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Thermococcus

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

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 mode 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 or at high temperatures, 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 to more than 100°C,[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] but they do require a low concentration of lithium ions 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] using elemental sulfur (S) and carbon sources including amino acids, carbohydrates, and organic acids such as pyruvate.[29]

Metabolism

Metabolically, Thermococcus spp. have developed a different form of glycolysis from 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, hydrolysis of the peptides to amino acids is catalyzed by peptidases,[30] then the conversion of the amino acids to keto acids is 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 in Thermococcus cell growth.[31] Nutrients that affect cell growth the most in thermococcal species are carbon and nitrogen sources.[31] Since thermococcal 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

Thermococcal species can grow between 60 and 80°C, which gives them a great ecological advantage to be the first organisms to colonize new hydrothermal environments.[36][30][37] Some thermococcal species produce CO2, H2, and H2S as products of metabolism and respiration.[34] The releases of these molecules are then used by other autotrophic species, aiding the diversity of hydrothermal microbial communities.[30] This type of continuous enrichment culture plays a crucial role in the ecology of deep-sea hydrothermal vents,[38] suggesting that thermococci interact with other organisms via metabolite exchange, which supports the growth of autotrophs.[30] 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.[39]

Transportation mechanisms

Thermococcus species are naturally competent in taking up DNA and incorporating donor DNA into their genomes via homologous recombination.[40] These species can produce membrane vesicles (MVs),[40] formed by budding from the outermost cellular membranes,[40][41] which can capture and obtain plasmids from neighboring Archaea species to transfer the DNA into either themselves or surrounding species.[40] These MVs are secreted from the cells in clusters, forming nanospheres or nanotubes,[41] keeping the internal membranes continuous.[40]
Thermococcus species produce numerous MVs, transferring DNA, metabolites, and even toxins in some species;[41] moreover, these MVs protect their contents against thermodegradation by transferring these macromolecules in a protected environment.[40][41] MVs also prevent infections by capturing viral particles.[41] Along with transporting macromolecules, Thermococcus species use MVs to communicate to each other.[40] Furthermore, these MVs are used by a specific species (Thermococcus coalescens) to indicate when aggregation should occur,[40] so these typically single-celled miroorganisms can fuse into one massive single cell.[40]
It has been reported that Thermococcus kodakarensis has four virus-like integrated gene elements containing subtilisin-like serine protease precursors.[42] To date, only two viruses have been isolated from Thermococcus spp., PAVE1 and TPV1.[42] These viruses exist in their hosts in a carrier state.[42]
The process of DNA replication and elongation has been extensively studied in T. kodakarensis.[42] The DNA molecule is a circular structure consisting of about 2 million base pairs in length, and has more than 2,000 sequences that code for proteins.[42]

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.[43] Tk-SP, another enzyme from T. kodakarensis,[43][44] can degrade abnormal prion proteins (PrPSc);[43] prions are misfolded proteins that can cause fatal diseases in all organisms.[43] Tk-SP shows broad substrate specificity, and degraded prions exponentially in the lab setting.[43] This enzyme does not require calcium or any other substrate to fold, so is showing great potential in studies thus far.[43] Additional studies have been coordinated on the phosphoserine phosphatase (PSP) enzyme of T. onnurineus, which provided an essential component in the regulation of PSP activity.[44] 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.[44]
Thermococcus spp. can increase gold mining efficiency up to 95% due to their specific abilities in bioleaching.[45]

References

  1. ^ See the NCBI webpage on Thermococcus. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information. Retrieved 2007-03-19.
  2. ^ a b c d e f g Amenabar, M. J.; et al. (2013). "Archaeal diversity from hydrothermal systems of Deception Island, Antarctica". Polar Biology. 36 (3): 373–380. doi:10.1007/s00300-012-1267-3.
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  19. ^ a b c d e 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. doi:10.1128/jb.00655-12. PMC 3393502. PMID 22740682.
  20. ^ a b c d Annmarie Neumer, H. W. J.; Belkin, Shimshon; Stetter, Karl O. (1990). "Thermococcus litoralis sp. nov.: A new species of extremely thermophilic marine archaebacteria". Arch Microbiology. 153 (1): 3.
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  22. ^ a b Elisabeth Antoine, J. G.; Meunier, J. R.; Lesongeur, F.; Barbier, G. (1995). "Isolation and Characterization of Extremely Thermophilic Archaebacteria Related to the Genus Thermococcus from Deep-Sea Hydrothermal Guaymas Basin". Current Microbiology. 31 (3): 7. doi:10.1007/bf00293552.
  23. ^ Kazuo Tori, S. I.; Kiyonari, Shinichi; Tahara, Saki; Ishino, Yoshizumi (2013). "A Novel Single-Strand Specific 3'-5' Exonuclease Found in the Hyperthermophilic Archaeon, Pyrococcus furiosus". PLoS ONE. 8 (3): 9. doi:10.1371/journal.pone.0058497. PMC 3591345. PMID 23505520.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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. doi:10.1007/s00792-012-0461-0. PMID 22622648.
  25. ^ Uehara, Ryo; Takano, Kazufumi; Koga, Yuichi; Kanaya, Shigenori (2012). "Requirement of insertion sequence IS1 for thermal adaptation of Pro-Tk-subtilisin from hyperthermophilic archaeon". Extremophiles. 16 (6): 841. doi:10.1007/s00792-012-0479-3.
  26. ^ Cubonova, L.; et al. (2012). "An Archaeal Histone Is Required for Transformation of Thermococcus kodakarensis". Journal of Bacteriology. 194 (24): 6864–6874. doi:10.1128/jb.01523-12. PMC 3510624. PMID 23065975.
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  28. ^ Eberly, Jed O. (2008). "Thermotolerant Hydrogenases: Biological Diversity, Properties, and Biotechnological Applications". Critical Reviews in Microbiology. 34 (3–4): 117–30. doi:10.1080/10408410802240893. PMID 18728989.
  29. ^ a b c d e 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. doi:10.1016/j.jbiosc.2012.02.014. PMID 22608551.
  30. ^ a b c d e f g h Zhang, Y.; et al. (2012). "Sulfur Metabolizing Microbes Dominate Microbial Communities in Andesite-Hosted Shallow-Sea Hydrothermal Systems". PLoS ONE. 7 (9): e44593. doi:10.1371/journal.pone.0044593. PMC 3436782. PMID 22970260.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  31. ^ a b c d e f g h Davidova, I. A.; et al. (2012). "Involvement of thermophilic archaea in the biocorrosion of oil pipelines". Environmental Microbiology. 14 (7): 1762–1771. doi:10.1111/j.1462-2920.2012.02721.x. PMID 22429327.
  32. ^ Duffaud, Guy D.; d'Hennezel, Olga B.; Peek, Andrew S.; Reysenbach, Anna-Louise; Kelly, Robert M. (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. doi:10.1016/s0723-2020(98)80007-6.
  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. 68 (12): 1440–1447. doi:10.1107/s1744309112043394. PMC 3509962. PMID 23192021.
  34. ^ a b c 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. 68 (12): 1482–1487. doi:10.1107/S1744309112032447. PMC 3509969. PMID 23192028.
  36. ^ Itoh, T (2003). "Taxonomy of Nonmethanogenic Hyperthermophilic and Related Thermophilic Archaea". Journal of Bioscience and Bioengineering. 96 (3): 10. doi:10.1263/jbb.96.203.
  37. ^ Yumani Kuba, S. I.; Yamagami, Takeshi; Tokuhara, Masahiro; Kanai, Tamotsu; Ryosuke; Daiyasu, Hiromi; Atomi, Haruyuki; Ishino, Yoshizumi (2012). "Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis". Genes to Cells. 17 (11): 923–937. doi:10.1111/gtc.12007. PMID 23078585.
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  40. ^ a b c d e f g h i Marguet, E.; et al. (2013). "Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus". Biochemical Society Transactions. 41 (1): 436–442. doi:10.1042/bst20120293. PMID 23356325.
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  43. ^ a b c d e f Azumi Hirata, Y. H.; Okada, Jun; Sakudo, Akikazu; Ikuta, Kazuyoshi; Kanaya, Shigenori; Takano, Kazufumi (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.
  44. ^ a b c Trofimov, A. A.; et al. (2012). "Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus". Acta Crystallographica Section F. 68 (11): 1275–1278. doi:10.1107/s174430911203761x. PMC 3515363. PMID 23143231.
  45. ^ Muhammad Nisar, N. R.; Bashir, Qamar; Gardener, Qurra-tul-Ann; Shafiq, Muhammad; Akhtar, Muhammad (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): 39–44. doi:10.1016/j.jbiosc.2013.01.020. PMID 23453203.

Further reading

  • Judicial Commission of the International Committee on Systematics of Prokaryotes (2005). "The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79". Int. J. Syst. Evol. Microbiol. 55 (Pt 1): 517–518. doi:10.1099/ijs.0.63548-0. PMID 15653928.
  • Mora, Maximilian; Bellack, Annett; Ugele, Matthias; Hopf, Johann; Wirth, Reinhard (August 2014). "The Temperature Gradient-Forming Device, an Accessory Unit for Normal Light Microscopes To Study the Biology of Hyperthermophilic Microorganisms". Applied and Environmental Microbiology. 80 (15): 4764–70. doi:10.1128/AEM.00984-14. PMC 4148812. PMID 24858087.
  • Zillig W; Holz I; Klenk HP; et al. (1987). "Pyrococcus woesei, sp. nov., an ultra-thermophilic marine Archaebacterium, representing a novel order, Thermococcales". Syst. Appl. Microbiol. 9 (1–2): 62–70. doi:10.1016/S0723-2020(87)80057-7.
  • Zillig W; Holz L; Janekovic D; Schafer W; Reiter WD (1983). "The archaebacterium Thermococcus celer represents a novel genus within the thermophilic branch of the archaebacteria". Syst. Appl. Microbiol. 4: 88–94. doi:10.1016/S0723-2020(83)80036-8.

Template:Taxonomic references

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