Thermococcus Explained

In taxonomy, Thermococcus is a genus of thermophilic Archaea in the family the Thermococcaceae.[1]

Members of the genus Thermococcus are typically irregularly shaped coccoid species, ranging in size from 0.6 to 2.0 μm in diameter.[2] Some species of Thermococcus are immobile, and some species have motility, using flagella as their main mode of movement. These flagella typically exist at a specific pole of the organism. This movement has been seen at room or at high temperatures, depending on the specific organism.[3] In some species, these microorganisms can aggregate and form white-gray plaques.[4] Species under Thermococcus typically thrive at temperatures between 60 and 105 °C, either in the presence of black smokers (hydrothermal vents), or freshwater springs.[5] Species in this genus are strictly anaerobes,[6] [7] and are thermophilic, found in a variety depths, such as in hydrothermal vents 2500m below the ocean surface,[8] but also centimeters below the water surface in geothermal springs.[9] These organisms thrive at pH levels of 5.6-7.9.[10] Members of this genus have been found in many hydrothermal vent systems in the world, including from the seas of Japan,[11] to off the coasts of California.[12] Sodium Chloride salt is typically present in these locations at 1%-3% concentration, but is not a required substrate for these organisms,[13] [14] as one study showed Thermococcus members living in fresh hot water systems in New Zealand, but they do require a low concentration of lithium ions for growth.[15] Thermococcus members are described as heterotrophic, chemotrophic,[16] [17] and are organotrophic sulfanogens; using elemental sulfur and carbon sources including amino acids, carbohydrates, and organic acids such as pyruvate.[18]

Phylogeny

Unassigned species:

Metabolism

Metabolically, Thermococcus spp. have developed a different form of glycolysis from eukaryotes and prokaryotes.[25] [26] One example of a metabolic pathway for these organisms is the metabolism of peptides, which occurs in three steps: first, hydrolysis of the peptides to amino acids is catalyzed by peptidases, then the conversion of the amino acids to keto acids is catalyzed by aminotransferases, and finally CO2 is released from the oxidative decarboxylation or the keto acids by four different enzymes, which produces coenzyme A derivatives that are used in other important metabolic pathways. Thermococcus species also have the enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase),[27] which is made from enzymes involved in the metabolism of nucleic acids in Thermococcus kodakarensis, showing how integrated these metabolic systems truly are for these hyperthermophilic microorganisms. Some nutrients are limiting in Thermococcus cell growth. Nutrients that affect cell growth the most in thermococcal species are carbon and nitrogen sources. 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). When Thermococcus species are supplemented with these amino acids, they can metabolize them and produce acetyl-CoA or succinyl-CoA, which are important precursors used in other metabolic pathways essential for cellular growth and respiration. Thermococcus onnurineus lacks the genes for purine nucleotide biosynthesis and thus relies on environmental sources to meet its purine requirements.[28] With today's technology, Thermococcus members are relatively easy to grow in labs,[29] and are therefore considered model organisms for studying the physiological and molecular pathways of extremophiles.[30] [31] Thermococcus kodakarensis is one example of a model Thermococcus species, a microorganism in which has had its entire genome examined and replicated.[32] [33]

Ecology

Thermococcal species can grow between 60 and 102 °C,optimal temperature at 85 °C which gives them a great ecological advantage to be the first organisms to colonize new hydrothermal environments.[34] [35] As hyperthermophiles, there is a need for extreme environmental conditions, including temperature, pH, and salt. These conditions lead to the production of stress proteins and molecular chaperones that protect DNA as well as housekeeping cellular machinery. Thermococcus also thrives under gluconeogenic conditions. Some thermococcal species produce CO2, H2, and H2S as products of metabolism and respiration. The releases of these molecules are then used by other autotrophic species, aiding the diversity of hydrothermal microbial communities. This type of continuous enrichment culture plays a crucial role in the ecology of deep-sea hydrothermal vents,[36] suggesting that thermococci interact with other organisms via metabolite exchange, which supports the growth of autotrophs. 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.[37]

Transportation mechanisms

Thermococcus species are naturally competent in taking up DNA and incorporating donor DNA into their genomes via homologous recombination.[38] These species can produce membrane vesicles (MVs), formed by budding from the outermost cellular membranes,[39] which can capture and obtain plasmids from neighboring Archaea species to transfer the DNA into either themselves or surrounding species. These MVs are secreted from the cells in clusters, forming nanospheres or nanotubes, keeping the internal membranes continuous. Competence for DNA transfer and integration of donor DNA into the recipient genome by homologous recombination is common in the archaea and appears to be an adaptation for repairing DNA damage in the recipient cells (see Archaea subsection "Gene transfer and genetic exchange").

Thermococcus species produce numerous MVs, transferring DNA, metabolites, and even toxins in some species; moreover, these MVs protect their contents against thermodegradation by transferring these macromolecules in a protected environment. MVs also prevent infections by capturing viral particles. Along with transporting macromolecules, Thermococcus species use MVs to communicate to each other. Furthermore, these MVs are used by a specific species (Thermococcus coalescens) to indicate when aggregation should occur, so these typically single-celled miroorganisms can fuse into one massive single cell.

It has been reported that Thermococcus kodakarensis has four virus-like integrated gene elements containing subtilisin-like serine protease precursors.[40] To date, only two viruses have been isolated from Thermococcus spp., PAVE1 and TPV1. These viruses exist in their hosts in a carrier state.
The process of DNA replication and elongation has been extensively studied in T. kodakarensis. 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.

Future technology

An enzyme from Thermococcus, Tpa-S DNA polymerase, has been found to be more efficient in long and rapid polymerase chain reaction (PCR) than Taq polymerase.[41] Tk-SP, another enzyme from T. kodakarensis,[42] can degrade abnormal prion proteins (PrPSc); prions are misfolded proteins that can cause fatal diseases in all organisms. Tk-SP shows broad substrate specificity, and degraded prions exponentially in the lab setting. This enzyme does not require calcium or any other substrate to fold, so is showing great potential in studies this far. 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. 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.

Thermococcus spp. can increase gold mining efficiency up to 95% due to their specific abilities in bioleaching.[43]

See also

Further reading

External links

Notes and References

  1. See the NCBI webpage on Thermococcus. Data extracted from the Web site: NCBI taxonomy resources . . 2007-03-19.
  2. Canganella F, Jones WJ, Gambacorta A, Antranikian G . 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 Pt 4 . 4 . 1181–5 . October 1998 . 9828419 . 10.1099/00207713-48-4-1181 . free .
  3. Tagashira K, Fukuda W, Matsubara M, Kanai T, Atomi H, Imanaka T . Genetic studies on the virus-like regions in the genome of hyperthermophilic archaeon, Thermococcus kodakarensis . Extremophiles . 17 . 1 . 153–60 . January 2013 . 23224520 . 10.1007/s00792-012-0504-6 . 15924402 .
  4. 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.
  5. Antoine E, Guezennec J, Meunier JR, Lesongeur F, Barbier G . 1995 . Isolation and Characterization of Extremely Thermophilic Archaebacteria Related to the Genus Thermococcus from Deep-Sea Hydrothermal Guaymas Basin . 10.1007/bf00293552 . Current Microbiology . 31 . 3. 7 . 25215530 .
  6. Amenábar MJ, Flores PA, Pugin B, Boehmwald FA, Blamey JM . 2013. Archaeal diversity from hydrothermal systems of Deception Island, Antarctica. Polar Biology. 36. 3. 373–380. 10.1007/s00300-012-1267-3. 2013PoBio..36..373A . 11705986.
  7. Kim BK, Lee SH, Kim SY, Jeong H, Kwon SK, Lee CH, Song JY, Yu DS, Kang SG, Kim JF . 6 . Genome sequence of an oligohaline hyperthermophilic archaeon, Thermococcus zilligii AN1, isolated from a terrestrial geothermal freshwater spring . Journal of Bacteriology . 194 . 14 . 3765–6 . July 2012 . 22740682 . 3393502 . 10.1128/jb.00655-12 .
  8. Krupovic M, Gonnet M, Hania WB, Forterre P, Erauso G . Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids . PLOS ONE . 8 . 1 . e49044 . 2013 . 23326305 . 3543421 . 10.1371/journal.pone.0049044 . 2013PLoSO...849044K . free .
  9. Hetzer A, Morgan HW, McDonald IR, Daughney CJ . Microbial life in Champagne Pool, a geothermal spring in Waiotapu, New Zealand . Extremophiles . 11 . 4 . 605–14 . July 2007 . 17426919 . 10.1007/s00792-007-0073-2 . 24239907 .
  10. Tori K, Ishino S, Kiyonari S, Tahara S, Ishino Y . A novel single-strand specific 3'-5' exonuclease found in the hyperthermophilic archaeon, Pyrococcus furiosus . PLOS ONE . 8 . 3 . e58497 . 2013 . 23505520 . 3591345 . 10.1371/journal.pone.0058497 . 2013PLoSO...858497T . Yoshizumi Ishino . free .
  11. Cui Z, Wang Y, Pham BP, Ping F, Pan H, Cheong GW, Zhang S, Jia B . 6 . High level expression and characterization of a thermostable lysophospholipase from Thermococcus kodakarensis KOD1 . Extremophiles . 16 . 4 . 619–25 . July 2012 . 22622648 . 10.1007/s00792-012-0461-0 . 17109990 .
  12. Uehara R, Tanaka S, Takano K, Koga Y, Kanaya S . Requirement of insertion sequence IS1 for thermal adaptation of Pro-Tk-subtilisin from hyperthermophilic archaeon . Extremophiles . 16 . 6 . 841–51 . November 2012 . 22996828 . 10.1007/s00792-012-0479-3 . 10924828 .
  13. Čuboňováa L, Katano M, Kanai T, Atomi H, Reeve JN, Santangelo TJ . An archaeal histone is required for transformation of Thermococcus kodakarensis . Journal of Bacteriology . 194 . 24 . 6864–74 . December 2012 . 23065975 . 3510624 . 10.1128/jb.01523-12 .
  14. Postec A, Lesongeur F, Pignet P, Ollivier B, Querellou J, Godfroy A . Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys . Extremophiles . 11 . 6 . 747–57 . November 2007 . 17576518 . 10.1007/s00792-007-0092-z . 24258675 . 20.500.11850/58941 . free .
  15. Eberly JO, Ely RL . Thermotolerant hydrogenases: biological diversity, properties, and biotechnological applications . Critical Reviews in Microbiology . 34 . 3–4 . 117–30 . 2008 . 18728989 . 10.1080/10408410802240893 . 86357193 .
  16. Schut GJ, Boyd ES, Peters JW, Adams MW . 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 . March 2013 . 22713092 . 10.1111/j.1574-6976.2012.00346.x . free . 2013FEMMR..37..182S .
  17. 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.
  18. Atomi H, Tomita H, Ishibashi T, Yokooji Y, Imanaka T . CoA biosynthesis in archaea . Biochemical Society Transactions . 41 . 1 . 427–31 . February 2013 . 23356323 . 10.1042/bst20120311 .
  19. Web site: The LTP . 20 November 2023.
  20. Web site: LTP_all tree in newick format. 20 November 2023.
  21. Web site: LTP_08_2023 Release Notes. 20 November 2023.
  22. Web site: GTDB release 08-RS214 . Genome Taxonomy Database. 10 May 2023.
  23. Web site: ar53_r214.sp_label . Genome Taxonomy Database. 10 May 2023.
  24. Web site: Taxon History . Genome Taxonomy Database. 10 May 2023.
  25. Ozawa Y, Siddiqui MA, Takahashi Y, Urushiyama A, Ohmori D, Yamakura F, Arisaka F, Imai T . 6 . Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus . Journal of Bioscience and Bioengineering . 114 . 1 . 23–7 . July 2012 . 22608551 . 10.1016/j.jbiosc.2012.02.014 .
  26. Zhang Y, Zhao Z, Chen CT, Tang K, Su J, Jiao N . Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems . PLOS ONE . 7 . 9 . e44593 . 2012 . 22970260 . 3436782 . 10.1371/journal.pone.0044593 . 2012PLoSO...744593Z . free .
  27. Davidova IA, Duncan KE, Perez-Ibarra BM, Suflita JM . Involvement of thermophilic archaea in the biocorrosion of oil pipelines . Environmental Microbiology . 14 . 7 . 1762–71 . July 2012 . 22429327 . 10.1111/j.1462-2920.2012.02721.x . 2012EnvMi..14.1762D .
  28. Brown AM, Hoopes SL, White RH, Sarisky CA . Purine biosynthesis in archaea: variations on a theme . Biology Direct . 6 . 63 . December 2011 . 22168471 . 10.1186/1745-6150-6-63 . 3261824 . free .
  29. Duffaud GD, d'Hennezel OB, Peek AS, Reysenbach AL, Kelly RM . Isolation and characterization of Thermococcus barossii, sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent flange formation . Systematic and Applied Microbiology . 21 . 1 . 40–9 . March 1998 . 9741109 . 10.1016/s0723-2020(98)80007-6 . 1998SyApM..21...40D .
  30. Petrova T, Bezsudnova EY, Boyko KM, Mardanov AV, Polyakov KM, Volkov VV, Kozin M, Ravin NV, Shabalin IG, Skryabin KG, Stekhanova TN, Kovalchuk MV, Popov VO . 6 . 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 . Pt 12 . 1440–7 . December 2012 . 23192021 . 3509962 . 10.1107/s1744309112043394 .
  31. Amend JP . 2009 . A brief review of microbial geochemistry in the shallow-sea hydrothermal system of Vulcano Island (Italy) . Freiberg Online Geoscience . 22 . 7 .
  32. Hughes RC, Coates L, Blakeley MP, Tomanicek SJ, Langan P, Kovalevsky AY, García-Ruiz JM, Ng JD . 6 . Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction . Acta Crystallographica. Section F, Structural Biology and Crystallization Communications . 68 . Pt 12 . 1482–7 . December 2012 . 23192028 . 3509969 . 10.1107/S1744309112032447 .
  33. Atomi H, Reeve J . Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon . Microbiology . 165 . 11 . 1166–1168 . November 2019 . 31436525 . 7137780 . 10.1099/mic.0.000839 . free .
  34. Itoh T . 2003 . Taxonomy of Nonmethanogenic Hyperthermophilic and Related Thermophilic Archaea . Journal of Bioscience and Bioengineering . 96 . 3. 203–212 . 10.1263/jbb.96.203. 16233511 .
  35. Kuba Y, Ishino S, Yamagami T, Tokuhara M, Kanai T, Fujikane R, Daiyasu H, Atomi H, Ishino Y . 6 . Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis . Genes to Cells . 17 . 11 . 923–37 . November 2012 . 23078585 . 10.1111/gtc.12007 . Yoshizumi . Hiromi . Haruyuki . 25416025 . free .
  36. 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.
  37. Ppyun H, Kim I, Cho SS, Seo KJ, Yoon K, Kwon ST . Improved PCR performance using mutant Tpa-S DNA polymerases from the hyperthermophilic archaeon Thermococcus pacificus . Journal of Biotechnology . 164 . 2 . 363–70 . December 2012 . 23395617 . 10.1016/j.jbiotec.2013.01.022 .
  38. Marguet E, Gaudin M, Gauliard E, Fourquaux I, le Blond du Plouy S, Matsui I, Forterre P . Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus . Biochemical Society Transactions . 41 . 1 . 436–42 . February 2013 . 23356325 . 10.1042/bst20120293 .
  39. Gaudin M, Gauliard E, Schouten S, Houel-Renault L, Lenormand P, Marguet E, Forterre P . Hyperthermophilic archaea produce membrane vesicles that can transfer DNA . Environmental Microbiology Reports . 5 . 1 . 109–16 . February 2013 . 23757139 . 10.1111/j.1758-2229.2012.00348.x . 2013EnvMR...5..109G .
  40. Li Z, Kelman LM, Kelman Z . Thermococcus kodakarensis DNA replication . Biochemical Society Transactions . 41 . 1 . 332–8 . February 2013 . 23356307 . 10.1042/bst20120303 .
  41. Hirata A, Hori Y, Koga Y, Okada J, Sakudo A, Ikuta K, Kanaya S, Takano K . 6 . 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 . 19 . February 2013 . 23448268 . 10.1186/1472-6750-13-19 . 3599501 . free .
  42. Trofimov AA, Slutskaya EA, Polyakov KM, Dorovatovskii PV, Gumerov VM, Popov VO . Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus . Acta Crystallographica. Section F, Structural Biology and Crystallization Communications . 68 . Pt 11 . 1275–8 . November 2012 . 23143231 . 3515363 . 10.1107/s174430911203761x .
  43. Nisar MA, Rashid N, Bashir Q, Gardner QT, Shafiq MH, Akhtar M . TK1299, 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 . July 2013 . 23453203 . 10.1016/j.jbiosc.2013.01.020 .

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