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

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.

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.

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

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

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

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

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

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

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

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

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.

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

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

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

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

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.

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.