Pyrococcus furiosus

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 aldehyde ferredoxin oxidoreductase enzymes containing tungsten, an element rarely found in biological molecules.

Pyrococcus furiosus
Pyrococcus furiosus
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Thermococci
Order:
Thermococcales
Family:
Thermococcaceae
Genus:
Pyrococcus
Species:
P. furiosus
Binomial name
Pyrococcus furiosus
Erauso et al. 1993

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, called an S-layer.

It grows between 70 °C (158 °F) and 103 °C (217 °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 P. 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.

P. 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 an electrochemical 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.[1]

Uses

The enzymes of Pyrococcus furiosus are extremely thermostable. As a consequence, the DNA polymerase from P. furiosus (also known as Pfu DNA polymerase) can be used in the polymerase chain reaction (PCR) DNA amplification process.

In DNA amplification

A DNA polymerase was discovered in P. furiosus that was thought to be 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.[2] It has since been placed in the family B of polymerases, the same family as DNA Polymerase II. Its structure, which appears quite typical for Polymerase B, has been solved as well.[3][4]

In production of diols

One practical application of P. furiosus is in the production of diols for various industrial processes. It may be possible to use the enzymes of P. 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.[5]

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 species 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.[6]

By introducing the superoxide reductases of P. furiosus into plants, the levels of O2 can be rapidly reduced.[7] Scientists tested this method using the Arabidopsis thaliana 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.[8]

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 barophilic, 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.[9]

Besides yielding information about the barophilicity 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 barophilicity 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.[9]

Discovery

Pyrococcus furiosus was originally isolated anaerobically 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 Karl Stetter of the University of Regensburg in Germany, and a colleague, Gerhard Fiala. Pyrococcus furiosus actually originated a new genus of archaea with its relatively recent discovery in 1986.[10]

Genome

The sequencing of the complete genome 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[11]

Scientific name

The name Pyrococcus means "fireball" in Greek, to refer to the extremophile's round shape and ability to grow in temperatures of around 100 degrees Celsius. The species name furiosus means 'rushing' in Latin, and refers to the extremophile's doubling time and rapid swimming.[10][12]

References
  1. Sapra, R; Bagramyan, K; Adams, M. W. W (2003). "A simple energy-conserving system: Proton reduction coupled to proton translocation". Proceedings of the National Academy of Sciences. 100 (13): 7545–50. Bibcode:2003PNAS..100.7545S. doi:10.1073/pnas.1331436100. PMC 164623. PMID 12792025.
  2. Uemori, Takashi; Sato, Yoshimi; Kato, Ikunoshin; Doi, Hirofumi; Ishino, Yoshizumi (1997). "A novel DNA polymerase in the hyperthermophilic archaeon,Pyrococcus furiosus: Gene cloning, expression, and characterization". Genes to Cells. 2 (8): 499–512. doi:10.1046/j.1365-2443.1997.1380336.x. PMID 9348040.
  3. Ishino, S; Ishino, Y (2014). "DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field". Frontiers in Microbiology. 5: 465. doi:10.3389/fmicb.2014.00465. PMC 4148896. PMID 25221550.
  4. Kim, Suhng Wook; Kim, Dong-Uk; Kim, Jin Kwang; Kang, Lin-Woo; Cho, Hyun-Soo (May 2008). "Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus". International Journal of Biological Macromolecules. 42 (4): 356–361. doi:10.1016/j.ijbiomac.2008.01.010. PMID 18355915.
  5. Machielsen, Ronnie; Leferink, Nicole G. H; Hendriks, Annemarie; Brouns, Stan J. J; Hennemann, Hans-Georg; Dauβmann, Thomas; Van Der Oost, John (2008). "Laboratory evolution of Pyrococcus furiosus alcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures". Extremophiles. 12 (4): 587–94. doi:10.1007/s00792-008-0164-8. PMC 2467505. PMID 18452026.
  6. Im, Y. J; Ji, M; Lee, A; Killens, R; Grunden, A. M; Boss, W. F (2009). "Expression of Pyrococcus furiosus Superoxide Reductase in Arabidopsis Enhances Heat Tolerance". Plant Physiology. 151 (2): 893–904. doi:10.1104/pp.109.145409. PMC 2754621. PMID 19684226.
  7. Coker; et al. (2013). "Evolutionary significance of metabolism of reactive oxygen species and free radicals by Pyrococcus furiosus". Journal of Evolutionary Biology. 34 (10): 12–28.
  8. Karen Miller (August 5, 2005). "Prozac for Plants". National Space Science Data Center. NASA.
  9. Di Giulio, Massimo (2005). "A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi: Barophily in the physicochemical properties of amino acids and in the genetic code". Gene. 346: 1–6. doi:10.1016/j.gene.2004.10.008. PMID 15716096.
  10. Fiala, Gerhard; Stetter, Karl O (1986). "Pyrococcus furiosus sp. nov. Represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C". Archives of Microbiology. 145 (1): 56–61. doi:10.1007/BF00413027.
  11. Robb, Frank T; Maeder, Dennis L; Brown, James R; Diruggiero, Jocelyne; Stump, Mark D; Yeh, Raymond K; Weiss, Robert B; Dunn, Dianne M (2001). "Genomic sequence of hyperthermophile, Pyrococcus furiosus: Implications for physiology and enzymology". Hyperthermophilic Enzymes Part A. Methods in Enzymology. 330. pp. 134–57. doi:10.1016/S0076-6879(01)30372-5. ISBN 978-0-12-182231-6.
  12. Zaramela, Livia S; Vêncio, Ricardo Z. N; Ten-Caten, Felipe; Baliga, Nitin S; Koide, Tie (2014). "Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life". PLoS ONE. 9 (9): e107680. doi:10.1371/journal.pone.0107680. PMC 4169567. PMID 25238539.

Further reading
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