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Patrick Forterre - One of the best experts on this subject based on the ideXlab platform.
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Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Edmond Jolivet, Patrick Forterre, Erwan Corre, Stéphane L'haridon, Daniel PrieurAbstract:Enrichments for anaerobic organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected at the Guaymas Basin (27 degrees 01' N, 111 degrees 24' W). Positive enrichments were submitted to gamma-irradiation at a dose of 30 kGy. One of the resistant strains, designated strain EJ3(T), formed regular motile cocci. The new strain grew between 55 and 95 degrees C, with an optimum growth temperature of 88 degrees C. The optimal pH for growth was 6.0, and the optimum NaCl concentration for growth was around 20 g l(-1). Strain EJ3(T) was an obligately anaerobic heterotroph that utilized yeast extract, tryptone and peptone. Elemental sulfur or cystine was required for growth and reduced to hydrogen sulfide. The G + C content of the genomic DNA was 51.3 mol%. As determined by 16S rRNA gene sequence analysis, the organism was most closely related to Thermococcus celer, Thermococcus guaymasensis, Thermococcus hydrothermalis, Thermococcus profundus and Thermococcus gorgonarius. However, no significant homology was observed between them by DNA-DNA hybridization. The novel organism also possessed phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that this isolate, which constitutes the most radioresistant hyperthermophilic archaeon known to date, should be described as the type strain of a novel species, Thermococcus gammatolerans sp. nov. The type strain is EJ3(T) (= DSM 15229(T) = JCM 11827(T)).
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genome sequence of a hyperthermophilic archaeon Thermococcus nautili 30 1 that produces viral vesicles
Genome Announcements, 2014Co-Authors: Jacques Oberto, Marie Gaudin, Evelyne Marguet, Aurore Gorlas, Matteo Cossu, Alexei Slesarev, Patrick ForterreAbstract:Thermococcus nautili 30-1 (formerly Thermococcus nautilus), an anaerobic hyperthermophilic marine archaeon, was isolated in 1999 from a deep-sea hydrothermal vent during the Amistad campaign. Here, we present the complete sequence of T. nautili, which is able to produce membrane vesicles containing plasmid DNA. This property makes T. nautili a model organism to study horizontal gene transfer.
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Thermococcus nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent.
International journal of systematic and evolutionary microbiology, 2014Co-Authors: Aurore Gorlas, Emilie Gauliard, Patrick Forterre, Olivier Croce, Jacques Oberto, Evelyne MarguetAbstract:Thermococcus nautili, strain 30-1T (formerly reported as Thermococcus nautilus), was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at a depth of 2633 m on the 'La chainette PP57' area. Cells were motile, irregular cocci with a polar tuft of flagella (0.8-1.5 µm) and divided by constriction. The micro-organism grew optimally at 87.5 °C (range 55-95 °C), at pH 7 (range pH 4-9) and with 2% NaCl (range 1-4%). Doubling time was 64 min in Zillig's broth medium under optimal conditions. Growth was strictly anaerobic. It grew preferentially in the presence of elemental sulfur or cystine, which are reduced to H2S, on complex organic substrates such as yeast extract, tryptone, peptone, Casamino acids and casein. Slow growth was observed on starch and pyruvate. Strain 30-1T was resistant to chloramphenicol and tetracyclin (at 100 µg ml(-1)) but sensitive to kanamycin and rifampicin. The G+C content of the genomic DNA was 54 mol%. Strain 30-1T harboured three plasmids named pTN1, pTN2 and pTN3 and produced membrane vesicles that incorporate pTN1 and pTN3. As determined by 16S rRNA gene sequence analysis, strain 30-1T is related most closely to Thermococcus sp. AM4 (99.3% similarity) and Thermococcus gammatolerans DSM 15229T (99.2%). DNA-DNA hybridization values (in silico) with these two closest relatives were below the threshold value of 70% (33% with Thermococcus sp. AM4 and 32% with T. gammatolerans DSM 15229T) and confirmed that strain 30-1 represents a novel species. On the basis of the data presented, strain 30-1T is considered to represent a novel species of the genus Thermococcus, for which the name Thermococcus nautili sp. nov. is proposed. The type strain is 30-1T (=CNCM 4275=JCM 19601).
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living side by side with a virus characterization of two novel plasmids from Thermococcus prieurii a host for the spindle shaped virus tpv1
Applied and Environmental Microbiology, 2013Co-Authors: Aurore Gorlas, Patrick Forterre, Mart Krupovic, Claire GeslinAbstract:Microbial cells often serve as an evolutionary battlefield for different types of mobile genetic elements, such as viruses and plasmids. Here, we describe the isolation and characterization of two new archaeal plasmids which share the host with the spindle-shaped Thermococcus prieurii virus 1 (TPV1). The two plasmids, pTP1 and pTP2, were isolated from the hyperthermophilic archaeon Thermococcus prieurii (phylum Euryarchaeota), a resident of a deep-sea hydrothermal vent located at the East Pacific Rise at 2,700-m depth (7°25′24 S, 107°47′66 W). pTP1 (3.1 kb) and pTP2 (2.0 kb) are among the smallest known plasmids of hyperthermophilic archaea, and both are predicted to replicate via the rolling-circle mechanism. The two plasmids and the virus TPV1 do not have a single gene in common and stably propagate in infected cells without any apparent antagonistic effect on each other. The compatibility of the three genetic elements and the high copy number of pTP1 and pTP2 plasmids (50 copies/cell) might be useful for developing new genetic tools for studying hyperthermophilic euryarchaea and their viruses.
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membrane vesicles nanopods and or nanotubes produced by hyperthermophilic archaea of the genus Thermococcus
Biochemical Society Transactions, 2013Co-Authors: Evelyne Marguet, Marie Gaudin, Emilie Gauliard, Patrick Forterre, Isabelle Fourquaux, Stephane Le Blond Du Plouy, Ikuo MatsuiAbstract:Thermococcus species produce MVs (membrane vesicles) into their culture medium. These MVs are formed by a budding process from the cell envelope, similar to ectosome formation in eukaryotic cells. The major protein present in MVs of Thermococci is a peptide-binding receptor of the OppA (oligopeptide-binding protein A) family. In addition, some of them contain a homologue of stomatin, a universal membrane protein involved in vesiculation. MVs produced by Thermococcus species can recruit endogenous or exogenous plasmids and plasmid transfer through MVs has been demonstrated in Thermococcus kodakaraensis . MVs are frequently secreted in clusters surrounded by S-layer, producing either big protuberances (nanosphere) or tubular structures (nanotubes). Thermococcus gammatolerans and T. kodakaraensis produce nanotubes containing strings of MVs, resembling the recently described nanopods in bacteria, whereas Thermococcus sp. 5-4 produces filaments whose internal membrane is continuous. These nanotubes can bridge neighbouring cells, forming cellular networks somehow resembling nanotubes recently observed in Firmicutes. As suggested for bacteria, archaeal nanopods and/or nanotubes could be used to expand the metabolic sphere around cells and/or to promote intercellular communication.
Sung Gyun Kang - One of the best experts on this subject based on the ideXlab platform.
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Characterization of hyperthermostable fructose-1,6-bisphosphatase from Thermococcus onnurineus NA1.
Journal of Microbiology, 2020Co-Authors: Sung Gyun Kang, Youngho ChungAbstract:To understand the physiological functions of thermostable fructose-1,6-bisphosphatase (TNA1-Fbp) from Thermococcus onnurineus NA1, its recombinant enzyme was overexpressed in Escherichia coli, purified, and the enzymatic properties were characterized. The enzyme showed maximal activity for fructose-1,6-bisphosphate at 95°C and pH 8.0 with a half-life (t1/2) of about 8 h. TNA1-Fbp had broad substrate specificities for fructose-1,6-bisphosphate and its analogues including fructose-1-phosphate, glucose-1-phosphate, and phosphoenolpyruvate. In addition, its enzyme activity was increased five-fold by addition of 1 mM Mg2+, while Li+ did not enhance enzymatic activity. TNA1-Fbp activity was inhibited by ATP, ADP, and phosphoenolpyruvate, but AMP up to 100 mM did not have any effect. TNA1-Fbp is currently defined as a class V fructose-1,6-bisphosphatase (FBPase) because it is very similar to FBPase of Thermococcus kodakaraensis KOD1 based on sequence homology. However, this enzyme shows a different range of substrate specificities. These results suggest that TNA1-Fbp can establish new criterion for class V FBPases.
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Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri Vent Field of the Central Indian Ocean ridge
Journal of Microbiology, 2020Co-Authors: Jhung-ahn Yang, Sung Gyun Kang, Sung Hyun Yang, Teddy Namirimu, Mi-jeong Park, Yong Min Kwon, Kae Kyoung KwonAbstract:A strictly anaerobic, dissimilatory Fe(III)-reducing hyperthermophilic archaeon, designated as strain IOH1^T, was isolated from a new deep-sea hydrothermal vent (Onnuri Vent Field) area in the Central Indian Ocean ridge. Strain IOH1^T showed > 99% 16S rRNA gene sequence similarity with Thermococcus celericrescens TS2^T (99.4%) and T. siculi DSM 12349^T (99.2%). Additional three species T. barossii SHCK-94^T (99.0%), T. celer Vu13^T (98.8%), and ^T. piezophilus (98.6%) showed > 98.6% of 16S rRNA gene sequence similarity, however, the maximum OrthoANI value is 89.8% for the genome of T. celericrescens TS2^T. Strain IOH1^T cells are coccoid, 1.2–1.8 μm in diameter, and motile by flagella. Growth was at 70–82°C (optimum 80°C), pH 5.4–8.0 (optimum pH 6.0) with 2–4% (optimum 3%) NaCl. Growth of strain IOH1T was enhanced by starch, pyruvate, D(+)-maltose and maltodextrin as a carbon sources, and elemental sulfur as an electron acceptor; clearly different from those of related species T. celecrescens DSM 17994^T and T. siculi DSM 12349^T. Strain IOH1^T, T. celercrescence DSM 17994^T, and T. siculi DSM 12349^T reduced soluble Fe(III)-citrate present in the medium, whereas the amount of total cellular proteins increased with the concomitant accumulation of Fe(II). We determined a circular chromosome of 2,234 kb with an extra-chromosomal archaeal plasmid, pTI1, of 7.7 kb and predicted 2,425 genes. The DNA G + C content was 54.9 mol%. Based on physiological properties, phylogenetic, and genome analysis, we proposed that strain IOH1^T (= KCTC 15844^T = JCM 39077^T) is assigned to a new species in the genus Thermococcus and named Thermococcus indicus sp. nov.
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Screening of a novel strong promoter by RNA sequencing and its application to H_2 production in a hyperthermophilic archaeon
Applied Microbiology and Biotechnology, 2015Co-Authors: Hae Chang Jung, Sung Gyun KangAbstract:A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H_2 from carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. This promoter, P_ TN0510 , was introduced into the front of CO-responsible hydrogenase gene cluster encoding a carbon monoxide dehydrogenase (CODH), a hydrogenase, and a Na^+/H^+ antiporter. In the resulting mutant strain, KS0510, transcription and translation level of the gene cluster increased by 4- to 14-folds and 1.5- to 1.9-folds, respectively, in comparison with those of the wild-type strain. Additionally, H_2 production rate of KS0510 mutant was 4.8-fold higher than that of the wild-type strain. The P_ TN0510 was identified to be much stronger than the well-known two strong promoters, gdh and slp promoters from Thermococcus strains, through RT-qPCR and Western blotting analyses and kinetics of H_2 production. In this study, we demonstrated that the RNA-seq approach is a good strategy to mine novel strong promoters of use to a Thermococcus strain when developed as a biotechnologically promising strain to produce valuable products such as enzymes and metabolites through metabolic engineering.
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Molecular cloning and enzymatic characterization of cyclomaltodextrinase from hyperthermophilic archaeon Thermococcus sp. CL1.
Journal of Microbiology and Biotechnology, 2013Co-Authors: Jong-hyun Jung, Sung Gyun Kang, James F Holden, Cheon-seok ParkAbstract:Genome organization near cyclomaltodextrinases (CDases) was analyzed and compared for four different hyperthermophilic archaea: Thermococcus, Pyrococcus, Staphylothermus, and Thermofilum. A gene (CL1_0884) encoding a putative CDase from Thermococcus sp. CL1 (tccd) was cloned and expressed in Escherichia coli. TcCD was confirmed to be highly thermostable, with optimal activity at 85oC. The melting temperature of TcCD was determined to be 93oC by both differential scanning calorimetry and differential scanning fluorimetry. A size-exclusion chromatography experiment showed that TcCD exists as a monomer. TcCD preferentially hydrolyzed α-cyclodextrin (α-CD), and at the initial stage catalyzed a ring-opening reaction by cleaving one α-1,4-glycosidic linkage of the CD ring to produce the corresponding single maltooligosaccharide. Furthermore, TcCD could hydrolyze branched CDs (G1-α-CD, G1-β- CD, and G2-β-CD) to yield significant amounts (45%, 40%, and 46%) of isomaltooligosaccharides (panose and 62-α-maltosylmaltose) in addition to glucose and maltose. This enzyme is one of the most thermostable maltogenic amylases reported, and might be of potential value in the production of isomaltooligosaccharides in the food industry.
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proteome analyses of hydrogen producing hyperthermophilic archaeon Thermococcus onnurineus na1 in different one carbon substrate culture conditions
Molecular & Cellular Proteomics, 2012Co-Authors: Yoonjung Moon, Sung Gyun Kang, Jong-soon Choi, Joseph Kwon, Youngho ChungAbstract:Hyperthermophilic archaea can use a wide variety of carbon and energy sources. Hyperthermophiles are widely distributed in extreme habitats such as deep-sea thermal vents, hot springs, and deep oil reservoirs (1–3). So far, the most frequently studied hyperthermophiles are from the genera Thermococcus and Pyrococcus, which belong to the order Thermococcales (4). These are ecologically important hyperthermophilic archaea for understanding the physiology and metabolic activity of microbial consortia within marine hot-water ecosystems. Members of the order Thermococcales are anaerobic heterotrophs that utilize various complex substrates with elemental sulfur (S0) or protons as electron acceptors (4–6). Unlike other Thermococcales, Thermococcus strain AM4 (7) and Thermococcus onnurineus NA1 (8) are capable of lithotrophic carbon monoxide-dependent hydrogenogenic growth. These Thermococcus strains use CO as a carbon and energy source by converting it into carbon dioxide (CO2). In addition, several hyperthermophilic archaea of the genus Thermococcus can grow with formate as an electron donor, producing hydrogen gas (9). T. onnurineus NA1 is a sulfur-reducing hyperthermophilic archaeon isolated from a deep sea hydrothermal vent area in the Eastern Manus Basin of Papua New Guinea (10). It is one of the more metabolically versatile hyperthermophiles in that it can use one-carbon (C1) substrates such as formate and CO, as well as multi-carbon substrates such as starch as the sole source of carbon and energy. Despite new insights into the mechanisms involved in the coupling of formate oxidation to energy conservation in T. onnurineus NA1 (9), the metabolic processes unique to growth on formate remain to be characterized. Typically, many hyperthermophiles are heterotrophs or grow on acetate. Most enzymes in the catabolic pathway of hyperthermophilic archaea have been identified and characterized. However, the anabolic pathway used by T. onnurineus NA1 to anaerobically convert these one-carbon substrates into cellular carbon is poorly understood. Therefore, study of one-carbon metabolism involved in H2-producing growth in T. onnurineus NA1 is of considerable interest because one-carbon substrates (i.e. methanol, carbon dioxide, and formate) are important for energy metabolism and carbon fixation pathways in some archaea (e.g. methanogenic archaea) and thus are expected to have many potential applications to industrial processes. Recently, complete genome sequences have been determined for a number of Thermococcales, including three representative Pyrococcus species (11–13) and four Thermococcus strains: Thermococcus sibiricus (6), T. onnurineus NA1 (8), Thermococcus kodakaraensis KOD1 (14), and Thermococcus gammatolerans (15). Comparative genomic studies on these Thermococcales have paved the way for exploring the features and functions of genes involved in major metabolic pathways. Using a whole genome shotgun approach, the structure of the T. onnurineus NA1 genome was accurately determined, indicating that it contains 1,847,607 base pairs and 1976 predicted open reading frames (8). Moreover, genetic predictions based on these genomic data have provided clues for identifying genes correlated with biological functions (6, 8, 14). In particular, genomic analysis of T. onnurineus NA1 revealed several distinct hydrogenase gene clusters involved in H2 metabolism and carboxydotrophic pathways (16). Compared with genome analysis, only a handful of proteomic studies have been performed on Thermococcus strains. In T. gammatolerans, the first archaeal genome-wide proteome investigation was performed using an LC-MS/MS shotgun approach at the primary genome annotation stage (15). This study demonstrated that T. gammatolerans utilizes various metabolic pathways during growth in nutrient-rich medium (15). However, few studies have examined changes in the protein expression profile of T. onnurineus NA1 (17, 18). A previous 2-DE/MS-MS proteome analysis provided the first global view of the metabolic pathways of T. onnurineus NA1 during heterotrophic growth (17). Using an SDS-PAGE/LC-MS/MS shotgun proteomic approach, we recently made significant progress in identifying the metabolic enzymes specific for hydrogen production under carboxydotrophic culture conditions (18). Although recent genome analyses and proteomic characterizations have revealed general genomic features and metabolic pathways, a comprehensive understanding of the overall metabolism of T. onnurineus NA1 is lacking. Furthermore, a quantitative comparative analysis of all enzymes needed for central carbon flow, electron transfer, and/or energy conservation under different growth conditions has not been published. Here we describe a quantitative proteome analysis of T. onnurineus NA1 cells using one-dimensional SDS-PAGE coupled with nano-UPLC-MSE.1 We examined the metabolism of T. onnurineus NA1 during H2-producing growth on different substrates. The major metabolic pathways proposed from a genomic analysis were characterized by comparing the protein expression profiles of cultures grown in the presence of formate, CO, and starch as sole carbon and/or energy sources. For the first time, we can draw a more complete metabolic picture of T. onnurineus NA1 at the protein level, which may facilitate a greater understanding of the metabolic adaptation of hyperthermophiles to extreme environments.
Tadayuki Imanaka - One of the best experts on this subject based on the ideXlab platform.
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Chaperonin from Thermococcus kodakaraensis KOD1.
Methods in Enzymology, 2020Co-Authors: Shinsuke Fujiwara, Masahiro Takagi, Tadayuki ImanakaAbstract:Publisher Summary Chaperonins are a group of molecular chaperones that are classified into the GroEL/HSP60 (heat shock protein 60) family. They are widely distributed from prokaryotes to eukaryotes and first came to light because of their specific induction during the cellular response of all organisms to heat shock. It is now clear that the majority of these proteins are expressed constitutively and abundantly in the absence of any stress, and genetic studies show that many of them are essential for cell viability under normal conditions of growth. Many HSPs do not respond significantly to heat shock and are induced under a variety of other stress conditions, whose common denominator may be the accumulation of unfolded or malfolded proteins in cells. They also mediate the correct assembly of polypeptides and the translocation of proteins across membranes, but are themselves not components of the final structures. In hyperthermophilic archaea, chaperonins play an essential role in hindering protein denaturation. Thermostable chaperonins are potentially useful for industrial application. In this chapter, methods to study archaeal chaperonins are discussed, which use as model systems recombinant forms of CpkA and CpkB from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD 1, previously reported as Pyrococcus kodakaraensis KOD 1. The enhancing effect of chaperonin on enzyme stability is introduced using yeast alcohol dehydrogenase (ADH) as a model protein. In addition, a unique approach to prevent insoluble complex formation in Escherichia coli by coexpressing CpkB with a target protein is mentioned.
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Chitinase from Thermococcus kodakaraensis KOD1.
Methods in Enzymology, 2020Co-Authors: Tadayuki Imanaka, Toshiaki Fukui, Shinsuke FujiwaraAbstract:Publisher Summary Various chitinases and their genes from Eucarya and Bacteria have been investigated. However, studies on archaeal chitinase have been limited to those from hyperthermophilic archaeal strains Thermococcus chitonophagus and Thermococcus kodakaraensis KOD 1. T. chitonophagus produces a chitinase and utilizes chitin as a carbon source. The chitinoclastic enzyme system of the strain is oxygen stable, cell associated, and inducible by chitin. T. kodakaraensis KOD1 also produces a cell-associated thermostable chitinase. The Tk-chiA gene encoding the chitinase of KOD1 strain has been cloned and sequenced. This chapter describes basic procedures for the purification of recombinant chitinase, substrate preparation, enzyme assay, and determination of reaction product. In addition, a simple method to examine chitin-binding activity is introduced.
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Thiol protease from Thermococcus kodakaraensis KOD1.
Methods in Enzymology, 2020Co-Authors: Masaaki Morikawa, Tadayuki ImanakaAbstract:Publisher Summary Thiol proteases (cysteinyl proteinases) are grouped into three families. The largest and most familiar is the papain superfamily. Mammalian lysosomal thiol protease, cathepsins B, L, and H, are homologous with papain. Calcium-dependent thiol proteases, calpains, are also a member of this group. A second superfamily is composed of bacterial proteases, including Streptococcus proteinase and Clostridium proteinase, clostripain. Their primary structures are different from papain. The hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1 (previously classified as Pyrococcus), was isolated from Kodakara Island, Kagoshima, Japan. This strain produces at least three kinds of extracellular proteases with different molecular weights. This chapter describes the isolation and characterization of thiol protease from T. kodakaraensis .
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an ornithine ω aminotransferase required for growth in the absence of exogenous proline in the archaeon Thermococcus kodakarensis
Journal of Biological Chemistry, 2018Co-Authors: Tadayuki Imanaka, Renchao Zheng, Shinichi Hachisuka, Hiroya Tomita, Yuguo Zheng, Makoto Nishiyama, Haruyuki AtomiAbstract:: Aminotransferases are pyridoxal 5'-phosphate-dependent enzymes that catalyze reversible transamination reactions between amino acids and α-keto acids, and are important for the cellular metabolism of nitrogen. Many bacterial and eukaryotic ω-aminotransferases that use l-ornithine (Orn), l-lysine (Lys), or γ-aminobutyrate (GABA) have been identified and characterized, but the corresponding enzymes from archaea are unknown. Here, we examined the activity and function of TK2101, a gene annotated as a GABA aminotransferase, from the hyperthermophilic archaeon Thermococcus kodakarensis We overexpressed the TK2101 gene in T. kodakarensis and purified and characterized the recombinant protein and found that it displays only low levels of GABA aminotransferase activity. Instead, we observed a relatively high ω-aminotransferase activity with l-Orn and l-Lys as amino donors. The most preferred amino acceptor was 2-oxoglutarate. To examine the physiological role of TK2101, we created a TK2101 gene-disruption strain (ΔTK2101), which was auxotrophic for proline. Growth comparison with the parent strain KU216 and the biochemical characteristics of the protein strongly suggested that TK2101 encodes an Orn aminotransferase involved in the biosynthesis of l-Pro. Phylogenetic comparisons of the TK2101 sequence with related sequences retrieved from the databases revealed the presence of several distinct protein groups, some of which having no experimentally studied member. We conclude that TK2101 is part of a novel group of Orn aminotransferases that are widely distributed at least in the genus Thermococcus, but perhaps also throughout the Archaea.
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formate driven growth coupled with h 2 production
Nature, 2010Co-Authors: Rie Matsumi, Haruyuki Atomi, Tadayuki Imanaka, Elizaveta A Bonchosmolovskaya, Kae Kyoung Kwon, Alexander V. Lebedinsky, T G Sokolova, Darya A Kozhevnikova, Sung Gyun KangAbstract:The oxidation of formate to carbon dioxide and hydrogen is a common reaction in microorganisms in anaerobic environments, but it releases little energy and had not been shown to sustain growth in an isolated species. Now Kim et al. have discovered that that several hyperthermophilic archaea of the Thermococcus genus are indeed capable of using formate oxidation for growth. These organisms thrive at above 80 °C, a habitat that may give a competitive advantage to organisms using what is one of the simplest forms of anaerobic respiration so far described. The oxidation of formate and water to bicarbonate and H2 is relatively common in microorganisms under anaerobic conditions. But can this reaction sustain growth in an isolated species? Here it is shown that several individual Thermococcus species can use formate oxidation for growth. Moreover, the biochemical basis of this ability is delineated. Although a common reaction in anaerobic environments, the conversion of formate and water to bicarbonate and H2 (with a change in Gibbs free energy of ΔG° = +1.3 kJ mol−1) has not been considered energetic enough to support growth of microorganisms. Recently, experimental evidence for growth on formate was reported for syntrophic communities of Moorella sp. strain AMP and a hydrogen-consuming Methanothermobacter species and of Desulfovibrio sp. strain G11 and Methanobrevibacter arboriphilus strain AZ1. The basis of the sustainable growth of the formate-users is explained by H2 consumption by the methanogens, which lowers the H2 partial pressure, thus making the pathway exergonic2. However, it has not been shown that a single strain can grow on formate by catalysing its conversion to bicarbonate and H2. Here we report that several hyperthermophilic archaea belonging to the Thermococcus genus are capable of formate-oxidizing, H2-producing growth. The actual ΔG values for the formate metabolism are calculated to range between −8 and −20 kJ mol−1 under the physiological conditions where Thermococcus onnurineus strain NA1 are grown. Furthermore, we detected ATP synthesis in the presence of formate as a sole energy source. Gene expression profiling and disruption identified the gene cluster encoding formate hydrogen lyase, cation/proton antiporter and formate transporter, which were responsible for the growth of T. onnurineus NA1 on formate. This work shows formate-driven growth by a single microorganism with protons as the electron acceptor, and reports the biochemical basis of this ability.
Philippe Oger - One of the best experts on this subject based on the ideXlab platform.
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Complete Genome Sequences of 11 Type Species from the Thermococcus Genus of Hyperthermophilic and Piezophilic Archaea
Genome Announcements, 2018Co-Authors: Philippe OgerAbstract:ABSTRACT We report here the genome sequences of the type strains of the species Thermococcus barossii , T. celer , T. chitonophagus , T. gorgonarius , T. pacificus , T. peptonophilus , T. profundus , T. radiotolerans , T. siculi , and T. thioreducens , as well as the prototype of a possible type strain of a novel Thermococcus species, strain P6.
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Thermococcus piezophilus sp nov a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth isolated from a deepest hydrothermal vent at the mid cayman rise
Systematic and Applied Microbiology, 2016Co-Authors: Cecile Dalmasso, Philippe Oger, Gwendoline Selva, Damien Courtine, Stephane Lharidon, Alexandre GarlaschelliAbstract:Abstract A novel strictly anaerobic, hyperthermophilic archaeon, designated strain CDGST, was isolated from a deep-sea hydrothermal vent in the Cayman Trough at 4964 m water depth. The novel isolate is obligate anaerobe and grows chemoorganoheterotrophically with stimulation of growth by sulphur containing compounds. Its growth is optimal at 75 °C, pH 6.0 and under a pressure of 50 MPa. It possesses the broadest hydrostatic pressure range for growth that has ever been described for a microorganism. Its genomic DNA G + C content is 51.11 mol%. The novel isolate belongs to the genus Thermococcus. Phylogenetic analyses indicated that it is most closely related to Thermococcus barossii DSM17882T based on its 16S rRNA gene sequence, and to ‘Thermococcus onnurineus’ NA1 based on its whole genome sequence. The average nucleotide identity scores with these strains are 77.66% for T. barossii and 84.84% for ‘T. onnurineus’, respectively. Based on the draft whole genome sequence and phenotypic characteristics, strain CDGST is suggested to be separated into a novel species within the genus Thermococcus, with proposed name Thermococcus piezophilus (type strain CDGST = ATCC TSD-33T = UBOCC 3296T).
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genome expression of Thermococcus barophilus and Thermococcus kodakarensis in response to different hydrostatic pressure conditions
Research in Microbiology, 2015Co-Authors: P Vannier, Philippe Oger, Mohamed Jebbar, Gregoire Michoud, V MarteinssonAbstract:Abstract Transcriptomes were analyzed for two related hyperthermophilic archaeal species, the piezophilic Thermococcus barophilus strain MP and piezosensitive Thermococcus kodakarensis strain KOD1 subjected to high hydrostatic pressures. A total of 378 genes were differentially expressed in T. barophilus cells grown at 0.1, 40 and 70 MPa, whereas 141 genes were differentially regulated in T. kodakarensis cells grown at 0.1 and 25 MPa. In T. barophilus cells grown under stress conditions (0.1 and 70 MPa), 178 upregulated genes were distributed among three clusters of orthologous groups (COG): energy production and conversion (C), inorganic ion transport and metabolism (P) and carbohydrate transport and metabolism (G), whereas 156 downregulated genes were distributed among: amino acid transport and metabolism (E), replication, recombination and repair (L) and nucleotide transport and metabolism (F). The expression of 141 genes was regulated in T. kodakarensis cells grown under stress conditions (25 MPa); 71 downregulated genes belong to three COG: energy production and conversion (C), amino acid transport and metabolism (E) and transcription (K), whereas 70 upregulated genes are associated with replication, recombination and repair (L), coenzyme transport (H) and defense mechanisms (V).
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complete genome sequence of the hyperthermophilic piezophilic heterotrophic and carboxydotrophic archaeon Thermococcus barophilus mp
Journal of Bacteriology, 2011Co-Authors: P Vannier, Philippe Oger, Viggo Thor Marteinsson, Olafur H Fridjonsson, Mohamed JebbarAbstract:Thermococcus barophilus is a hyperthermophilic, anaerobic, mixed heterotrophic, and carboxydotrophic euryarchaeon isolated from the deep sea hydrothermal vent Snakepit site on the mid-Atlantic ridge at a depth of 3,550 m. T. barophilus is the first true piezophilic, hyperthermophilic archaeon isolated, having an optimal growth at 40 MPa. Here we report the complete genome sequence of strain MP, the type strain of T. barophilus. The genome data reveal a close proximity with Thermococcus sibiricus, another Thermococcus isolated from the deep biosphere and a possible connection to life in the depths.
Daniel Prieur - One of the best experts on this subject based on the ideXlab platform.
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Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation.
International journal of systematic and evolutionary microbiology, 2020Co-Authors: Edmond Jolivet, Patrick Forterre, Erwan Corre, Stéphane L'haridon, Daniel PrieurAbstract:Enrichments for anaerobic organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected at the Guaymas Basin (27 degrees 01' N, 111 degrees 24' W). Positive enrichments were submitted to gamma-irradiation at a dose of 30 kGy. One of the resistant strains, designated strain EJ3(T), formed regular motile cocci. The new strain grew between 55 and 95 degrees C, with an optimum growth temperature of 88 degrees C. The optimal pH for growth was 6.0, and the optimum NaCl concentration for growth was around 20 g l(-1). Strain EJ3(T) was an obligately anaerobic heterotroph that utilized yeast extract, tryptone and peptone. Elemental sulfur or cystine was required for growth and reduced to hydrogen sulfide. The G + C content of the genomic DNA was 51.3 mol%. As determined by 16S rRNA gene sequence analysis, the organism was most closely related to Thermococcus celer, Thermococcus guaymasensis, Thermococcus hydrothermalis, Thermococcus profundus and Thermococcus gorgonarius. However, no significant homology was observed between them by DNA-DNA hybridization. The novel organism also possessed phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that this isolate, which constitutes the most radioresistant hyperthermophilic archaeon known to date, should be described as the type strain of a novel species, Thermococcus gammatolerans sp. nov. The type strain is EJ3(T) (= DSM 15229(T) = JCM 11827(T)).
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tpv1 the first virus isolated from the hyperthermophilic genus Thermococcus
Environmental Microbiology, 2012Co-Authors: Aurore Gorlas, Daniel Prieur, Nadege Bienvenu, Eugene V Koonin, Claire GeslinAbstract:Summary We describe a novel virus, TPV1 (Thermococcus prieurii virus 1), which was discovered in a hyperthermophilic euryarchaeote isolated from a deep-sea hydrothermal chimney sample collected at a depth of 2700 m at the East Pacific Rise. TPV1 is the first virus isolated and characterized from the hyperthermophilic euryarchaeal genus Thermococcus. TPV1 particles have a lemon-shaped morphology (140 nm × 80 nm) similar to the structures previously reported for Fuselloviruses and for the unclassified virus-like particle PAV1 (Pyrococcus abyssi virus 1). The infection with TPV1 does not cause host lysis and viral replication can be induced by UV irradiation. TPV1 contains a double-stranded circular DNA of 21.5 kb, which is also present in high copy number in a free form in the host cell. The TPV1 genome encompasses 28 predicted genes; the protein sequences encoded in 16 of these genes show no significant similarity to proteins in public databases. Proteins predicted to be involved in genome replication were identified as well as transcriptional regulators. TPV1 encodes also a predicted integrase of the tyrosine recombinase family. The only two genes that are homologous between TPV1 and PAV1 are TPV1-22 and TPV1-23, which encode proteins containing a concanavalin A-like lectin/glucanase domain that might be involved in virus–host recognition.
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Thermococcus gammatolerans sp nov a hyperthermophilic archaeon from a deep sea hydrothermal vent that resists ionizing radiation
International Journal of Systematic and Evolutionary Microbiology, 2003Co-Authors: Edmond Jolivet, Patrick Forterre, Stephane Lharidon, Erwan Corre, Daniel PrieurAbstract:Enrichments for anaerobic organotrophic hyperthermophiles were performed with hydrothermal chimney samples collected at the Guaymas Basin (27° 01′ N, 111° 24′ W). Positive enrichments were submitted to γ-irradiation at a dose of 30 kGy. One of the resistant strains, designated strain EJ3T, formed regular motile cocci. The new strain grew between 55 and 95 °C, with an optimum growth temperature of 88 °C. The optimal pH for growth was 6·0, and the optimum NaCl concentration for growth was around 20 g l−1. Strain EJ3T was an obligately anaerobic heterotroph that utilized yeast extract, tryptone and peptone. Elemental sulfur or cystine was required for growth and reduced to hydrogen sulfide. The G+C content of the genomic DNA was 51·3 mol%. As determined by 16S rRNA gene sequence analysis, the organism was most closely related to Thermococcus celer, Thermococcus guaymasensis, Thermococcus hydrothermalis, Thermococcus profundus and Thermococcus gorgonarius. However, no significant homology was observed between them by DNA–DNA hybridization. The novel organism also possessed phenotypic traits that differ from those of its closest phylogenetic relatives. Therefore, it is proposed that this isolate, which constitutes the most radioresistant hyperthermophilic archaeon known to date, should be described as the type strain of a novel species, Thermococcus gammatolerans sp. nov. The type strain is EJ3T (=DSM 15229T=JCM 11827T).
