bacterial and Eukaryotic cells
• Archaea are similar to other prokaryotes in
most aspects of cell structure and
metabolism
• archaean translation uses eukaryotic-like
initiation and elongation factors, and their
transcription involves TATA-binding
proteins and TFIIB as in eukaryotes.

20. Characteristics of Bacterial Eucaryotic
Archaeal DNA
Bacteria Eukarya
Characteristics Archaea
Histones Absent present present
associated
with DNA
Present in
Intron Absent present
some genes
1st amino
1st amino 1st amino
Protein acid =
acid = acid =
synthesis formylmethio
methionine methionine
nine

21. Characteristics of Bacterial Eucaryotic Archaeal
cytoplasmic membranes
Characteri Bacteria Eucaryotic Archaea
stics
Protein High Low High
content
Lipid Phospholipid Phospholipids Sulfolipids,
compositio glycolipids,
n nonpolar
isoprenoid
lipids,
phospholipids
peptidoglyc Present Absent Absent
an
Lipid Ester linked Ester linked Ether linked
linkage
Sterols Absent Present Absent

22. Habitat
generally in extreme
habitats (swamps,
salt lakes, acidic hot
springs)

23. Based on environmental criteria,
archaea can be classified
Methanogens
extreme halophiles,
extreme thermophilies.

24. • Methanogens are archaea that produce
methane as a metabolic byproduct.
Methanogens are among the strictest
anaerobes.
• They live in swamps and marshes where
other microbes have consumed all the
oxygen.
– Methanogens are important decomposers in
sewage treatment.

25. • Extreme halophiles
• sometimes known as Halobacterium,
live in extremely saline environments

26. • Extreme thermophiles thrive in hot
environments.
– The optimum temperatures for most
thermophiles are 60oC-80oC.
Sulfolobus oxidizes sulfur in hot sulfur springs
Another sulfur-metabolizing thermophile lives
at 105oC water near deep-sea hydrothermal
vents.

27. Scientific classification
I. ARCHAEA
Crenarchaeota
Euryarchaeota
Korarchaeota
Nanoarchaeota

28. Euryarchaeota
• major group of Archaea
• They include the:
 methanogens
 halobacteria
 thermophilic

29. Family :Thermoplasmatales
• acidophiles, thermophilic. , growing
optimally at pH below 2.
• not contain a cell wall
• Genera:
Thermoplasma
Picrophilus
Ferroplasma

30. Thermoplasma
• , which thrive in acidic and high-temperature
environments
• facultative anaerobes and respire using sulfur
and organic carbon
• They do not contain a cell wall
• Thermoplasma contains two species, T.
acidophilum and T. volcanium.
• Both species are highly flagellated

31. Picrophilus
• extremely
acidophilic genus
• of two species: P.
oshimae and P.
torridus
• pH of -0.06.
• unable to maintain
their membrane
integrety at pH's
higher than 4
• contains an S-layer
cell wall.

32. Ferroplasma
• acidophilic iron-oxidizing
• mesophile with a temperature optimum of
approximately 35ºC, at which grows optimally at
pH of 1.7.
• does not contain a cell wall.
• cell membrane does not contain tetraether lipids.
• , F. acidophilum obtains energy by oxidation of
the ferrous iron in the pyrite using oxygen as a
terminal electron acceptor

33. Family : Archaeoglobaceae
• hyperthermophilic
Genera :
Archaeoglobus
Geoglobus
 Ferroglobus

34. Archaeoglobus
• The genus Archaeoglobus is a
hyperthermophilic
• two species
 A. fulgidus
 A. profundus
• Optimal growth at approximately 83ºC .
• Archaeoglobus can also live
chemolithoautotrophically by coupling the
oxidation of thiosulfate to the reduction of
hydrogen gas .

35. Geoglobus
• Geoglobus is a hyperthermophilic
• It consists of one species, G. ahangari
• it grows best at a temperature of 88ºC cannot grow at temperature
below 65ºC or above 90ºC.
• It possess an S-layer cell wall and a single flagellum.
• ( anaerobe )
• ferric iron (Fe3+) as a terminal electron acceptor.
• . It can grow either autotrophically using hydrogen gas
(H2) or heterotrophically using a large number of organic
compounds, including several types of fatty acids, as
energy sources.

36. Ferroglobus
• . It consists of one species,
F. Placidus
 best at 85ºC and a neutral pH
Cells possess an S-layer cell wall and flagella.
 anaerobically by oxidizing aromatic compounds such as
benzoate coupled to the reduction of ferric iron (Fe3+)
Hydrogen gas (H2) and sulfide (H2S) can also be used
as energy sources.
 nitrate (NO3-) is used as a terminal electron acceptor
whereby it is converted to nitrite
 Thiosulfate can also be used as a terminal electron
acceptor

37. Halobacterium: an example of an extreme
halophile
• They require salt concentrations
between 15% to 35% sodium chloride to live.
• Halobacteria also possess a second pigment,
bacteriorhodopsin.and halorhodopsin .
• They produce ATP by respiration or by
bacteriorhodopsin.
• The Red Sea was named after halobacterium
that turns the water red during massive blooms.

38. Bacteriorhodopsin
• It is the retinal molecule that changes its conformation when
absorbing a photon, resulting in a conformational change of the
surrounding protein and the proton pumping action.
• The bacteriorhodopsin molecule is purple and is most
efficient at absorbing green light (wavelength 500-650
nm, with the absorption maximum at 568 nm).

39. light-driven pump
bacteriorhodopsin
retinal

40. Lipids of Halobacteria
• The cytoplasmic membrane contains
unusual lipids, which are made up from C5
isoprenoid units
• isoprenoid chains are attached to glycerol
• The sulfate containing lipids are only found
in the purple membrane

41. Glycoprotein of Halobacteria
• . Instead their rod shape is maintained by
an outer layer of structural protein. This is
a glycoprotein
• below 4M Halobacteria become spherical
and finally lyse
• The first step is due to disintegration of the
glycoprotein envelope.

42. Family :Thermococcaceae
• Genus:Pyrococcus
• Species:P. furiosus
• The name Pyrococcus means
"fireberry" in Greek, The species name furiosus
means 'rushing' in Latin
 extremophile growth temperature of 100ºC
 Pyrococcus furiosus is noted for its rapid
doubling time of 37 minutes under optimal
conditions. It appears as mostly regular cocci
monopolar polytrichous flagellation

43. Methanopyrus
• Hyperthermophile
• methanogen
• single described species,
M. kandleri
• temperatures of 84-110
C
• . It lives in an hydrogen-
carbon dioxide rich
environment, and like
other methanogens
reduces the former to
methane.

44. Crenarchaeota
• extremeophiles
• have identified them as the most
abundant archaea in the marine
environment
• grow up to 113 C
• These organisms stain gram
negative and are morphologically
diverse having rod, cocci,

45. Family :Metallosphaera
• Hyperthermophiles
,growing between pH 1 and 5,
with pH 3 being optimum
• contains two species sedula and prunae
• This strain grows between 55C and 80C by
oxidation of pyrite, sphalerite,
chalcopyrite, or molecular hydrogen.

46. Family :Sulfolobaceae
• growth occurring at pH 2-3 and
temperatures of 75-80 C
• Sulfolobus cells are irregularly shaped and
flagellar
• their energy comes from the oxidation of
sulfur and/or cellular respiration in which
sulfur acts as the final electron acceptor

47. Sulfolobus as a viral host
• Lysogenic viruses infect Sulfolobus for
protection
• The viruses cannot survive in the extremely
acidic and hot conditions that Sulfolobus lives in,
• Rudiviridae is a family of recently discovered
viruses which infect crenarchaeota. Rudiviruses
were first isolated from acidic hot springs in
Iceland.

48. Korarchaeota
• extremophile
• they generate energy and obtain carbon,
are currently unknown

49. Nanoarchaeum
• Nanoarchaeum equitans –
archaea
– Hyperthermophile
– Diverged early in evolution from other archaea
– New kingdom of archaea?
• Obligate symbiont with Ignicoccus
• Smallest completely sequenced genome
– <500kB

50. How can archaea tolerate the
extremes of their environment ?
• that the proteins fold tightly and strongly to avoid
denaturation in heat or salinity.
• accumulate 2,3-diphosphoglycerate which reduces the
depurination of DNA
• The histone-like DNA binding proteins
• anzyme called gyrase; this supercoiling of the DNA can
stabilize it
• cell membrane structure

51. Chaperones
• (Chaperones are defined as proteins and protein assemblies that
help other proteins fold into their proper conformation)
• Hsp70 is a single, monomeric protein that is found
throughout the cell, Hsp70 plays many roles in the cell
• Hsp70 has two domains. The N-terminal This domain
contains an ATPase activity
• The C-terminal region is the substrate-binding domain
• hsp70 can exist in two conformations. These are the
ATP-bound state (before hydrolysis) and the ADP-bound
state

53. Archaea in the biotechnology
• Taq polymerase lacks a 3' to 5' exonuclease activity.
Thus, Taq has no error-proofreading activity
• Examples of polymerases with 3' to 5' exonuclease
activity include: KOD DNA polymerase, a recombinant
form of Thermococcus kodakaraensis KOD1; Vent,
which is extracted from Thermococcus litoralis; Pfu DNA
polymerase, which is extracted from Pyrococcus
furiosus; and Pwo, which is extracted from Pyrococcus
woesii. Tgo DNA polymerase, which is extracted from
Thermococcus. gorgonarius

54. Table. Comparison of Taq and Some
Proofreading DNA polymerases
DNA Taq Pfu Yes Vent
Polymeras 1.3 x 10-6
e
Organism Thermus Pyrococcus Thermococcus
Aquaticus Furiosus Litoralis
5'-3' Yes No NO
Exonuclease
Activity
3'-5' No Yes Yes
Exonuclease
Activity
Error Rate 8 x 10-6 1.3 x 10-6 2.8 x 10-6
(error/bp
incorporated)