Thermococcus

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Thermococcus
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Thermococci
Order:
Thermococcales
Family:
Thermococcaceae
Genus:
Thermococcus
Species
Synonyms
  • Thermococcus Zillig 1983

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In taxonomy, Thermococcus is a genus of extreme thermophiles in the family the Thermococcaceae.[1]
Members of the genus Thermococcus are all Archaea, having thermophillic-hyperthermophillic characteristics.[2] These microorganisms are typically irregularly shaped coccoid species, ranging in size from 0.6-2.0 μm in diameter.[3] Some species of Thermococcus are immobile, and some species have motility, using flagella as their main source of movement.[2][3][4][5][6][7][8][9][10][11][12][13] These flagella typically exist at a specific pole of the organism.[13] This movement has been seen at room temperature or at high temperature, depending on the specific organism.[14] In some species, these microorganisms can aggregate and form white-gray plaques,[13] while all of these organisms dwell in temperatures from 70-<100oC,[2][3][4][5][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] either in the presence of black smokers (hydrothermal vents), or freshwater springs,[22] amongst salt (NaCl) concentrations of 1%-3%.[19] Species in this genus are strictly anaerobes,[2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] and most are barophiles as well as thermophiles,[2][3][4][5][6][7][8] living in depths between 200-<1000 ft.[11][12][13][14][15][16][17][18][19][20][21] These organisms thrive at pH levels of 5.6-7.9.[23] Members of this genus have been found in many hydrothermal vent systems in the world, including from the seas of Japan,[24] to off the coasts of California.[25] Surprisingly salt (NaCl) is not a required substrate for these organisms,[26][27] as one study showed Thermococcus members living in fresh hot water systems in New Zealand,[22] however they do require a low concentration of lithium ion for growth.[28] Thermococcus members are described as heterotrophic, chemotrophic[2][3][4][5] and organotrophic sulfanogens;[2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21] utilizing elemental sulfur (So) and carbon sources including amino acids, carbohydrates, and organic acids such as pyruvate.[29]

Metabolism

Metabolically, Thermococcus have developed a different form of glycolysis than eukaryotes and prokaryotes.[29][30] One example of a metabolic pathway for these organisms is the metabolism of peptides,[29] which occurs in three steps: first, there is hydrolysis of the peptides to amino acids catalyzed by peptidases,[30] then there is conversion of the amino acids to keto acids catalyzed by aminotransferases,[29] and finally CO2 is released from the oxidative decarboxylation or the keto acids by four different enzymes,[30] which produces coenzyme A derivatives that are used in other important metabolic pathways.[30] Thermococcus species also have the enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase),[31] which is made from enzymes involved in the metabolism of nucleic acids in Thermococcus kodakarensis,[29][30][31] showing how integrated these metabolic systems truly are for these hyperthermophilic microorganisms.[31] Some nutrients are limiting when it comes to Thermococcus cell growth.[31] Nutrients that affect cell growth the most in thermococci species are carbon and nitrogen sources.[31] Since thermococci species do not metabolically generate all necessary amino acids, some have to be provided by the environment in which these organisms thrive. Some of these needed amino acids are leucine, isoleucine, and valine (the branched chain amino acids).[31] When Thermococcus species are supplemented with these amino acids, they can metabolize them and produce acetyl-CoA or succinyl-CoA,[31] which are important precursors used in other metabolic pathways essential for cellular growth and respiration.[31] With today's technology, Thermococcus members are relatively easy to grow in labs,[32] and are therefore considered model organisms for studying the physiological and molecular pathways of extremophiles.[33][34] Thermococcus kodakarensis is one example of a model Thermococcus species, a microorganism in which has had its entire genome examined and replicated.[34][35]

Ecology

Thermococci species can grow at anywhere between 60-80oC (1-20), which gives thermococci species a great ecological advantage to be the first organisms to colonize new hydrothermal environments.[36][37][38] Some thermococci species produce CO2, H2, and H2S as products of metabolism and respiration.[34] The release of these molecules are then used by other autotrophic species, aiding to the diversity of hydrothermal microbial communities.[37] This type of continuous enrichment culture plays a crucial role in the ecology of deep sea hydrothermal vents,[39] suggesting that thermococci interact with other organisms via metabolite exchange which supports the growth of autotrophs.[37] Thermococcus species that release H2 with the use of multiple hydrogenases (including CO-dependent hydrogenases) have been regarded as potential biocatalysts for water-gas shift reactions.[40]

Transportation Mechanisms

Thermococcus members are naturally competent in taking up DNA and incorporating donor DNA into their genomes via homologous recombination.[41] These species can produce membrane vesicles (MVs),[41] formed by budding from the outermost cellular membranes,[41][42] which can capture and obtain plasmids from neighboring archaea species in order to transfer the DNA into either themselves or surrounding species.[41] These MVs are secreted from the cells in clusters, forming nanospheres or nanotubes,[42] keeping the internal membranes continuous.[41]
A study has shown that Thermococcus species produce numerous MVs, transferring DNA, metabolites, and even toxins in some species;[42] moreover, these MVs protect their contents against thermodegradation by transferring these macromolecules in a protected environment.[41][42] MVs also prevent infections by capturing viral particles.[42] Along with transporting macromolecules, Thermococcus members use MVs to communicate to each other.[41] Furthermore, these MVs are used by a specific species (Thermococcus coalescens) to indicate when aggregation should occur,[41] so that these typically single-celled miroorganisms can fuse into one massive single cell.[41]
It has been reported that Thermococcus kodakarensis has four virus-like integrated gene elements containing subtilisin-like serine protease precursors.[43] To date, only two viruses have been isolated from Thermococcus members, PAVE1 and TPV1.[43] These viruses exist in their hosts in a carrier state.[43]
The process of DNA replication and elongation has been extensively studied in Thermococcus kodakarensis.[43] The DNA molecule is a circular structure consisting of approximately 2 million base pairs in length, and has more than 2,000 sequences that code for proteins.[43]

Future Technology

An enzyme from Thermococcus, Tpa-S DNA polymerase, has been found to be more efficient in long and rapid PCR than Taq-polymerase.[44] Tk-SP, another enzyme from T. kodakarensis,[44][45] can degrade abnormal prion proteins (PrPSc);[44] prions are misfolded proteins that can cause fatal diseases in all organisms.[44] Tk-SP shows broad substrate specificity, and degraded prions exponentially in the lab setting.[44] This enzyme does not require calcium or any other substrate to fold, and therefore is showing great potential in studies thus far.[44] Additional studies have been coordinated on the PSP (phosphoserine phosphatase) enzyme of Thermococcus onnurineus, which provided an essential component in the regulation of PSP activity.[45] This information is useful for drug companies, because abnormal PSP activity leads to a major decrease in serine levels of the nervous system, causing neurological diseases and complications.[45]
One study has shown that members of the family Thermococcus can increase gold mining efficiency up to 85-95% due to their specific abilities in bioleaching.[46]

References

  1. ↑ See the NCBI webpage on Thermococcus. Data extracted from the Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Amenabar, M. J., et al. (2013). "Archaeal diversity from hydrothermal systems of Deception Island, Antarctica." Polar Biology 36(3): 373-380.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Francesco Canganella, W. J. J., Agata Gambacorta, and Garabed Antranikian (1998). "Thermococcus guaymasensis sp. nov. and Thermococcus aggregans sp. nov., two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site." International Journal of Systematic Bacteriology 48(1): 6.
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 Schut, G. J., et al. (2013). "The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications."Fems Microbiology Reviews 37(2): 182-203.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 Yuusuke Tokooji, T. S., Shinsuke Fujiwara, Tadayuki Imanaka and Haruyuki Atomi (2013). "Genetic Examination of Initial Amino Acid Oxidation and Glutamate Catabolism in the Hyperthermophilic Archaeon Thermococcus kodakarensis." Journal of Bacteriology: 10.
  6. ↑ 6.0 6.1 6.2 6.3 Bezsudnova, E. Y., et al. (2012). "Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus." Biochimie 94(12): 2628-2638.
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Cho, S. S., et al. (2012). "Characterization and PCR application of a new high-fidelity DNA polymerase from Thermococcus waiotapuensis." Enzyme and Microbial Technology 51(6-7): 334-341.
  8. ↑ 8.0 8.1 8.2 8.3 8.4 Atomi, H., et al. (2013). "CoA biosynthesis in archaea." Biochemical Society Transactions 41: 427-431.
  9. ↑ 9.0 9.1 9.2 9.3 Lee, J., et al. (2012). "Hydrogen production from C1 compounds by a novel marine hyperthermophilic archaeon Thermococcus onnurineus NA1." International Journal of Hydrogen Energy 37(15): 11113-11121.
  10. ↑ 10.0 10.1 10.2 10.3 Aono, R., et al. (2012). "Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway." Journal of Bacteriology 194(24): 6847-6855.
  11. ↑ 11.0 11.1 11.2 11.3 11.4 Jaime Andres Rivas-Pardo, A. H.-M., Victor Castro-Fernandez, Francisco J. Fernandez, M. Cristina Vega, and Victoria Guixe (2013). "Crystal Structure, SAXS and Kinetic Mechanism of Hyperthermophilic ADP-Depended Glucokinase from Thermococcus litoralis Reveal a Conserved Mechanism for Catalysis " PLoS ONE: 12.
  12. ↑ 12.0 12.1 12.2 12.3 12.4 Rogatykh, S. V., et al. (2013). "Evaluation of Quantitative and Qualitative Composition of Cultivated Acidophilic Microorganisms by Real-Time PCR and Clone Library Analysis." Microbiology 82(2): 210-214.
  13. ↑ 13.0 13.1 13.2 13.3 13.4 13.5 13.6 Tae-Yang Jung, Y.-S. K., Byoung-Ha Oh, and Euijeon Woo (2012). "Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus." Wiley Periodicals: 11.
  14. ↑ 14.0 14.1 14.2 14.3 14.4 Tagashira, K., et al. (2013). "Genetic studies on the virus-like regions in the genome of hyperthermophilic archaeon, Thermococcus kodakarensis." Extremophiles 17(1): 153-160.
  15. ↑ 15.0 15.1 15.2 15.3 Gorlas, A. and C. Geslin (2013). "A simple procedure to determine the infectivity and host range of viruses infecting anaerobic and hyperthermophilic microorganisms." Extremophiles 17(2): 349-355.
  16. ↑ 16.0 16.1 16.2 16.3 Krupovic, M., et al. (2013). "Insights into Dynamics of Mobile Genetic Elements in Hyperthermophilic Environments from Five New Thermococcus Plasmids." PLoS ONE 8(1).
  17. ↑ 17.0 17.1 17.2 17.3 Adrian Hetzer, H. W. M., Ian R. McDonald, Christopher J. Daughney (2007). "Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand." Extremophiles 11:10.
  18. ↑ 18.0 18.1 18.2 18.3 Tomohiro Kato, X. L., Hiroyuki Asanuma (2012). "Model of Elongation of Short DNA Sequence by Thermophilic DNA Polymerase under Isothermal Conditions." Biochemistry 51: 8.
  19. ↑ 19.0 19.1 19.2 19.3 19.4 Kim, B. K., et al. (2012). "Genome Sequence of an Oligohaline Hyperthermophilic Archaeon, Thermococcus zilligii AN1, Isolated from a Terrestrial Geothermal Freshwater Spring." Journal of Bacteriology 194(14): 3765-3766.
  20. ↑ 20.0 20.1 20.2 20.3 Annmarie Neumer, H. W. J., Shimshon Belkin, and Karl O. Stetter (1990). "Thermococcus litoralis sp. nov.: A new species of extremely thermophilic marine archaebacteria." Arch Microbiology 153(1): 3.
  21. ↑ 21.0 21.1 21.2 21.3 James F. Holden, K. T., Melanie Summit, Sheryl Bolton, Jamie Zyskowski, John A. Baross (2000). "Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean." FEMS Microbiology Ecology 36: 10.
  22. ↑ 22.0 22.1 Elisabeth Antoine, J. G., J. R. Meunier, F. Lesongeur, G. Barbier (1995). "Isolation and Characterization of Extremely Thermophilic Archaebacteria Related to the Genus Thermococcus from Deep-Sea Hydrothermal Guaymas Basin." Current Microbiology 31: 7.
  23. ↑ Kazuo Tori, S. I., Shinichi Kiyonari, Saki Tahara, Yoshizumi Ishino (2013). "A Novel Single-Strand Specific 3'-5' Exonuclease Found in the Hyperthermophilic Archaeon, Pyrococcus furiosus." PLoS ONE 8: 9.
  24. ↑ Cui, Z. C., et al. (2012). "High level expression and characterization of a thermostable lysophospholipase from Thermococcus kodakarensis KOD1." Extremophiles 16(4): 619-625.
  25. ↑ Ryo Uehara, S.-i. T., Kazufumi Takano, Yuichi Koga, Shigenori Kanaya (2012). "Requirement of insertion sequence IS1 for thermal adaptation of Pro-Tk-subtilisin from hyperthermophilic archaeon." Extremophiles 16: 11.
  26. ↑ Cubonova, L., et al. (2012). "An Archaeal Histone Is Required for Transformation of Thermococcus kodakarensis." Journal of Bacteriology 194(24): 6864-6874.
  27. ↑ Anne Postec, F. L., Patricia Pignet, Bernard Ollivier, Joel Querellou, Anne Godfroy (2007). "Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys." Extremophiles 11: 10.
  28. ↑ Jed O. Eberly, R. L. E. (2008). "Thermotolerant Hydrogenases: Biological Diversity, Properties, and Biotechnological Applications." Critical Reviews in Microbiology 34: 14.
  29. ↑ 29.0 29.1 29.2 29.3 29.4 Ozawa, Y., et al. (2012). "Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus." Journal of Bioscience and Bioengineering 114(1): 23-27.
  30. ↑ 30.0 30.1 30.2 30.3 30.4 Zhang, Y., et al. (2012). "Sulfur Metabolizing Microbes Dominate Microbial Communities in Andesite-Hosted Shallow-Sea Hydrothermal Systems." PLoS ONE 7(9).
  31. ↑ 31.0 31.1 31.2 31.3 31.4 31.5 31.6 31.7 Davidova, I. A., et al. (2012). "Involvement of thermophilic archaea in the biocorrosion of oil pipelines." Environmental Microbiology 14(7): 1762-1771.
  32. ↑ Guy D. Duffaud, O. B. d. H., Andrew S. Peek, Anna-Louise Reysenbach, Robert M. Kelly (1998). "Isolation and Characterization of Thermococcus barossii, sp. nov., a Hyperthermophilic Archaeon Isolated from a Hydrothermal Vent Flange Formation." Systematic and Applied Microbiology 21: 10.
  33. ↑ Petrova, T., et al. (2012). "ATP-dependent DNA ligase from Thermococcus sp 1519 displays a new arrangement of the OB-fold domain." Acta Crystallographica Section F-Structural Biology and Crystallization Communications 68: 1440-1447.
  34. ↑ 34.0 34.1 34.2 Amend, J. P. (2009). "A brief review of microbial geochemistry in the shallow-sea hydrothermal system of Vulcano Island (Italy)." Freiberg Online Geology 22: 7.
  35. ↑ Hughes, R. C., et al. (2012). "Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction." Acta Crystallographica Section F-Structural Biology and Crystallization Communications 68: 1482-1487.
  36. ↑ Itoh, T. (2003). "Taxonomy of Nonmethanogenic Hyperthermophilic and Related Thermophilic Archaea." Journal of Bioscience and Bioengineering 96(3): 10.
  37. ↑ 37.0 37.1 37.2 Yao Zhang, Z. Z., Chen-Tung Arthur Chen, Kai Tang, Jianqiang Su, Nianzhi Jiao (2012). "Sulfur Metabolizing Microbes Dominate Microbial Communities in Andesite-Hosted Shallow-Sea Hydrothermal Systems." PLoS ONE 7(9): 11.
  38. ↑ Yumani Kuba, S. I., Takeshi Yamagami, Masahiro Tokuhara, Tamotsu Kanai, Ryosuke Fujikane, Hiromi Daiyasu, Haruyuki Atomi, Yoshizumi Ishino (2012). "Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis." Genes to Cells 17: 15.
  39. ↑ Hakon Dahle, F. G., Marit Madsen, Nils-Kare Birkeland (2008). "Microbial community structure analysis of produced water from a high-temperature North Sea oil-field." Antonie van Leeuwenhoek 93: 13.
  40. ↑ Ppyun, H., et al. (2012). "Improved PCR performance using mutant Tpa-S DNA polymerases from the hyperthermophilic archaeon Thermococcus pacificus." Journal of Biotechnology 164(2): 363-370.
  41. ↑ 41.0 41.1 41.2 41.3 41.4 41.5 41.6 41.7 41.8 Marguet, E., et al. (2013). "Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus." Biochemical Society Transactions 41: 436-442.
  42. ↑ 42.0 42.1 42.2 42.3 42.4 Gaudin, M., et al. (2013). "Hyperthermophilic archaea produce membrane vesicles that can transfer DNA." Environmental Microbiology Reports 5(1): 109-116.
  43. ↑ 43.0 43.1 43.2 43.3 43.4 Li, Z., et al. (2013). "Thermococcus kodakarensis DNA replication." Biochemical Society Transactions 41: 332-338.
  44. ↑ 44.0 44.1 44.2 44.3 44.4 44.5 Azumi Hirata, Y. H., Jun Okada, Akikazu Sakudo, Kazuyoshi Ikuta, Shigenori Kanaya, and Kazufumi Takano (2013). "Enzymatic activity of a subtilisin homolog, Tk-SP, from Thermococcus kodakarensis in detergents and its ability to degrade the abnormal prion protein " BMC Biotechnology 13: 7.
  45. ↑ 45.0 45.1 45.2 Trofimov, A. A., et al. (2012). "Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus." Acta Crystallographica Section F-Structural Biology and Crystallization Communications 68: 1275-1278.
  46. ↑ Muhammad Nisar, N. R., Qamar Bashir, Qurra-tul-Ann Gardener, Muhammad Shafiq, and Muhammad Akhtar (2013). "TK 1299, a highly thermostable NAD(P)H oxidase from Thermococcus kodakaraensis exhibiting higher enzymatic activity with NADPH." Journal of Bioscience and Bioengineering 116(1): 5.

Further reading

Scientific journals

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Scientific books

Scientific databases

External links

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