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Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents. Res Microbiol 2015; 166:742-52. [DOI: 10.1016/j.resmic.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
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Gorlas A, Croce O, Oberto J, Gauliard E, Forterre P, Marguet E. Thermococcus
nautili sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal deep-sea vent. Int J Syst Evol Microbiol 2014; 64:1802-1810. [DOI: 10.1099/ijs.0.060376-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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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Affiliation(s)
- Aurore Gorlas
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Olivier Croce
- Université Aix-Marseille, Faculté de médecine, CNRS UMR7278, Marseille, France
| | - Jacques Oberto
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Emilie Gauliard
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
| | - Evelyne Marguet
- Institut de Génétique et Microbiologie, Université Paris-Sud, CNRS UMR8621, 91405 Orsay Cedex, France
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Gorlas A, Alain K, Bienvenu N, Geslin C. Thermococcus
prieurii sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2013; 63:2920-2926. [DOI: 10.1099/ijs.0.026419-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel hyperthermophilic, anaerobic archaeon, strain Bio-pl-0405IT2T, was isolated from a hydrothermal chimney sample collected from the East Pacific Rise at 2700 m depth in the ‘Sarah Spring’ area (7° 25′ 24″ S 107° 47′ 66″ W). Cells were irregular, motile cocci (0.8–1.5 µm in diameter) and divided by constriction. Growth was observed at temperatures between 60 °C and 95 °C with an optimum at 80 °C. The pH range for growth was between pH 4.0 and pH 8.0 with an optimum around pH 7.0. Strain Bio-pl-0405IT2T grew at salt concentrations of 1–5 % (w/v) NaCl with an optimum at 2 %. The novel isolate grew by fermentation or sulphur respiration on a variety of organic compounds. It was a chemoorganoheterotrophic archaeon growing preferentially with yeast extract, peptone and tryptone as carbon and energy sources and sulphur and organic compounds as electron acceptors; it also grew on maltose and starch. Sulphur or l-cystine were required for growth and were reduced to hydrogen sulfide. The strain was resistant to rifampicin, chloramphenicol, vancomycin and kanamycin (all at 100 µg ml−1) but was sensitive to tetracycline. The G+C content of its genomic DNA was 53.6 mol%. Phylogenetic analysis of the almost complete 16S rRNA gene sequence (1450 bp) of strain Bio-pl-0405IT2T showed that the novel isolate belonged to the genus
Thermococcus
. DNA–DNA hybridization values with the two closest relatives
Thermococcus hydrothermalis
AL662T and
Thermococcus celer
JCM 8558T were below the threshold value of 70 %. On the basis of the physiological and genotypic distinctness, we propose a novel species,
Thermococcus
prieurii sp. nov. The type strain is Bio-pl-0405IT2T ( = CSUR P577T = JCM 16307T).
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Affiliation(s)
- Aurore Gorlas
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Karine Alain
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Nadège Bienvenu
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
| | - Claire Geslin
- UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IUEM, Technopôle Brest-Iroise, F-29280 Plouzané, France
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Norais C, Moisan A, Gaspin C, Clouet-d'Orval B. Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol 2013; 10:659-70. [PMID: 23422322 DOI: 10.4161/rna.23927] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Pyrococcales are members of the order Thermococcales, a group of hyperthermophilic euryarchaea that are frequently found in deep sea hydrothermal vents. Infectious genetic elements, such as plasmids and viruses, remain a threat even in this remote environment and these microorganisms have developed several ways to fight their genetic invaders. Among these are the recently discovered CRISPR systems. In this review, we have combined and condensed available information on genetic elements infecting the Thermococcales and on the multiple CRISPR systems found in the Pyrococcales to fight them. Their organization and mode of action will be presented with emphasis on the Type III-B system that is the only CRISPR system known to target RNA molecules in a process reminiscent of RNA interference. The intriguing case of Pyrococcus abyssi, which is among the rare strains to present a CRISPR system devoid of the universal cas1 and cas2 genes, is also discussed.
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Affiliation(s)
- Cédric Norais
- Laboratoire de Biochimie, UMR CNRS 7654, Département de Biologie, Ecole Polytechnique, Palaiseau, France
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5
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Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS One 2013; 8:e49044. [PMID: 23326305 PMCID: PMC3543421 DOI: 10.1371/journal.pone.0049044] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 10/03/2012] [Indexed: 12/04/2022] Open
Abstract
Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.
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Defining components of the chromosomal origin of replication of the hyperthermophilic archaeon Pyrococcus furiosus needed for construction of a stable replicating shuttle vector. Appl Environ Microbiol 2011; 77:6343-9. [PMID: 21784908 DOI: 10.1128/aem.05057-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We report the construction of a series of replicating shuttle vectors that consist of a low-copy-number cloning vector for Escherichia coli and functional components of the origin of replication (oriC) of the chromosome of the hyperthermophilic archaeon Pyrococcus furiosus. In the process of identifying the minimum replication origin sequence required for autonomous plasmid replication in P. furiosus, we discovered that several features of the origin predicted by bioinformatic analysis and in vitro binding studies were not essential for stable autonomous plasmid replication. A minimum region required to promote plasmid DNA replication was identified, and plasmids based on this sequence readily transformed P. furiosus. The plasmids replicated autonomously and existed in a single copy. In contrast to shuttle vectors based on a plasmid from the closely related hyperthermophile Pyrococcus abyssi for use in P. furiosus, plasmids based on the P. furiosus chromosomal origin were structurally unchanged after transformation and were stable without selection for more than 100 generations.
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Gonnet M, Erauso G, Prieur D, Le Romancer M. pAMT11, a novel plasmid isolated from a Thermococcus sp. strain closely related to the virus-like integrated element TKV1 of the Thermococcus kodakaraensis genome. Res Microbiol 2010; 162:132-43. [PMID: 21144896 DOI: 10.1016/j.resmic.2010.11.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 10/05/2010] [Indexed: 10/18/2022]
Abstract
A novel extrachromosomal element that we called pAMT11 was discovered in a deep-sea vent isolate belonging to the hyperthermophilic euryarchaeal order Thermococcales. It consists of a double-stranded DNA of 20,534bp which encodes 30 putative open reading frames (ORFs) of which six could be assigned to a putative function on the basis of sequence similarity to known genes or to protein domain families. Most of the ORFs of pAMT1 showed homology and synteny with a genomic island of Thermococcus kodakaraensis KOD1. This region, named TKV1, was previously described as a "virus-like integrated element" and assumed to integrate into the host chromosome by a site-specific recombination mechanism similar to that of Sulfolobus solfataricus virus 1. While most of the genes shared by pAMT11 and TKV1 encode putative membrane proteins presumably involved in virus particle formation, attempts to induce production of virus particles by mitomycin treatment of AMT11 cultures failed, suggesting that pAMT11 may represent the genome of a defective virus or a plasmid. Genomes of mobile elements usually contain two regions: a core of conserved genes mainly involved in replication, maintenance or spreading of the genetic element, and a variable set of accessory genes. Surprisingly, genes presumably implied in the replication process are quite divergent between TKV1 and pAMT11. Indeed, TKV1 possesses a MCM-like protein that may function as a replication initiator, while pAMT11 encodes a putative non-conventional protein distantly related to the Rep protein previously described in a small plasmid of Pyrococcus sp. strain JT1, assumed to replicate by a rolling-circle (RC) mechanism. However, in the case of pAMT11, this mode of plasmid replication could not be experimentally proven and is questionable given the lack of significant similarities with any other members of the RC-Rep superfamily and its unusual large size compared to other RC plasmids.
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Affiliation(s)
- Mathieu Gonnet
- Unité d'Epidémiologie Animale, UR356, INRA centre de Clermont-Ferrand Theix, Route de Theix, 63122 Saint Genès Champanelle, France.
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8
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Soler N, Justome A, Quevillon-Cheruel S, Lorieux F, Le Cam E, Marguet E, Forterre P. The rolling-circle plasmid pTN1 from the hyperthermophilic archaeon Thermococcus nautilus. Mol Microbiol 2007; 66:357-70. [PMID: 17784911 DOI: 10.1111/j.1365-2958.2007.05912.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The hyperthermophilic archaeon Thermococcus nautilus carries a plasmid, pTN1, which encodes a rolling-circle (RC) replication initiator protein of 74 kDa (Rep74) and an orphan protein of 24 kDa (p24). The Rep74 protein is homologous to the Rep75 protein encoded by the RC plasmid pGT5 from Pyrococcus abyssi. Comparative analysis of Rep74 and Rep75 sequences shows that these proteins correspond to a new family of RC initiators formed by the fusion of a Rep domain with an N-terminal domain of unknown function. Surprisingly, the Rep domain of Rep74/75 is more closely related to transposases encoded by IS elements than to Rep proteins of other RC plasmids. The p24 protein contains a hydrophobic segment, a highly charged region and a zinc finger motif. A recombinant p24 protein lacking the hydrophobic segment binds and condenses both single- and double-stranded DNA, and forms DNA aggregates with extreme compaction at high protein to DNA ratio. In addition to encoding proteins of significant interest, pTN1 is remarkable by being the only characterized plasmid isolated from a Thermococcus strain, thus being useful to develop genetic tools in Thermococcus kodakaraensis for which gene disruption methods became recently available.
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Affiliation(s)
- Nicolas Soler
- Institut de Génétique et Microbiologie, Univ Paris-Sud, CNRS UMR 8621 and 8619, 91405 Orsay Cedex, France
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9
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Näther DJ, Rachel R, Wanner G, Wirth R. Flagella of Pyrococcus furiosus: multifunctional organelles, made for swimming, adhesion to various surfaces, and cell-cell contacts. J Bacteriol 2006; 188:6915-23. [PMID: 16980494 PMCID: PMC1595509 DOI: 10.1128/jb.00527-06] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrococcus furiosus ("rushing fireball") was named for the ability of this archaeal coccus to rapidly swim at its optimal growth temperature, around 100 degrees C. Early electron microscopic studies identified up to 50 cell surface appendages originating from one pole of the coccus, which have been called flagella. We have analyzed these putative motility organelles and found them to be composed primarily (>95%) of a glycoprotein that is homologous to flagellins from other archaea. Using various electron microscopic techniques, we found that these flagella can aggregate into cable-like structures, forming cell-cell connections between ca. 5% of all cells during stationary growth phase. P. furiosus cells could adhere via their flagella to carbon-coated gold grids used for electron microscopic analyses, to sand grains collected from the original habitat (Porto di Levante, Vulcano, Italy), and to various other surfaces. P. furiosus grew on surfaces in biofilm-like structures, forming microcolonies with cells interconnected by flagella and adhering to the solid supports. Therefore, we concluded that P. furiosus probably uses flagella for swimming but that the cell surface appendages also enable this archaeon to form cable-like cell-cell connections and to adhere to solid surfaces.
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Affiliation(s)
- Daniela J Näther
- Lehrstuhl für Microbiology, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Lepage E, Marguet E, Geslin C, Matte-Tailliez O, Zillig W, Forterre P, Tailliez P. Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis. Appl Environ Microbiol 2004; 70:1277-86. [PMID: 15006744 PMCID: PMC368356 DOI: 10.1128/aem.70.3.1277-1286.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Members of the Thermococcales are anaerobic Archaea belonging to the kingdom Euryarchaea that are studied in many laboratories as model organisms for hyperthermophiles. We describe here a molecular analysis of 86 new Thermococcales isolates collected from six different chimneys of a single hydrothermal field located in the 13 degrees N 104 degrees W segment of the East Pacific ridge at a depth of 2,330 m. These isolates were sorted by randomly amplified polymorphic DNA (RAPD) fingerprinting into nine groups, and nine unique RAPD profiles were obtained. One RAPD group corresponds to new isolates of Thermococcus hydrothermalis, whereas all other groups and isolates with unique profiles are different from the 22 reference strains included in this study. Analysis of 16S rRNA gene sequences of representatives of each RAPD group and unique profiles showed that one group corresponds to Pyrococcus strains, whereas all the other isolates are Thermococcus strains. We estimated that our collection may contain at least 11 new species. These putative species, isolated from a single area of hydrothermal deep-sea vents, are dispersed in the 16S rRNA tree among the reference strains previously isolated from diverse hot environments (terrestrial, shallow water, hydrothermal vents) located around the world, suggesting that there is a high degree of dispersal of Thermococcales: About one-half of our isolates contain extrachromosomal elements that could be used to search for novel replication proteins and to develop genetic tools for hyperthermophiles.
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Affiliation(s)
- Elodie Lepage
- Unité de Recherches Laitières et Génétique Appliquée, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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11
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Geslin C, Le Romancer M, Erauso G, Gaillard M, Perrot G, Prieur D. PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, "Pyrococcus abyssi". J Bacteriol 2003; 185:3888-94. [PMID: 12813083 PMCID: PMC161591 DOI: 10.1128/jb.185.13.3888-3894.2003] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the first virus-like particle of a hyperthermophilic euryarchaeote which was discovered in a strain of "Pyrococcus abyssi" previously characterized in our laboratory. This particle, named PAV1, is lemon-shaped (120 nm x 80 nm), with a short tail terminated by fibers, and resembles the virus SSV1, the type member of the Fuselloviridae, isolated from Sulfolobus shibatae. Sensitivity of the virus-like particle to organic solvents and detergents suggested that the envelope of PAV1 may contain lipids in addition to proteins. It contains a double-stranded circular DNA of 18 kb which is also present in high copy number in a free form in the host cytoplasm. No integrated form of the PAV1 genome could be detected in the host chromosome. Under standard growth conditions, the host cells continuously release PAV1 particles into the culture supernatant without spontaneous lysis, with a maximum reached in the late stationary phase. UV, gamma irradiation, treatment with mitomycin C, and various physiological stresses had no effect on PAV1 production. Screening of a large number of Thermococcales isolates did not permit to find a sensitive host. These results suggest that PAV1 persists in the host strain in a stable carrier state rather than a prophage.
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Affiliation(s)
- C Geslin
- Université de Bretagne Occidentale, CNRS UMR 6539, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, 29280 Plouzané, France.
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12
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Sato T, Fukui T, Atomi H, Imanaka T. Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 2003; 185:210-20. [PMID: 12486058 PMCID: PMC141832 DOI: 10.1128/jb.185.1.210-220.2003] [Citation(s) in RCA: 237] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In contrast to the high accumulation in sequence data for hyperthermophilic archaea, methodology for genetically manipulating these strains is still at an early stage. This study aimed to develop a gene disruption system for the hyperthermophilic euryarchaeon Thermococcus kodakaraensis KOD1. Uracil-auxotrophic mutants with mutations in the orotidine-5'-monophosphate decarboxylase gene (pyrF) were isolated by positive selection using 5-fluoroorotic acid (5-FOA) and used as hosts for further transformation experiments. We then attempted targeted disruption of the trpE locus in the host strain by homologous recombination, as disruption of trpE was expected to result in tryptophan auxotrophy, an easily detectable phenotype. A disruption vector harboring the pyrF marker within trpE was constructed for double-crossover recombination. The host cells were transformed with the exogenous DNA using the CaCl(2) method, and several transformants could be selected based on genetic complementation. Genotypic and phenotypic analyses of a transformant revealed the unique occurrence of targeted disruption, as well as a phenotypic change of auxotrophy from uracil to tryptophan caused by integration of the wild-type pyrF into the host chromosome at trpE. As with the circular plasmid, gene disruption with linear DNA was also possible when the homologous regions were relatively long. Shortening these regions led to predominant recombination between the pyrF marker in the exogenous DNA and the mutated allele on the host chromosome. In contrast, we could not obtain trpE disruptants by insertional inactivation using a vector designed for single-crossover recombination. The gene targeting system developed in this study provides a long-needed tool in the research on hyperthermophilic archaea and will open the way to a systematic, genetic approach for the elucidation of unknown gene function in these organisms.
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Affiliation(s)
- Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501
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Abstract
Archaea, members of the third domain of life, are bacterial-looking prokaryotes that harbour many unique genotypic and phenotypic properties, testifying for their peculiar evolutionary status. The archaeal ancestor was probably a hyperthermophilic anaerobe. Two archaeal phyla are presently recognized, the Euryarchaeota and the Crenarchaeota. Methanogenesis was the main invention that occurred in the euryarchaeal phylum and is now shared by several archaeal groups. Adaptation to aerobic conditions occurred several times independently in both Euryarchaeota and Crenarchaeota. Recently, many new groups of Archaea that have not yet been cultured have been detected by PCR amplification of 16S ribosomal RNA from environmental samples. The phenotypic and genotypic characterization of these new groups is now a top priority for further studies on archaeal evolution.
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Affiliation(s)
- Patrick Forterre
- Institut de Génétique et Microbiologie, UMR 8621 CNRS, Bat 409, Université Paris-Sud, 91405 Orsay Cedex, France.
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14
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Ward DE, Revet IM, Nandakumar R, Tuttle JH, de Vos WM, van der Oost J, DiRuggiero J. Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1. J Bacteriol 2002; 184:2561-6. [PMID: 11948174 PMCID: PMC134983 DOI: 10.1128/jb.184.9.2561-2566.2002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon Pyrococcus sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some resemblance to motifs typically found in plasmids that replicate via a rolling-circle mechanism. The presence of single-stranded DNA replication intermediates of pRT1 was detected, confirming this mode of replication.
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Affiliation(s)
- Donald E Ward
- Laboratory for Microbiology, Wageningen University, 6703CT Wageningen, The Netherlands.
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