1. Mic 101: L 13 STT Archaea : General Characteristics
Morphological feature
Physiological diversity

2. Archaea
According to Woese’ 3 domain concept, the archaea form a domain of their own.
Prokaryotes with extreme tolerance of environmental parameters, ether-linked lipids, methionine as the first amino acid in proteins and complex RNA polymerase enzyme.
The archaea are recently discovered and characterized because of their extreme habitats.

3. Phylogenetic Overview
The domain Archaea is divided into two major and one kingdoms: The major kingdoms are Euryarchaeota and Crenarchaeota, the minor kingdom is Korarchaeota
The basis of division into kindoms is the 16s rRNA. The Archaea evolve from a common ancestor, which are most closely resembled by Korarchaeota. The Crenarchaeota had evolved in extreme hot and cold locations. The Euryarchaeota are the most evolved and diversified kingdom with a wide range of tolerance, requirement and utilizations of certain elements and compounds.

4. General Characteristics
Prokaryotic; DNA is covalently closed circular form. Plasmids are present.
70s ribosome; sensitive to diphtheria toxin
Need transcription factors for gene expression
Not sensitive to chloramphenicol, streptomycin, kanamycin
Methanogenesis is exclusive ability of Archaea
Not able to photosynthesize

5. Morphological Diversity
Chemolithotrophs can oxidize inorganic compounds as their source of energy. Eg. Sulphur is the electron donor for Sulfolobus.
Chemoautotrophs can use Carbon di oxide as their only source of carbon. Eg. Pyrococcus
Chemo-organotroph only oxidize organic compounds as source of energy; eg. Methanol and formate are oxidized by the methanogens Halophile
Methanogen produce methane gas from organic substrates.
Methanotrophs can oxidize methane as a source of energy.
Picrophiles are archaea with extreme low pH as a growth requirement

6. Physiological Diversity
Hypersaline environment has 4 M NaCl
Anoxic sediment is the bottom or a water body without molecular Oxygen
Self-heating swamp is an aquatic habitat with high organic component concentration, where excessive anaerobic metabolism creates methane and heat
Sumarine habitat is at the deep ends of the ocean
Thermal vent is an opening under water which emits warm current due to presence of hot magma in deep layers
A black smoker is a thermal vent which emits heavy concentrations of sulphur and other volcanic minerals
A solfataras is a location of boiling mud from geothermal activity
Fumaroles are opening crust of surface volcanoes

7. Extreme Halophiles An extreme halophile needs 1.5 M NaCl for growth
The highest limit for salt tolerance is 5.5M, the amount found in the dead sea
Metabolism at high salinity: the glycoproteins and cytoplasmic proteins of halophiles need high concentration of cations (Na and K) to stabilize. These proteins have a high amount of acidic amino acid residues, which can only stabilize in an ionic solution.
Organisms adapted to 0.85% NaCl solution are put to extreme osmotic pressure when they are in high NaCl concentration. As a result, water is diffused out of the cell into the extra-cellular suspension. The cell is dehydrated and dead. But halophiles can stop water diffusion through maintaining a positive pressure inside the cell. This can happen either by producing glycerol-phosphates or accumulating potassium ions.
Examples: Halo bacterium, Halorubrum, Haloferax, Haloarcula

8. Methanogens Archaea with pseudomurein in the cell wall
Strict anaerobes, require carbon monoxide, carbon dioxide, formate, methyl group and acetate as substrate
The common reaction of methanogenesis is CO2 + 4H2 = CH4 + 2H2O
Methanogens are found in swamps, rumen digestive tract, geo-thermal source, sewage sludge digestor etc.
Example: Methanococcus, Methanosarcina, Methanopyrus

9. Thermophiles Most members are obligate anaerobic chemoautotroph
Grow optimally at 55 degree Celcius
In case of mesophilic organisms, high temperature denatures proteins, rupture the membrane and melt the DNA and RNA. Thermophiles have high basic proteins surruonding the DNA so that DNA is stable at high temperature. The tetraether residue in the cell membrane lipids allow them to tolerate high temperature.
Example: Thermoplasma

10. Acidophiles Extreme acidophilic archaea can grow at pH -0.06.
Low pH destroys the cell membrane due to destruction of membrane phopholipids. But acidophiles have unusual amino acids that are sensitive to alkali but stable at low pH and impermeable to Hydrogen ion.
At pH the cell membrane of acidophiles disintegrate, killing the cell.
Example: Picrophilus

11. Sulfer-metabolizers
Oxidize H2S and S to H2SO4 and create an acidic environment in its natural habitat
pH value is below 1
Sulphur oxidation under high heat causes environmental hazard
Example: Sulfolobus

12. Crenarchaeotes
Includes members that can tolerate extreme heat and extreme cold
There are Crenarchaeotes at the Arctic region, which grow in 2 degree C and nutrient-poor water. The cells are often suspended as planktons.
Eg. Pyrolobus, Pyrodictium, Staphylothermus.

13. Korarchaeota: Hydrogen Metabolizers
Utilization of Hydrogen as an electron donor enables a cell to survive in pre-biotic conditions; ie. Conditions without organic compunds, photosynthetic carbon fixation and Oxygen dependent respiration
A hydrgen-metabolizing cell has not been isolated but the genome and proteome has been found in a mixed population from an Obsidian pool
Theoretically these cells can grow at 85 degree Celcius

14. Archaea and Evolution
If we summarize the properties of Archaea we find that these organisms have anaerobic metabolism; able to live in high temperature, pressure, acidity; able to use inorganic elements as respiratory electron donors or ultimate electron receptor; natural habitat in volcanoes, acid springs, thermal vents and ability to use Hydrogen as a substrate.
These properties match the physiological description of earth in pre-biotic conditions.
The chronological clock of archaea (16 s r RNA) shows little evolutionary changes compared to rapidly evolving cells
Therefore the Archaea are considered to be the earliest examples of cell or the least-evolved cell

15. Similarities with Eukaryotes
Some Archaea contain histone proteins bound to DNA
The ribosomes of both are sensitive to diphtheria toxin
RNA polymerase enzyme has multiple subunits
TATA sequenes present in the promoters of gene
Not sensitive to chloramphenicol, streptomycin, kanamycin

16. Similarity with bacteria
Prokaryote, DNA and plasmid structure and gene organization are same
m RNAs not poly-A tailed
Capable of nitrification, denitrification, nitogen fixation and chemolithotrophy
Synthesizes similar carbon storage component poly-beta-hydroxy butyrate
Can survive above 80 degree Celcius temperate

17. Environment and limits of life
Proteins adapted to high temperature have ionic interaction between amino acid residues (salt bridges) together with di-sulfide bonds. Heat-shock proteins continuously repair partially denatured proteins to make them active under high temperature. Special heat resistant proteins called thermosomes associate with all other proteins to adjust their thermal stability. Presence of a heat-absorbent sticky glycoprotein allows the proteins to stay in their natural form.
The DNA in the Archaea are protected from depurination and melting by the help of potassium cyclic diphosphoglycerate, archaeal histones and small heat-stable Sac 7d (unique to Archaea). High proportion of basic proteins and their interaction with acidic DNA/RNA allow the nucleic acids to render easy folding/unfolding. Besides, the Archaea replicate DNA at an extremely slow rate, allowing constant repairing of possible heat/acidic damages.
Ester linkage and biphytanyl tetraether make the cell membrane lipids stay solid at extreme conditions.
However the heat tolerance of NAD and ATP in Archaea have not been stuided yet.

18. Questions What are the unique features of Archaea?
Why are Archaea considered prokaryotes?
Why are Archaea a separate domain in the 3 Domain classification?
What are the metabolic diversities of Archaeal members?
Discuss the heat-resistance mechanisms of Archaeal nucleic acids.