Pyrococcus furiosus
Encyclopedia
Pyrococcus furiosus is an extremophilic
species of Archaea
. It can be classified as a hyperthermophile
because it thrives best under extremely high temperatures—higher than those preferred of a thermophile
. It is notable for having an optimum growth temperature of 100°C (a temperature that would destroy most living organisms), and for being one of the few organisms identified as possessing enzymes containing tungsten
, an element rarely found in biological molecules.
It grows between 70 °C (158 °F) and 103 °C (217.4 °F), with an optimum temperature of 100 °C (212 °F), and between pH 5 and 9 (with an optimum at pH 7). It grows well on yeast extract, maltose
, cellobiose
, β-glucans, starch
, and protein sources (tryptone, peptone, casein, and meat extracts). This is a relatively wide range when compared to other archaea. Growth is very slow, or nonexistent, on amino acids, organic acids, alcohols, and most carbohydrates (including glucose
, fructose
, lactose
, and galactose
). The metabolic products of pyrococcus furiosus are CO2
and H2
. The presence of hydrogen severely inhibits its growth and metabolism; this effect can be circumvented, however, by introducing sulfur
into the organism's environment. In this case, H2S
can be produced through its metabolic processes, although no energy seems to be derived from this series of reactions. Interesting to note is that, while many other hyperthermophiles depend on sulfur for growth, P. furiosus does not.
The ability to grow on polysaccharides (maltose, cellobiose, starch) but not on the monomeric sugars suggests that oligosaccharides with various degrees of polymerization may be imported into the cell, and only afterwards hydrolyzed to glucose
.
Pyrococcus furiosus is also notable for an unusual and intriguingly simple respiratory system, which obtains energy by reducing protons to hydrogen gas and uses this energy to create a proton
gradient across its cell membrane, thereby driving ATP synthesis. Such a system could be a very early evolutionary precursor of respiratory systems in all higher organisms today.
A DNA polymerase
was discovered in P. furiosus that is unrelated to other known DNA polymerases, as no significant sequence homology was found between its two proteins and those of other known DNA polymerases. This DNA polymerase has strong 3'-5' exonucleolytic activity and a template-primer preference which is characteristic of a replicative DNA polymerase, leading scientists to believe that this enzyme may be the replicative DNA polymerase of p. furiosus. Although archaea are, in general, more like eukaroyotes than prokaryotes in terms of transcription, translation, and replication of their DNA, scientists have not been able to find many examples of DNA polymerases in archaea that are similar in structure to DNA polymerases of eukaryotes. Obtaining more information about these enzymes would allow a more comprehensive understanding of the mechanism of DNA replication in archaea[citation needed].
from Pyrococcus furiosus (also known as Pfu DNA polymerase
) can be used in the polymerase chain reaction
(PCR) DNA amplification process.
for various industrial processes. It may be possible to use the enzymes of pyrococcus furiosus for applications in such industries as food, pharmaceuticals, and fine-chemicals in which alcohol dehydrogenases
are necessary in the production of enantio- and diastereomerically pure diols. Enzymes from hyperthermophiles such as P. furiosus can perform well in laboratory processes because they are relatively resistant: they generally function well at high temperatures and high pressures, as well as in high concentrations of chemicals.
In order to make naturally-derived enzymes useful in the laboratory, it is often necessary to alter their genetic makeup. Otherwise, the naturally-occurring enzymes may not be efficient in an artificially-induced procedure. Although the enzymes of P. furiosus function optimally at a high temperature, scientists may not necessarily want to carry out a procedure at 100 °C (212 °F). Consequently, in this case, the specific enzyme AdhA was taken from P. furiosus and put through various mutations in a laboratory in order to obtain a suitable alcohol dehydrogenase for use in artificial processes. This allowed scientists to obtain a mutant enzyme that could function efficiently at lower temperatures and maintain productivity.
which can result in cell death. If these free radicals are removed, cell death can be delayed. Enzymes in plants called superoxide dismutases
remove superoxide anion radicals
from cells, but increasing the amount and activity of these enzymes is difficult and not the most efficient way to go about improving the durability of plants.
By introducing the superoxide reductases
of P. furiosus into plants, the levels of O2 can be rapidly reduced. Scientists tested this method using the arabidopsis
plant. As a result of this procedure, cell death in plants occurs less often, therefore resulting in a reduction in the severity of responses to environmental stress. This enhances the survival of plants, making them more resistant to light, chemical, and heat stress.
This study could potentially be used as a starting point to creating plants that could survive in more extreme climates on other planets such as Mars. By introducing more enzymes from extremophiles like P. furiosus into other species of plants, it may be possible to create incredibly resistant species.
, while P. abyssi is, meaning that it functions optimally at very high pressures. Using two hyperthermophilic species of archaea lessens the possibility of deviations having to do with temperature of the environment, essentially reducing the variables in the experimental design.
Besides yielding information about the barophily of certain amino acids, the experiment also provided valuable insight into the origin of the genetic code and its organizational influences. It was found that most of the amino acids that determined barophily were also found to be important in the organization of the genetic code. It was also found that more polar amino acids and smaller amino acids were more likely to be barophilic. Through the comparison of these two archaea, the conclusion was reached that the genetic code was likely structured under high hydrostatic pressure, and that hydrostatic pressure was a more influential factor in determining genetic code than temperature.
.
from geothermally heated marine sediments with temperatures between 90 °C (194 °F) and 100 °C (212 °F) collected at the beach of Porto Levante, Vulcano Island, Italy. It was first described by Dr. Karl Stetter
of the University of Regensburg
in Germany, and a colleague, Dr. Gerhard Fiala. Pyrococcus furiosus actually originated a new genus of archaea with its relatively recent discovery in 1986.
of Pyrococcus furiosus was completed in 2001 by scientists at the University of Maryland Biotechnology Institute
. The Maryland team found that the genome has 1,908 kilobases, coding for some 2,065 proteins.
, to refer to the extremophile's round shape and ability to grow in temperatures of around 100 degrees Celsius. The species name means 'rushing' in Latin
, and refers to the extremophile's doubling time.
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...
species of Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
. It can be classified as a hyperthermophile
Hyperthermophile
A hyperthermophile is an organism that thrives in extremely hot environments— from 60 degrees C upwards. An optimal temperature for the existence of hyperthermophiles is above 80°C . Hyperthermophiles are a subset of extremophiles, micro-organisms within the domain Archaea, although some bacteria...
because it thrives best under extremely high temperatures—higher than those preferred of a thermophile
Thermophile
A thermophile is an organism — a type of extremophile — that thrives at relatively high temperatures, between 45 and 122 °C . Many thermophiles are archaea...
. It is notable for having an optimum growth temperature of 100°C (a temperature that would destroy most living organisms), and for being one of the few organisms identified as possessing enzymes containing tungsten
Tungsten
Tungsten , also known as wolfram , is a chemical element with the chemical symbol W and atomic number 74.A hard, rare metal under standard conditions when uncombined, tungsten is found naturally on Earth only in chemical compounds. It was identified as a new element in 1781, and first isolated as...
, an element rarely found in biological molecules.
Properties
The species was taken from the thermal marine sediments and studied by growing it in culture in a lab. Pyrococcus furiosus is noted for its rapid doubling time of 37 minutes under optimal conditions, meaning that every 37 minutes, the number of individual organisms is multiplied by 2, yielding an exponential growth curve. It appears as mostly regular cocci—meaning that it is roughly spherical—of 0.8 µm to 1.5 µm diameter with monopolar polytrichous flagellation. Each organism is surrounded by a cellular envelope composed of glycoprotein, distinguishing them from bacteria.It grows between 70 °C (158 °F) and 103 °C (217.4 °F), with an optimum temperature of 100 °C (212 °F), and between pH 5 and 9 (with an optimum at pH 7). It grows well on yeast extract, maltose
Maltose
Maltose , or malt sugar, is a disaccharide formed from two units of glucose joined with an αbond, formed from a condensation reaction. The isomer "isomaltose" has two glucose molecules linked through an α bond. Maltose is the second member of an important biochemical series of glucose chains....
, cellobiose
Cellobiose
Cellobiose is a disaccharide with the formula [HOCH2CHO3]2O. Cellobiose consists of two glucose molecules linked by a β bond. It can be hydrolyzed to glucose enzymatically or with acid. Cellobiose has eight free alcohol groups, one acetal linkage and one hemiacetal linkages, which give rise to...
, β-glucans, starch
Starch
Starch or amylum is a carbohydrate consisting of a large number of glucose units joined together by glycosidic bonds. This polysaccharide is produced by all green plants as an energy store...
, and protein sources (tryptone, peptone, casein, and meat extracts). This is a relatively wide range when compared to other archaea. Growth is very slow, or nonexistent, on amino acids, organic acids, alcohols, and most carbohydrates (including glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...
, fructose
Fructose
Fructose, or fruit sugar, is a simple monosaccharide found in many plants. It is one of the three dietary monosaccharides, along with glucose and galactose, that are absorbed directly into the bloodstream during digestion. Fructose was discovered by French chemist Augustin-Pierre Dubrunfaut in 1847...
, lactose
Lactose
Lactose is a disaccharide sugar that is found most notably in milk and is formed from galactose and glucose. Lactose makes up around 2~8% of milk , although the amount varies among species and individuals. It is extracted from sweet or sour whey. The name comes from or , the Latin word for milk,...
, and galactose
Galactose
Galactose , sometimes abbreviated Gal, is a type of sugar that is less sweet than glucose. It is a C-4 epimer of glucose....
). The metabolic products of pyrococcus furiosus are CO2
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...
and H2
Hydrogen
Hydrogen is the chemical element with atomic number 1. It is represented by the symbol H. With an average atomic weight of , hydrogen is the lightest and most abundant chemical element, constituting roughly 75% of the Universe's chemical elemental mass. Stars in the main sequence are mainly...
. The presence of hydrogen severely inhibits its growth and metabolism; this effect can be circumvented, however, by introducing sulfur
Sulfur
Sulfur or sulphur is the chemical element with atomic number 16. In the periodic table it is represented by the symbol S. It is an abundant, multivalent non-metal. Under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a bright yellow...
into the organism's environment. In this case, H2S
Hydrogen sulfide
Hydrogen sulfide is the chemical compound with the formula . It is a colorless, very poisonous, flammable gas with the characteristic foul odor of expired eggs perceptible at concentrations as low as 0.00047 parts per million...
can be produced through its metabolic processes, although no energy seems to be derived from this series of reactions. Interesting to note is that, while many other hyperthermophiles depend on sulfur for growth, P. furiosus does not.
The ability to grow on polysaccharides (maltose, cellobiose, starch) but not on the monomeric sugars suggests that oligosaccharides with various degrees of polymerization may be imported into the cell, and only afterwards hydrolyzed to glucose
Glucose
Glucose is a simple sugar and an important carbohydrate in biology. Cells use it as the primary source of energy and a metabolic intermediate...
.
Pyrococcus furiosus is also notable for an unusual and intriguingly simple respiratory system, which obtains energy by reducing protons to hydrogen gas and uses this energy to create a proton
Proton
The proton is a subatomic particle with the symbol or and a positive electric charge of 1 elementary charge. One or more protons are present in the nucleus of each atom, along with neutrons. The number of protons in each atom is its atomic number....
gradient across its cell membrane, thereby driving ATP synthesis. Such a system could be a very early evolutionary precursor of respiratory systems in all higher organisms today.
A DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
was discovered in P. furiosus that is unrelated to other known DNA polymerases, as no significant sequence homology was found between its two proteins and those of other known DNA polymerases. This DNA polymerase has strong 3'-5' exonucleolytic activity and a template-primer preference which is characteristic of a replicative DNA polymerase, leading scientists to believe that this enzyme may be the replicative DNA polymerase of p. furiosus. Although archaea are, in general, more like eukaroyotes than prokaryotes in terms of transcription, translation, and replication of their DNA, scientists have not been able to find many examples of DNA polymerases in archaea that are similar in structure to DNA polymerases of eukaryotes. Obtaining more information about these enzymes would allow a more comprehensive understanding of the mechanism of DNA replication in archaea[citation needed].
Uses
The enzymes of Pyrococcus furiosus are extremely thermostable. As a consequence, the DNA PolymeraseDNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
from Pyrococcus furiosus (also known as Pfu DNA polymerase
Pfu DNA polymerase
Pfu DNA polymerase is an enzyme found in the hyperthermophilic archaeon Pyrococcus furiosus, where it functions in vivo to replicate the organism's DNA...
) can be used in the polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
(PCR) DNA amplification process.
In Production of Diols
One practical application of P. furiosus is in the production of diolsDiol
A diol or glycol is a chemical compound containing two hydroxyl groups A geminal diol has two hydroxyl groups bonded to the same atom...
for various industrial processes. It may be possible to use the enzymes of pyrococcus furiosus for applications in such industries as food, pharmaceuticals, and fine-chemicals in which alcohol dehydrogenases
Alcohol dehydrogenase
Alcohol dehydrogenases are a group of dehydrogenase enzymes that occur in many organisms and facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of nicotinamide adenine dinucleotide...
are necessary in the production of enantio- and diastereomerically pure diols. Enzymes from hyperthermophiles such as P. furiosus can perform well in laboratory processes because they are relatively resistant: they generally function well at high temperatures and high pressures, as well as in high concentrations of chemicals.
In order to make naturally-derived enzymes useful in the laboratory, it is often necessary to alter their genetic makeup. Otherwise, the naturally-occurring enzymes may not be efficient in an artificially-induced procedure. Although the enzymes of P. furiosus function optimally at a high temperature, scientists may not necessarily want to carry out a procedure at 100 °C (212 °F). Consequently, in this case, the specific enzyme AdhA was taken from P. furiosus and put through various mutations in a laboratory in order to obtain a suitable alcohol dehydrogenase for use in artificial processes. This allowed scientists to obtain a mutant enzyme that could function efficiently at lower temperatures and maintain productivity.
In Plants
The expression of a certain gene found in P. furiosus in plants can also render them more durable by increasing their tolerance for heat. In response to environmental stresses such as heat exposure, plants produce reactive oxygen speciesReactive oxygen species
Reactive oxygen species are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. Reactive oxygen species are highly reactive due to the presence of unpaired valence shell electrons....
which can result in cell death. If these free radicals are removed, cell death can be delayed. Enzymes in plants called superoxide dismutases
Superoxide dismutase
Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen...
remove superoxide anion radicals
Superoxide
A superoxide, also known by the obsolete name hyperoxide, is a compound that possesses the superoxide anion with the chemical formula O2−. The systematic name of the anion is dioxide. It is important as the product of the one-electron reduction of dioxygen O2, which occurs widely in nature...
from cells, but increasing the amount and activity of these enzymes is difficult and not the most efficient way to go about improving the durability of plants.
By introducing the superoxide reductases
Superoxide reductase
Superoxide reductase is an enzyme that catalyzes the conversion of highly reactive and toxic superoxide into less toxic hydrogen peroxide and molecular oxygen :Hydrogen peroxide in turn is converted to molecular oxygen by the enzyme catalase...
of P. furiosus into plants, the levels of O2 can be rapidly reduced. Scientists tested this method using the arabidopsis
Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
plant. As a result of this procedure, cell death in plants occurs less often, therefore resulting in a reduction in the severity of responses to environmental stress. This enhances the survival of plants, making them more resistant to light, chemical, and heat stress.
This study could potentially be used as a starting point to creating plants that could survive in more extreme climates on other planets such as Mars. By introducing more enzymes from extremophiles like P. furiosus into other species of plants, it may be possible to create incredibly resistant species.
In Researching Amino Acids
By comparing P. furiosus with a related species of archaea, Pyrococcus abyssi, scientists have tried to determine the correlation between certain amino acids and affinity for certain pressures in different species. P. furiosus is not barophilicPiezophile
A piezophile is an organism which thrives at high pressures, such as deep sea bacteria or archaea. They are generally found on ocean floors, where pressure often exceeds 380 atm . Some have been found at the bottom of the Pacific Ocean where the maximum pressure is roughly 117 MPa...
, while P. abyssi is, meaning that it functions optimally at very high pressures. Using two hyperthermophilic species of archaea lessens the possibility of deviations having to do with temperature of the environment, essentially reducing the variables in the experimental design.
Besides yielding information about the barophily of certain amino acids, the experiment also provided valuable insight into the origin of the genetic code and its organizational influences. It was found that most of the amino acids that determined barophily were also found to be important in the organization of the genetic code. It was also found that more polar amino acids and smaller amino acids were more likely to be barophilic. Through the comparison of these two archaea, the conclusion was reached that the genetic code was likely structured under high hydrostatic pressure, and that hydrostatic pressure was a more influential factor in determining genetic code than temperature.
Involvement in Space Research
As Pyrococcus furiosus can withstand large variations in temperature (100+ °C), it is being used to do research into bio-engineering plants suitable for growing in greenhouses on Mars. The research involves taking a gene from Pyrococcus furiosus and introducing into the plant arabidopsisArabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
.
Discovery
Pyrococcus furiosus was originally isolated anaerobicallyAnaerobic organism
An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It could possibly react negatively and may even die if oxygen is present...
from geothermally heated marine sediments with temperatures between 90 °C (194 °F) and 100 °C (212 °F) collected at the beach of Porto Levante, Vulcano Island, Italy. It was first described by Dr. Karl Stetter
Karl Stetter
Karl Otto Stetter is a German microbiologist and authority on astrobiology. He is an expert on microbial life at high temperatures.-Career:...
of the University of Regensburg
University of Regensburg
The University of Regensburg is a public research university located in the medieval city of Regensburg, Bavaria, a city that is listed as a UNESCO World Heritage Site. The university was founded on July 18, 1962 by the Landtag of Bavaria as the fourth full-fledged university in Bavaria...
in Germany, and a colleague, Dr. Gerhard Fiala. Pyrococcus furiosus actually originated a new genus of archaea with its relatively recent discovery in 1986.
Genome
The sequencing of the complete genomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of Pyrococcus furiosus was completed in 2001 by scientists at the University of Maryland Biotechnology Institute
University of Maryland Biotechnology Institute
Formed in 1985, the University of Maryland Biotechnology Institute is part of the University System of Maryland. It was created to provide a unified focus for Maryland's biotechnology research and education.-About UMBI:...
. The Maryland team found that the genome has 1,908 kilobases, coding for some 2,065 proteins.
The extremophile's scientific name
The name means "fireberry" in GreekAncient Greek
Ancient Greek is the stage of the Greek language in the periods spanning the times c. 9th–6th centuries BC, , c. 5th–4th centuries BC , and the c. 3rd century BC – 6th century AD of ancient Greece and the ancient world; being predated in the 2nd millennium BC by Mycenaean Greek...
, to refer to the extremophile's round shape and ability to grow in temperatures of around 100 degrees Celsius. The species name means 'rushing' in Latin
Latin
Latin is an Italic language originally spoken in Latium and Ancient Rome. It, along with most European languages, is a descendant of the ancient Proto-Indo-European language. Although it is considered a dead language, a number of scholars and members of the Christian clergy speak it fluently, and...
, and refers to the extremophile's doubling time.