User:Jotapefh/Hyperthermophile

Hyperthermophile its a group of organisms that have optimal growth between 80-110°C. Microorganisms are composed of aerobic and anaerobic, autotrophic and heterotrophic organisms, also in the two domains, Bacteria and Archaea. This microorganism cannot grow at a temperature lower than 50°C.

History
Life on earth evolved at temperatures as high as 110°C and the discovery that most hyperthermophiles belong to the field of archaea has led to speculation about the thermal origin of life and the properties of hyperthermophiles. Nowadays there are 2 theories about the evolution of hyperthermophiles. In particular, some authors believe that hyperthermophiles are close relatives of the last common ancestor. This hypothesis is based on the archaeal and bacterial phylogenetic tree constructed based on 16S rRNA sequence comparison. Hyperthermophiles gather at the base of these trees, and most of their branches are short, indicating that they retain the phenotypic characteristics of their ancestors. Pasteur, thanks to several experiments found that bacteria’s vegetative cells are killed at temperatures between 80-100°C, but in 1980 Karl O. Stetter and Wolfram Zillig found that there are a few bacteria species that grow fastest at higher temperatures (75°C). In fact, it was found that Sulfolobus acidocaldarius, with an aerobic lifestyle, lives at a temperature of 75°C, with a maximum of 85°C, in acid mud ponds.

One of the discoveries, that brought to do the Hyperthermophiles taxa, was that after have took some water samples in Iceland (in 1980) and boiled them, there were a lot of microorganisms with uncommon shapes, it was poured resazurin ( redox pH indicator) that indicated that these microorganisms were anaerobic living in high temperature.

Another experiment was made at Vulcano Island, the sample was taken from a submarine solfataric field close at Porto di Levante, thanks to these samples it was isolated an aerobic archaeon called Pyrodictium, ranging from 0.3 to 2.5 µm that is able to grow at a temperature above 100°C, with an optimal temperature of 105°C and a limit to 110°C. after these experiments, it was found that there is life also in the deep subterranean water with the temperature above 100°C and also in 3500M below the bottom of the North sea, and thanks to these it was described 50 new hyperthermophiles species:


 * Bacteria: Thermotog a, Thermosipho, Aquifex,  Thermocrinis.
 * Archae: Acidianus,  Metallosphaera,  Stygiolobus,  Thermoproteus, Pyrobaculum,  Thermofilum,  Desulfurococcus,  Staphylothermus,  Thermosphaera,  Thermodiscus,  Pyrodictium, Pyrolobus,  Thermococcus,  Pyrococcus,  Archaeoglobus.

For sampling and cultivating these types of genera, it needs primary material as hot waters, soils, rocks, or sediments, and very important thing is that must be avoided the oxygen’s contamination of the sample because at high temperature it becomes toxic but at low temperatures can survive for years. Positive enrichment culteres can be identified in 1 to 7 days, but pure cultures are required

The idea of ​​hyperthermophilic LCA (the last common ancestor) is also supported by protein phylogeny, which places the roots of the tree of life on bacterial branches. Only a few articles challenge these explanations. Since the comparative analysis of the three-domain of life shows that LCA is already very complicated, many evolutionary steps are beyond any "primitive" first cell-one that can speculate about how life appeared in the cold and evolved in the warm environment before LCA appeared. It is very important to clarify whether the temperature "adaptation" of today's hyperthermophiles is indeed an adaptation or a main feature so that we can correctly interpret the specific features found in these microorganisms.

The origin of reverse gyrase activity is the central issue of the debate on the nature of hyperthermophiles infact that topoisomerase is not present in all mesophilic, thermophilic organisms and it is really important because it coordinates the job of two domains or components membered of two different protein. This problem has been clarified to a certain extent through the analysis of the gene encoding the retrograde from Sulfolobus acidicola. This indicates that reverse gyrase is formed by the combination of two very different enzymes, topoisomerase and putative helicase. The helicase domain belongs to a large family of ATP-binding proteins, including DNA metabolizing enzymes, transporters, and elongation factors, while the topoisomerase domain belongs to one of two known types of DNA topoisomerase families. Therefore, these two domains cannot be combined to produce reverse gyrase activity until their respective families diversify and if reverse gyrase is a prerequisite for hyperthermophilic life, then the original microorganisms that undergo these mutations are not hyperthermophilic organisms.

This does not exclude the possibility of reverse rotation before the advent of LCA. Recently, eukaryotic type I DNA topoisomerases have been shown to interact with helicases involved in DNA recombination in vivo. This indicates that topoisomerase and helicase first appeared and evolved independently in the mesophilic or thermophilic DNA world. Some co-evolve to provide reverse gyrase-like activity; this activity is then collected into thermophilic bacteria to control the entire DNA topology, allowing certain offspring to invade the biological community at temperatures as high as 110°C. The formation of unique lipids in hyperthermophiles is also an indicator of evolutionary innovation. Many archaea and some thermophilic and hyperthermophilic bacteria have huge lipids that cover the entire width of the membrane and form a single lipid layer. This requires a new enzymatic system to concentrate two classic diesters or dieting agents. The research on the molecular biology of hyperthermophiles has just begun, so it is clear that more specific thermal adaptation mechanisms have yet to be discovered. For example, at temperatures close to the boiling point of water, the rate of DNA depurination and subsequent lysis is about 1,000 times higher than 37°C, which indicates that there are powerful DNA protection and repair mechanisms in hyperthermophiles. The first signs of support for this idea were recently described in Pyrococcus furiosus. The study reported that the DNA in P. furiosus cells exposed at 100°C is higher than the DNA in E. coli cells cultured at the same temperature. The resistance is about 20 times higher. It is not easy to imagine the original version of all the putative heat-resistant mechanisms found so far in hyperthermophiles. They seem more likely to come from systems that originally evolved in less thermophilic or even mesophilic ancestors, and they were recruited to adapt to extreme temperatures.

As mentioned earlier, the idea that hyperthermophiles are directly related to the warm origin of life comes from the hypothesis that LCA is a superthermophile. Conversely, if hyperthermophiles were previously less thermophilic or even mesophilic ancestors, it is necessary to explain why LCA is hyperthermophilic, because hyperthermophilic bacteria may outperform primitive mesophilic bacteria in adapting to lower temperatures, this may be due to the increased production of heat shock proteins.

General Physiology
Due to the fact of living in extreme environments, hyperthermophiles can be adapted to several variety of factors, like pH, redox potential, level of salinity, and temperature. They grow-similar to mesophiles-within a temperature range of about 25-30ºC between the minimal and maximal temperature. The fastest growth is obtained at their optimal growth temperature which may be up to 106ºC. The main characteristics they present in their morphology are:


 * Cell wall: the outermost part of archaea, it is arranged around the cell and protects the cell contents. It does not contain peptidoglycan, which makes them naturally resistant to lysozyme.The most common wall is a paracrystalline surface layer formed by proteins or glycoproteins of hexagonal symmetry. An exceptional peculiarity comes from the hand of the genus that lacks a wall, a deficiency that is filled by the development of a cell membrane whose unique chemical structure: it contains a lipid tetraether with and glucose in a very high proportion to the total lipids. In addition, it is accompanied by glycoproteins that together with lipids give the membrane of Thermoplasma spp stability against the acidic and thermophilic conditions in which it lives.
 * Cytoplasmic membrane: it is the main adaptation to temperature. This membrane is radically different from that known from and to eukaryotes. The membrane of Archaeabacteria is built on a tetraether unit, thus establishing ether bonds between glycerol molecules and hydrophobic side chains that do not consist of fatty acids. These side chains are mainly composed of repeating isoprene units. At certain points of the membrane, side chains linked by covalent bonds and a monolayer are found at these points. Thus, the membrane is much more stable and resistant to temperature alterations than the acidic bilayers present in eukaryotic organisms and bacteria.
 * Proteins: they denature at elevated temperatures so they must also adapt. To achieve this, they use proteins and protein complexes also known as heat shock proteins. Their function is to bind or engulf the protein during synthesis, creating an environment conducive to its correct, helping it to reach its tertiary conformation. In addition, they can collaborate in transporting news to their site of action.
 * DNA: will also adapt to elevated temperatures by several mechanisms.The first is cyclic potassium 2,3-diphosphoglycerate, which has been isolated in only a few species of the genus . Methanopyrus is characterized by the fact that it prevents DNA damage at these temperatures. Topoisomerase is an enzyme found in all hyperthermophiles. It is responsible for the introduction of positive spins in which it confers greater stability against high temperatures. Sac7d this protein has been found in the genus and characterized by an increase, up to 40 °C, in the melting temperature of DNA. And finally the histones with which these proteins are associated and collaborate in its supercoiling.

Adaptations
As a rule, hyperthermophiles do not propagate at 50ºC or below, some not even below 80 or 90º. Although unable to grow at ambient temperatures, they are able to survive there for many years. Based on their simple growth requirements, hyperthermophiles could grow on any hot water-containing site, even on other planets and moons like Mars and Europa. Thermophiles-hyperthermophiles employ different mechanisms to adapt their cells to heat, especially to the cell wall, plasma membrane and its biomolecules (DNA, proteins, etc) :


 * The presence in their plasma membrane of long-chain and saturated fatty acids in bacteria and "ether" bonds (diether or tetraether) in archaea. In some archaea the membrane has a monolayer structure which further increases its heat resistance.
 * Overexpression of GroES and GroEL chaperones that help the correct folding of proteins in situations of cellular stress such as the temperature in which they grow.
 * Accumulation of compounds such as potassium diphosphoglycerate that prevent chemical damage (depurination or depyrimidination) to DNA.
 * Production of spermidine that stabilizes DNA, RNA and ribosomes.
 * Presence of a DNA reverse DNA gyrase that produces positive supercoiling and stabilizes DNA against heat.
 * Presence of proteins with higher content in α-helix regions, more resistant to heat.

Metabolism
Hyperthermophiles have a great diversity in metabolism including chemolithoautotrophs and chemoorganoheterotrophs, while there are not phototrophic hyperthermophiles known. Sugar catabolism involves non-phosphorylated versions of the Entner-Doudoroff pathway some modified versions of the Embden-Meyerhof pathway, the canonical Embden-Meyerhof pathway is present only in hyperthermophilic Bacteria but not Archaea.

Most of informations about sugar catabolism came from observation on Pyrococcus furiosus. It grows on many different sugars such as starch, maltose, and cellobiose, that once in the cell they are transformed in glucose, but they can use even others organic substrate as carbon and energy source. Some evidences showed that glucose is catabolysed by a modified Embden-Meyerhof pathway, that is the canonical version of well-known glycolysis, present in both eukaryotes and bacteria.

Some differences discovered concerned the sugar kinase of starting reactions of this pathway: instead of conventional glucokinase and phosphofructokinase, two novel sugar kinase have been discovered. These enzymes are ADP-dependent glucokinase (ADP-GK) and ADP-dependent phosphofructokinase (ADP-PFK), they catalyse the same reactions but use ADP as phosphoryl donor, instead of ATP, producing AMP.

Ecology
The growth and survival of all microrganisms are controlled by various physical and chemical factors, including biological and non-biological. An Hypertermophile is an organism that can live outside the "normal" range of at least one environmental factor and is considered to be an organism that finds optimal growth conditions outside of the "normal" environment. Far away from the normal environment, species diversity decreases and environmental pressure increases and the latter affects the dynamic properties of proteins by distorting the protein energy profile. Environmental stress factors are usually additive, one increase increases the susceptibility of one organism to the other. There are several biological factors that determine the growth of Hypertermophiles, but the most important may be sources of nutrition and energy. For hyperthermophilic microorganisms and all organisms, liquid water is necessary for their activities, so any organisms that grow above 100°C must also be under pressure and the most important are deep-sea hydrothermal vent (found in 1977) that is a thermal anoxic area on the seafloor, where chemical-rich water is released into cold aerobic conditions. These areas, which are widely distributed around the world, are defined by biophysical and biochemical characteristics. The water is heated by the discharge of acidic fluids and thanks to the high temperature (from 407°C to 500°C) and thanks also to the contained hot rocks, chemicals, and volatile gases there is a buoyancy hydrothermal fluid that rises and flows out of orifices on the seafloor, and then rapidly mixes with cold seawater, providing a redox interface where chemical energy supports the vent ecosystem, and then everything will settle and often deposit. The steep thermal and chemical gradients in the active hydrothermal chimneys create multiple niches: Deltaproteobacteria, Epsilonproteobacteria, and Gammaproteobacteria, which are a broad family of hyperthermophiles. There also also other areas where hyperthermophile can live:


 * Freshwater alkaline hot springs: Freshwater hot springs and geysers with neutral to alkaline pH are mainly located outside the volcanic activity area. The water temperature at a depth of 500-3000m is usually below 150°C; the groundwater seeps, that are inside these high-temperature areas, heats up and returns to the surface containing dissolved minerals (such as silica), and dissolved gas as CO2 and H2S.


 * Area of the acid Solfafara field: there are a lot of sulfur, acid soil, acidic hot springs and boiling mud pots; these waters are usually characterized by a water temperature of 150 to 300°C at a depth of 500 to 3000 meters. The gases released in this area due to volcanic activity are mainly N2, CO2, H2S and H2, and methane, ammonia and CO are usually found.

Hyperthermophiles don’t live only in deep sea water, but there are also some of them that are terrestrial, living in terrestrial solfataric field so they are also acidophilic living in a pH of 1 to pH 5 with an optimum of pH3.
 * Anaerobic geothermal mud and soil: The soil of the solfatara field is hardly as acidic as the hot spring itself. The soil is usually very dense, moist, and reduced by high sulfide. The main energy sources, sulfide and hydrogen, are rich in reserves, but the biological and chemical production of sulfur and sulfate is large. Oxidized sulfur compounds and CO are the main inorganic oxidants used in this habitat.

Applied uses
Most industrial starch processes involve the hydrolysis of starch into glucose, maltose or oligosaccharide syrup. These syrups are then used as fermentation syrups to produce various chemicals (such as ethanol, lysine, and citric acid). High fructose corn syrup (HFCS) is produced by enzymatic isomerization of high glucose syrup. Starch bioprocessing usually includes two steps, liquefaction and saccharification, both of which operate at high temperatures. During the liquefaction process, starch granules are gelatinized in an aqueous solution (pH 5.8 to 6.5) at 105 to 110°C for 5 minutes in a jet cooker, and then partially hydrolyzed at a-1,4.

The characterization of T.aquaticus Taq DNA polymerase followed by the rapid popularization of technologies related to PCR a  contributed to the growing interest of scientific and industrial  communities for enzymes and hyperthermophils. The ever increasing number of enzymes characterized from organisms and the recent advent of powerful protein engineering tools suggest thermophilic and hyperthermophilic enzymes will be increasingly used in a variety applications.

Another uses is related to the DNA ligases. Thermophilic DNA ligases are commercially available. Optimally active in the range of 45 to 80 °C, they  represent an excellent complement to the PCR technology. These enzymes are great for ligating adjacent oligonucleotides are hybridized to the same target DNA. This property can be used for ligase reaction, for mutational analysis or gene synthesis.

Hyperthermophiles are also used to cellulose degradation and ethanol production. An enzymatic saccharification step makes the cellulose and degradation products suitable for ethanologenic or bacterial yeasts. Since the alkaline pretreatment of cellulose is carried out at temperature, hyperthermophilic cellulases should be the best catalysts for the degradation of cellulose. The industrial production of ethanol is currently based on corn which is first liquefied and saccharified. The use of cellulases for to increase the yields of liquefaction and saccharification of starch has been described. Since the liquefaction of starch is carried out at high temperatures, the use of thermophilic endoglucanases in the unwinding steps is an option.