Thermococcus

Unassigned species:

• T. coalescens Kuwabara et al. 2005
• T. marinus Jolivet et al. 2004
• T. mexicalis Antoine 1996
• T. thermotolerans Yang et al. 2023
• "T. waimanguensis" Goetz & Morgan 1999

Metabolically, Thermococcus spp. have developed a different form of glycolysis from eukaryotes and prokaryotes.{{cite journal | vauthors = Ozawa Y, Siddiqui MA, Takahashi Y, Urushiyama A, Ohmori D, Yamakura F, Arisaka F, Imai T | display-authors = 6 | title = Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus | journal = Journal of Bioscience and Bioengineering | volume = 114 | issue = 1 | pages = 23–7 | date = July 2012 | pmid = 22608551 | doi = 10.1016/j.jbiosc.2012.02.014 }}{{cite journal | vauthors = Zhang Y, Zhao Z, Chen CT, Tang K, Su J, Jiao N | title = Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems | journal = PLOS ONE | volume = 7 | issue = 9 | pages = e44593 | year = 2012 | pmid = 22970260 | pmc = 3436782 | doi = 10.1371/journal.pone.0044593 | bibcode = 2012PLoSO...744593Z | doi-access = free }} 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),{{cite journal | vauthors = Davidova IA, Duncan KE, Perez-Ibarra BM, Suflita JM | title = Involvement of thermophilic archaea in the biocorrosion of oil pipelines | journal = Environmental Microbiology | volume = 14 | issue = 7 | pages = 1762–71 | date = July 2012 | pmid = 22429327 | doi = 10.1111/j.1462-2920.2012.02721.x | bibcode = 2012EnvMi..14.1762D }} 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.{{cite journal | vauthors = Brown AM, Hoopes SL, White RH, Sarisky CA | title = Purine biosynthesis in archaea: variations on a theme | journal = Biology Direct | volume = 6 | pages = 63 | date = December 2011 | pmid = 22168471 | doi = 10.1186/1745-6150-6-63 | pmc = 3261824 | doi-access = free }} With today's technology, Thermococcus members are relatively easy to grow in labs,{{cite journal | vauthors = Duffaud GD, d'Hennezel OB, Peek AS, Reysenbach AL, Kelly RM | title = Isolation and characterization of Thermococcus barossii, sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent flange formation | journal = Systematic and Applied Microbiology | volume = 21 | issue = 1 | pages = 40–9 | date = March 1998 | pmid = 9741109 | doi = 10.1016/s0723-2020(98)80007-6 | bibcode = 1998SyApM..21...40D }} and are therefore considered model organisms for studying the physiological and molecular pathways of extremophiles.{{cite journal | vauthors = 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 | display-authors = 6 | title = ATP-dependent DNA ligase from Thermococcus sp. 1519 displays a new arrangement of the OB-fold domain | journal = Acta Crystallographica. Section F, Structural Biology and Crystallization Communications | volume = 68 | issue = Pt 12 | pages = 1440–7 | date = December 2012 | pmid = 23192021 | pmc = 3509962 | doi = 10.1107/s1744309112043394 }}{{cite journal | vauthors = Amend JP | year = 2009 | title = A brief review of microbial geochemistry in the shallow-sea hydrothermal system of Vulcano Island (Italy) | journal = Freiberg Online Geoscience | volume = 22 | page = 7 }} Thermococcus kodakarensis is one example of a model Thermococcus species, a microorganism in which has had its entire genome examined and replicated.{{cite journal | vauthors = Hughes RC, Coates L, Blakeley MP, Tomanicek SJ, Langan P, Kovalevsky AY, García-Ruiz JM, Ng JD | display-authors = 6 | title = Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction | journal = Acta Crystallographica. Section F, Structural Biology and Crystallization Communications | volume = 68 | issue = Pt 12 | pages = 1482–7 | date = December 2012 | pmid = 23192028 | pmc = 3509969 | doi = 10.1107/S1744309112032447 }}{{cite journal | vauthors = Atomi H, Reeve J | title = Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon | journal = Microbiology | volume = 165 | issue = 11 | pages = 1166–1168 | date = November 2019 | pmid = 31436525 | pmc = 7137780 | doi = 10.1099/mic.0.000839 | doi-access = free }}

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.{{cite journal | vauthors = Itoh T | year = 2003 | title = Taxonomy of Nonmethanogenic Hyperthermophilic and Related Thermophilic Archaea | journal = Journal of Bioscience and Bioengineering | volume = 96 | issue = 3| pages = 203–212 | doi=10.1263/jbb.96.203| pmid = 16233511 }}{{cite journal | vauthors = Kuba Y, Ishino S, Yamagami T, Tokuhara M, Kanai T, Fujikane R, Daiyasu H, Atomi H, Ishino Y | display-authors = 6 | title = Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis | journal = Genes to Cells | volume = 17 | issue = 11 | pages = 923–37 | date = November 2012 | pmid = 23078585 | doi = 10.1111/gtc.12007 | first8 = Yoshizumi | first6 = Hiromi | first7 = Haruyuki | s2cid = 25416025 | doi-access = free }} 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,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. 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.{{cite journal | vauthors = Ppyun H, Kim I, Cho SS, Seo KJ, Yoon K, Kwon ST | title = Improved PCR performance using mutant Tpa-S DNA polymerases from the hyperthermophilic archaeon Thermococcus pacificus | journal = Journal of Biotechnology | volume = 164 | issue = 2 | pages = 363–70 | date = December 2012 | pmid = 23395617 | doi = 10.1016/j.jbiotec.2013.01.022 }}

Thermococcus species are naturally competent in taking up DNA and incorporating donor DNA into their genomes via homologous recombination.{{cite journal | vauthors = Marguet E, Gaudin M, Gauliard E, Fourquaux I, le Blond du Plouy S, Matsui I, Forterre P | title = Membrane vesicles, nanopods and/or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus | journal = Biochemical Society Transactions | volume = 41 | issue = 1 | pages = 436–42 | date = February 2013 | pmid = 23356325 | doi = 10.1042/bst20120293 }} These species can produce membrane vesicles (MVs), formed by budding from the outermost cellular membranes,{{cite journal | vauthors = Gaudin M, Gauliard E, Schouten S, Houel-Renault L, Lenormand P, Marguet E, Forterre P | title = Hyperthermophilic archaea produce membrane vesicles that can transfer DNA | journal = Environmental Microbiology Reports | volume = 5 | issue = 1 | pages = 109–16 | date = February 2013 | pmid = 23757139 | doi = 10.1111/j.1758-2229.2012.00348.x | bibcode = 2013EnvMR...5..109G }} 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.{{cite journal | vauthors = Li Z, Kelman LM, Kelman Z | title = Thermococcus kodakarensis DNA replication | journal = Biochemical Society Transactions | volume = 41 | issue = 1 | pages = 332–8 | date = February 2013 | pmid = 23356307 | doi = 10.1042/bst20120303 }} 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.

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.{{cite journal | vauthors = Hirata A, Hori Y, Koga Y, Okada J, Sakudo A, Ikuta K, Kanaya S, Takano K | display-authors = 6 | title = Enzymatic activity of a subtilisin homolog, Tk-SP, from Thermococcus kodakarensis in detergents and its ability to degrade the abnormal prion protein | journal = BMC Biotechnology | volume = 13 | pages = 19 | date = February 2013 | pmid = 23448268 | doi = 10.1186/1472-6750-13-19 | pmc = 3599501 | doi-access = free }} Tk-SP, another enzyme from T. kodakarensis,{{cite journal | vauthors = Trofimov AA, Slutskaya EA, Polyakov KM, Dorovatovskii PV, Gumerov VM, Popov VO | title = Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus | journal = Acta Crystallographica. Section F, Structural Biology and Crystallization Communications | volume = 68 | issue = Pt 11 | pages = 1275–8 | date = November 2012 | pmid = 23143231 | pmc = 3515363 | doi = 10.1107/s174430911203761x }} 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.{{cite journal | vauthors = Nisar MA, Rashid N, Bashir Q, Gardner QT, Shafiq MH, Akhtar M | title = TK1299, a highly thermostable NAD(P)H oxidase from Thermococcus kodakaraensis exhibiting higher enzymatic activity with NADPH | journal = Journal of Bioscience and Bioengineering | volume = 116 | issue = 1 | pages = 39–44 | date = July 2013 | pmid = 23453203 | doi = 10.1016/j.jbiosc.2013.01.020 }}

• List of Archaea genera

{{reflist}}

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• {{cite journal | author = Judicial Commission of the International Committee on Systematics of Prokaryotes | title = 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 | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 55 | issue = Pt 1 | pages = 517–518 | date = January 2005 | pmid = 15653928 | doi = 10.1099/ijs.0.63548-0 | doi-access = free }}
• {{cite journal | vauthors = Mora M, Bellack A, Ugele M, Hopf J, Wirth R | title = The temperature gradient-forming device, an accessory unit for normal light microscopes to study the biology of hyperthermophilic microorganisms | journal = Applied and Environmental Microbiology | volume = 80 | issue = 15 | pages = 4764–70 | date = August 2014 | pmid = 24858087 | pmc = 4148812 | doi = 10.1128/AEM.00984-14 | bibcode = 2014ApEnM..80.4764M }}
• {{ cite journal | vauthors = Zillig W, Holz I, Klenk HP, Trent J, Wunderl S, Janekovic D, Imsel E, Haas B | date = 1987 | title = Pyrococcus woesei, sp. nov., an ultra-thermophilic marine Archaebacterium, representing a novel order, Thermococcales | journal = Syst. Appl. Microbiol. | volume = 9 | issue = 1–2 | pages = 62–70 | doi=10.1016/S0723-2020(87)80057-7| bibcode = 1987SyApM...9...62Z }}
• {{ cite journal | vauthors = Zillig W, Holz L, Janekovic D, Schafer W, Reiter WD | date = 1983 | title = The archaebacterium Thermococcus celer represents a novel genus within the thermophilic branch of the archaebacteria | journal = Syst. Appl. Microbiol. | volume = 4 | issue = 1 | pages = 88–94 | doi = 10.1016/S0723-2020(83)80036-8 | pmid = 23196302 | bibcode = 1983SyApM...4...88Z }}

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• {{Cite web|url=http://www.cas.muohio.edu/~stevenjr/mbi202/evolution202.html|title=Microbial Evolution and Systematics|access-date=2008-07-13|author=John R. Stevenson|work=General Microbiology II }}
• [http://bacdive.dsmz.de/index.php?search=Thermococcus&submit=Search Thermococcus at BacDive - the Bacterial Diversity Metadatabase]

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Category:Archaea genera

Category:Euryarchaeota