ContentsHistoryMorphology, Genetics,Comparison of Archaean, Bacterial and Eukaryotic cellsHabitatScientific classificationChaperonesArchaea in the biotechnology
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
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
Cell Wall• pseudopeptidoglycan, which is a peptide cross-linked (beta 1,3 polysaccharide (NAGlucosamine and NATalosaminuronic acid).
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
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 phosphoglycohydrocarbonslive isotonic environments rather than in, say, freshwater environments.
• Gram positive like:• they retain the bluedye-iodine complex inside thethick 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
• 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.
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
Structure flagella• composed of 3 parts; the filament, hook and anchoring structure.• Filament thinner than the bacterial flagella filament but thicker than bacterial pili
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
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.
Characteristics of Bacterial Eucaryotic Archaeal DNA Bacteria EukaryaCharacteristics 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
Characteristics of Bacterial Eucaryotic Archaeal cytoplasmic membranesCharacteri Bacteria Eucaryotic Archaea stics Protein High Low High content Lipid Phospholipid Phospholipids Sulfolipids,compositio glycolipids, n nonpolar isoprenoid lipids, phospholipidspeptidoglyc Present Absent Absentan Lipid Ester linked Ester linked Ether linked linkage Sterols Absent Present Absent
Habitatgenerally in extremehabitats (swamps,salt lakes, acidic hotsprings)
Based on environmental criteria, archaea can be classifiedMethanogensextreme halophiles,extreme thermophilies.
• 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.
• Extreme halophiles• sometimes known as Halobacterium, live in extremely saline environments
• 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.
Euryarchaeota• major group of Archaea• They include the: methanogens halobacteria thermophilic
Family :Thermoplasmatales• acidophiles, thermophilic. , growing optimally at pH below 2.• not contain a cell wall• Genera:Thermoplasma PicrophilusFerroplasma
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
Picrophilus• extremely acidophilic genus• of two species: P. oshimae and P. torridus• pH of -0.06.• unable to maintain their membrane integrety at pHs higher than 4• contains an S-layer cell wall.
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
Family : Archaeoglobaceae• hyperthermophilicGenera :ArchaeoglobusGeoglobus Ferroglobus
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 .
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.
Ferroglobus• . It consists of one species,F. Placidus best at 85ºC and a neutral pHCells 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
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.
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).
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
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.
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
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.
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,
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.
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
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.
Korarchaeota• extremophile• they generate energy and obtain carbon, are currently unknown
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
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
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
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
Table. Comparison of Taq and Some Proofreading DNA polymerasesDNA Taq Pfu Yes VentPolymeras 1.3 x 10-6e Organism Thermus Pyrococcus Thermococcus Aquaticus Furiosus Litoralis 5-3 Yes No NOExonuclease Activity 3-5 No Yes YesExonuclease Activity Error Rate 8 x 10-6 1.3 x 10-6 2.8 x 10-6 (error/bpincorporated)