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| Registros recuperados: 38 | |
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| Henneke, Ghislaine. |
| Using model DNA substrates and purified recombinant proteins from Pyrococcus abyssi. I have reconstituted the enzymatic reactions involved in RNA primer elimination in vitro. In my dual-labelled system, polymerase D performed efficient strand displacement DNA synthesis, generating 5'-RNA flaps which were subsequently released by Fen1, before ligation by Lig1. In this pathway, the initial cleavage event by RNase HII facilitated RNA primer removal of Okazaki fragments. In addition, I have shown that polymerase B was able to displace downstream DNA strands with a single ribonucleotide at the 5'-end, a product resulting from a single cut in the RNA initiator by RNase HII. After RNA elimination, the combined activities of strand displacement DNA synthesis by... |
| Tipo: Text |
Palavras-chave: Archaea; DNA ligase; DNA polymerase; Nuclease; Okazaki fragment. |
| Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00107/21841/20923.pdf |
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| Omoregie, Enoma O.; Niemann, Helge; Mastalerz, Vincent; De Lange, Gert J.; Stadnitskaia, Alina; Mascle, Jean; Foucher, Jean-paul; Boetius, Antje. |
| The Eastern Mediterranean hosts a variety of active cold seep systems, such as gas chimneys, mud volcanoes and pockmarks, in water depths of 500 to 3200 m. As part of the NAUTINIL expedition in 2003, the sediments of cold seeps on the Nile Deep Sea Fan (NDSF) were sampled for the first time for biogeochemical and microbiological analyses. Here we compare rates of the anaerobic oxidation of methane (AOM) and sulfate reduction (SR) as well as the microbial community structure of a variety of cold seep systems including mud volcanoes, pockmarks and brine seeps. Our results revealed strong differences in microbial activity among the different seep systems of the Eastern, Central and Western provinces of the NDSF, as well as the Olimpi field (Central... |
| Tipo: Text |
Palavras-chave: Methane oxidation; Sulfate reduction; Archaea; Cold seeps; Mud volcano; Pockmarks; Nile Deep Sea Fan. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/00000/11087/7910.pdf |
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| Malfatti, Matilde Clarissa; Henneke, Ghislaine; Balachander, Sathya; Koh, Kyung Duk; Newnam, Gary; Uehara, Ryo; Crouch, Robert J.; Storici, Francesca; Tell, Gianluca. |
| The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 ribonuclease H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damaged, that is, ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus... |
| Tipo: Text |
Palavras-chave: Ribonuclease; Bacteria; Escherichia coli (E coli); Archaea; Oxidative stress; Abasic-ribose; Oxidized-ribonucleotides; Pyrococcus abyssi; Type 2 RNase H. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00506/61796/65801.pdf |
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| Lossouarn, Julien; Dupont, Samuel; Gorlas, Aurore; Mercier, Coraline; Bienvenu, Nadege; Marguet, Evelyne; Forterre, Patrick; Geslin, Claire. |
| Mobile genetic elements (MGEs) such as viruses, plasmids, vesicles, gene transfer agents (GTAs), transposons and transpovirions, which collectively represent the mobilome, interact with cellular organisms from all three domains of life, including those thriving in the most extreme environments. While efforts have been made to better understand deep-sea vent microbial ecology, our knowledge of the mobilome associated with prokaryotes inhabiting deep-sea hydrothermal vents remains limited. Here we focus on the abyssal mobilome by reviewing accumulating data on viruses, plasmids and vesicles associated with thermophilic and hyperthermophilic Bacteria and Archaea present in deep-sea hydrothermal vents. |
| Tipo: Text |
Palavras-chave: Deep-sea hydrothermal vent; Bacteria; Archaea; (Hyper-)thermophiles; Mobilome. |
| Ano: 2015 |
URL: http://archimer.ifremer.fr/doc/00260/37145/36731.pdf |
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| Henneke, Ghislaine; Gueguen, Yannick; Flament, Didier; Azam, Philippe; Querellou, Joel; Dietrich, Jacques; Hubscher, Ulrich; Raffin, Jean-paul. |
| The molecular organization of the replication complex in archaea is similar to that in eukaryotes. Only two proteins homologous to subunits of eukaryotic replication factor C (RFC) have been detected in Pyrococcus abyssi (Pab). The genes encoding these two proteins are arranged in tandem. We cloned these two genes and co-expressed the corresponding recombinant proteins in Escherichia coli. Two inteins present in the gene encoding the small subunit (Pab RFC-small) were removed during cloning. The recombinant protein complex was purified by anion-exchange and hydroxyapatite chromatography. Also, the Pab RFC-small subunit could be purified, while the large subunit (Pab RFC-large) alone was completely insoluble. The highly purified Pab RFC complex possessed an... |
| Tipo: Text |
Palavras-chave: PCNA binding domain; Pyrococcus abyssi; Hyperthermophile; Archaea; Replication factor C. |
| Ano: 2002 |
URL: https://archimer.ifremer.fr/doc/2002/publication-675.pdf |
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| Birien, Tiphaine; Thiel, Axel; Henneke, Ghislaine; Flament, Didier; Moalic, Yann; Jebbar, Mohamed. |
| A gene disruption system for Thermococcus barophilus was developed using simvastatin (HMG-CoA reductase encoding gene) for positive selection and 5-Fluoroorotic acid (5-FOA), a pyrF gene for negative selection. Multiple gene mutants were constructed with this system, which offers the possibility of complementation in trans, but produces many false positives (<80%). To significantly reduce the rate of false positives, we used another counterselective marker, 6-methylpurine (6-MP), a toxic analog of adenine developed in Thermococcus kodakarensis, consistently correlated with the TK0664 gene (encoding a hypoxanthine-guanine phosphoribosyl-transferase). We thus replaced pyrF by TK0664 on our suicide vector and tested T. barophilus strain sensitivity to 6-MP... |
| Tipo: Text |
Palavras-chave: Archaea; Piezophiles; Hyperthermophiles; Genetics; Gene deletion; Deep sea; Hydrothermal vents. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00425/53679/54523.pdf |
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| Zeng, Xiang; Birrien, Jean-louis; Fouquet, Yves; Cherkashov, Georgy; Jebbar, Mohamed; Querellou, Joel; Oger, Philippe; Cambon-bonavita, Marie-anne; Xiao, Xiang; Prieur, Daniel. |
| A novel hydrothermal site was discovered in March 2007, on the mid-Atlantic ridge during the cruise 'Serpentine'. At a depth of 4100 m, the site 'Ashadze' is the deepest vent field known so far. Smoker samples were collected with the ROV 'Victor 6000' and processed in the laboratory for the enrichment of anaerobic heterotrophic microorganisms under high-temperature and high-hydrostatic pressure conditions. Strain CH1 was successfully isolated and assigned to the genus Pyrococcus, within the Euryarchaeota lineage within the Archaea domain. This organism grows within a temperature range of 80 to 108 degrees C and a pressure range of 20 to 120 MPa, with optima for 98 degrees C and 52 MPa respectively. Pyrococcus CH1 represents the first obligate piezophilic... |
| Tipo: Text |
Palavras-chave: Thermococcales; Extremophile; Deep sea hydrothermal vent; High hydrostatic pressure; Archaea. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6812.pdf |
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| Lazar, Cassandre Sara. |
| A large portion of the greenhouse gas methane on Earth is trapped in marine sediments. However, little methane actually reaches the hydrsphere and the atmosphere, because it is efficiently consumed by anaerobic methane-oxidizing Archaea (ANME). This methane is mainly biogenic in marine sédiments, and is produced by methanogenic Archaea. Methane ascends from deep sources to the seabed, in cold seep sites of continental margins. In order to study microbial community diversity in cold seeps, and to determine geochemical factors that control these microbial communities, we compared four geochemically and geologically distinct sites. In this work, molecular tools (PCR, RT-PCR, DGGE, cloning) as well as genetic markers (16S rRNA, mcrA, dsrB) were employed, to... |
| Tipo: Text |
Palavras-chave: Diversité moléculaire; Archaea; Méthanogène; ANME; McrA; DsrB; DGGE; Volcan de boue; Pockmark; Saumures; Fluides froids; Méthane; Mer de Norvège; Mer Méditerranée; Sédiments.; Molecular diversity; Archaea; Methanogen; ANME; McrA; DsrB; DGGE; Mud volcano; Pockmark; Brines; Cold seep; Methane; Norwegian Sea; Mediterranean Sea; Sediments.. |
| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00031/14250/11534.pdf |
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| Hugoni, Mylene; Escalas, Arthur; Bernard, Cecile; Nicolas, Sebastien; Jezequel, Didier; Vazzoler, Fanny; Sarazin, Gerard; Leboulanger, Christophe; Bouvy, Marc; Got, Patrice; Ader, Magali; Troussellier, Marc; Agogue, Helene. |
| Thalassohaline ecosystems are hypersaline environments originating from seawater in which sodium chloride is the most abundant salt and the pH is alkaline. Studies focusing on microbial diversity in thalassohaline lakes are still scarce compared with those on athalassohaline lakes such as soda lakes that have no marine origin. In this work, we investigated multiple facets of bacterial, archaeal and eukaryotic diversity in the thalassohaline Lake Dziani Dzaha using a metabarcoding approach. We showed that bacterial and archaeal diversity were mainly affected by contrasting physicochemical conditions retrieved at different depths. While photosynthetic microorganisms were dominant in surface layers, chemotrophic phyla (Firmicutes or Bacteroidetes) and... |
| Tipo: Text |
Palavras-chave: Archaea; Bacteria; Eukaryotes; Extreme environment; Metabarcoding; Thalassohaline lake. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00464/57564/59738.pdf |
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| Ribeiro,Catherine Gérikas; Steffens,Maria Berenice Reynaud; Etto,Rafael Mazer; Galvão,Carolina Weigert; Martins,César de Castro; Pedrosa,Fábio de Oliveira; Kolm,Hedda Elisabeth. |
| The mangrove's sediments from the coastal areas under human activities may contain significant contaminations by hydrocarbons, even when there are no visual evidences of it. The microorganisms are essential to these ecosystems, especially in the control of their chemical environment. Sediment samples were collected in two regions under different environment conditions (pristine and contaminated) of the Paranaguá Estuarine Complex (Paranaguá Bay and Laranjeiras Bay), Brazil. Aliphatic hydrocarbons were determined by the GC-FID to assess the status of contamination of the studied areas. The total DNA was extracted from these samples. The 16S rRNA gene was amplified by the PCR reactions with the pair of primers 21F and 958R for the archaeal domain, and 27F... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Diversity; Mangroves; Archaea; Bacteria; 16S rRNA; ARDRA; Aliphatic hydrocarbons. |
| Ano: 2013 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132013000200013 |
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| Alquéres,S.M.C.; Almeida,R.V.; Clementino,M.M.; Vieira,R.P.; Almeida,W.I.; Cardoso,A.M.; Martins,O.B.. |
| Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. The extremophilic nature of many archaea has stimulated intense efforts to understand the physiological adaptations for living in extreme environments. Their unusual properties make them a potentially valuable resource in the development of novel biotechnological processes and industrial applications as new pharmaceuticals, cosmetics, nutritional supplements, molecular probes, enzymes, and fine chemicals. In the present mini-review, we show and discuss some exclusive characteristics of Archaea domain and the current knowledge about the biotechnological uses of... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Archaea; Biotechnology; Extremozymes; Genomic; Molecular Phylogeny. |
| Ano: 2007 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822007000300002 |
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| Hong,Sung-Jun; Park,Chang Eon; Park,Gun-Seok; Kim,Min-Chul; Jung,Byung Kwon; Shin,Jae-Ho. |
| Abstract Thermococcus thioreducens DSM 14981T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications. |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Archaea; Hyperthermophile; Thermococcus thioreducens. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822017000100003 |
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| Registros recuperados: 38 | |
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