Role of Ori in Thermococcus Barophilus
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Thermococcus Piezophilus Sp. Nov., a Novel Hyperthermophilic And
1 Systematic and Applied Microbiology Achimer October 2016, Volume 39, Issue 7, Pages 440-444 http://dx.doi.org/10.1016/j.syapm.2016.08.003 http://archimer.ifremer.fr http://archimer.ifremer.fr/doc/00348/45949/ © 2016 Elsevier GmbH. All rights reserved. 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 ✯ Dalmasso Cécile 1, 2, 3, Oger Philippe 4, Selva Gwendoline 1, 2, 3, Courtine Damien 1, 2, 3, L'Haridon Stéphane 1, 2, 3, Garlaschelli Alexandre 1, 2, 3, Roussel Erwan 1, 2, 3, Miyazaki Junichi 5, Reveillaud Julie 1, 2, 3, Jebbar Mohamed 1, 2, 3, Takai Ken 5, Maignien Lois 1, 2, 3, Alain Karine 1, 2, 3, * 1 Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) − UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France 2 CNRS, IUEM − UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Place Nicolas Copernic, F-29280 Plouzané, France 3 Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France 4 Université de Lyon, INSA Lyon, CNRS UMR 5240, 11 Avenue Jean Capelle, F-69621 Villeurbanne, France 5 Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan * Corresponding author : Karine Alain, email address : [email protected] ✯ Note: The EMBL/GenBank/DDBJ 16S rRNA gene sequence accession number of strain CDGST is LN 878294. -
In Search for the Membrane Regulators of Archaea Marta Salvador-Castell, Maxime Tourte, Philippe Oger
In Search for the Membrane Regulators of Archaea Marta Salvador-Castell, Maxime Tourte, Philippe Oger To cite this version: Marta Salvador-Castell, Maxime Tourte, Philippe Oger. In Search for the Membrane Regula- tors of Archaea. International Journal of Molecular Sciences, MDPI, 2019, 20 (18), pp.4434. 10.3390/ijms20184434. hal-02283370 HAL Id: hal-02283370 https://hal.archives-ouvertes.fr/hal-02283370 Submitted on 12 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. International Journal of Molecular Sciences Review In Search for the Membrane Regulators of Archaea Marta Salvador-Castell 1,2 , Maxime Tourte 1,2 and Philippe M. Oger 1,2,* 1 Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France 2 Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France * Correspondence: [email protected] Received: 7 August 2019; Accepted: 6 September 2019; Published: 9 September 2019 Abstract: Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. -
An Integrative Genomic Island Affects the Adaptations of the Piezophilic Hyperthermophilic Archaeon Pyrococcus Yayanosii to High
fmicb-07-01927 November 25, 2016 Time: 18:18 # 1 ORIGINAL RESEARCH published: 29 November 2016 doi: 10.3389/fmicb.2016.01927 An Integrative Genomic Island Affects the Adaptations of the Piezophilic Hyperthermophilic Archaeon Pyrococcus yayanosii to High Temperature and High Hydrostatic Pressure Zhen Li1,2, Xuegong Li2,3, Xiang Xiao1,2 and Jun Xu1,2* 1 State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China, 2 Institute of Oceanology, Shanghai Jiao Tong University, Shanghai, China, 3 Deep-Sea Cellular Microbiology, Department of Deep-Sea Science, Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China Deep-sea hydrothermal vent environments are characterized by high hydrostatic pressure and sharp temperature and chemical gradients. Horizontal gene transfer is Edited by: thought to play an important role in the microbial adaptation to such an extreme Philippe M. Oger, UMR CNRS 5240 Institut National environment. In this study, a 21.4-kb DNA fragment was identified as a genomic des Sciences Appliquées, France island, designated PYG1, in the genomic sequence of the piezophilic hyperthermophile Reviewed by: Pyrococcus yayanosii. According to the sequence alignment and functional annotation, Federico Lauro, University of New South Wales, the genes in PYG1 could tentatively be divided into five modules, with functions related Australia to mobility, DNA repair, metabolic processes and the toxin-antitoxin system. Integrase Amy Michele Grunden, can mediate the site-specific integration and excision of PYG1 in the chromosome of North Carolina State University, USA R Anaïs Cario, P. yayanosii A1. Gene replacement of PYG1 with a Sim cassette was successful. -
Biogeography and Evolution of Thermococcus Isolates from Hydrothermal Vent Systems of the Pacific
ORIGINAL RESEARCH published: 24 September 2015 doi: 10.3389/fmicb.2015.00968 Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific Mark T. Price, Heather Fullerton and Craig L. Moyer * Department of Biology, Western Washington University, Bellingham, WA, USA Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, Edited by: Beth Orcutt, making biogeographic patterns and evolutionary relationships apparent. Isolates were Bigelow Laboratory for Ocean differentiated into regionally endemic populations; however, there was also evidence in Sciences, USA some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus Reviewed by: isolates and presence of distinct lineages within the same vent site suggests the Julie L. Meyer, University of Florida, USA utilization of varying ecological niches in this genus. In addition to resolving biogeographic Sean Patrick Jungbluth, patterns in Thermococcus, this study has raised new questions about the closely related University -
Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus Barophilus
G C A T T A C G G C A T genes Article Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus barophilus Tiphaine Birien 1,2,3, Axel Thiel 1,2,3, Ghislaine Henneke 1,2,3, Didier Flament 1,2,3, Yann Moalic 1,2,3 ID and Mohamed Jebbar 1,2,3,* ID 1 Université de Brest (UBO, UBL), Institut Universitaire Européen de la Mer (IUEM)–UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d’Urville, F-29280 Plouzané, France; [email protected] (T.B.); [email protected] (A.T.); [email protected] (G.H.); [email protected] (D.F.); [email protected] (Y.M.) 2 CNRS, IUEM–UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Rue Dumont d’Urville, F-29280 Plouzané, France 3 Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Technopôle Pointe du diable, F-29280 Plouzané, France * Correspondence: [email protected]; Tel.: +33-298-498-817; Fax: +33-298-498-705 Received: 8 January 2018; Accepted: 2 February 2018; Published: 7 February 2018 Abstract: 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). -
Deep Conservation of Histone Variants in Thermococcales Archaea
bioRxiv preprint doi: https://doi.org/10.1101/2021.09.07.455978; this version posted September 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Deep conservation of histone variants in Thermococcales archaea 2 3 Kathryn M Stevens1,2, Antoine Hocher1,2, Tobias Warnecke1,2* 4 5 1Medical Research Council London Institute of Medical Sciences, London, United Kingdom 6 2Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, 7 United Kingdom 8 9 *corresponding author: [email protected] 10 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.09.07.455978; this version posted September 7, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Abstract 2 3 Histones are ubiquitous in eukaryotes where they assemble into nucleosomes, binding and 4 wrapping DNA to form chromatin. One process to modify chromatin and regulate DNA 5 accessibility is the replacement of histones in the nucleosome with paralogous variants. 6 Histones are also present in archaea but whether and how histone variants contribute to the 7 generation of different physiologically relevant chromatin states in these organisms remains 8 largely unknown. Conservation of paralogs with distinct properties can provide prima facie 9 evidence for defined functional roles. -
Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes
GBE Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes Dennifier Costa Brandao~ Cruz1, Lenon Lima Santana1, Alexandre Siqueira Guedes2, Jorge Teodoro de Souza3,*, and Phellippe Arthur Santos Marbach1,* 1CCAAB, Biological Sciences, Recoˆ ncavo da Bahia Federal University, Cruz das Almas, Bahia, Brazil 2Agronomy School, Federal University of Goias, Goiania,^ Goias, Brazil 3 Department of Phytopathology, Federal University of Lavras, Minas Gerais, Brazil Downloaded from https://academic.oup.com/gbe/article/11/4/1235/5345563 by guest on 27 September 2021 *Corresponding authors: E-mails: [email protected]fla.br; [email protected]. Accepted: February 16, 2019 Abstract The last two steps of the purine biosynthetic pathway may be catalyzed by different enzymes in prokaryotes. The genes that encode these enzymes include homologs of purH, purP, purO and those encoding the AICARFT and IMPCH domains of PurH, here named purV and purJ, respectively. In Bacteria, these reactions are mainly catalyzed by the domains AICARFT and IMPCH of PurH. In Archaea, these reactions may be carried out by PurH and also by PurP and PurO, both considered signatures of this domain and analogous to the AICARFT and IMPCH domains of PurH, respectively. These genes were searched for in 1,403 completely sequenced prokaryotic genomes publicly available. Our analyses revealed taxonomic patterns for the distribution of these genes and anticorrelations in their occurrence. The analyses of bacterial genomes revealed the existence of genes coding for PurV, PurJ, and PurO, which may no longer be considered signatures of the domain Archaea. Although highly divergent, the PurOs of Archaea and Bacteria show a high level of conservation in the amino acids of the active sites of the protein, allowing us to infer that these enzymes are analogs. -
In Search for the Membrane Regulators of Archaea
International Journal of Molecular Sciences Review In Search for the Membrane Regulators of Archaea Marta Salvador-Castell 1,2 , Maxime Tourte 1,2 and Philippe M. Oger 1,2,* 1 Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France 2 Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France * Correspondence: [email protected] Received: 7 August 2019; Accepted: 6 September 2019; Published: 9 September 2019 Abstract: Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs. Keywords: archaea; membrane organization; membrane modulators; polyterpenes; carotenoids; polyprenols; quinones; polyisoprenoids; adaptation 1. Introduction In 1972, Singer and Nicolson reconciled the numerous observations about cell membranes to construct the now well-established fluid mosaic model [1]. -
Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus Pacificus DY20341T from Deep-Sea Hydrothermal Sediments
International Journal of Molecular Sciences Article Metabolic Adaptation to Sulfur of Hyperthermophilic Palaeococcus pacificus DY20341T from Deep-Sea Hydrothermal Sediments Xiang Zeng 1, Xiaobo Zhang 1,2 and Zongze Shao 1,* 1 Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No.178 Daxue Road, Xiamen 361005, China; [email protected] (X.Z.); [email protected] (X.Z.) 2 School of public health, Xinjiang Medical University, No.393 Xinyi Road, Urumchi 830011, China * Correspondence: [email protected]; Tel.: +86-592-2195321 Received: 4 December 2019; Accepted: 29 December 2019; Published: 6 January 2020 Abstract: The hyperthermo-piezophilic archaeon Palaeococcus pacificus DY20341T, isolated from East Pacific hydrothermal sediments, can utilize elemental sulfur as a terminal acceptor to simulate growth. To gain insight into sulfur metabolism, we performed a genomic and transcriptional analysis of Pa. pacificus DY20341T with/without elemental sulfur as an electron acceptor. In the 2001 protein-coding sequences of the genome, transcriptomic analysis showed that 108 genes increased (by up to 75.1 fold) and 336 genes decreased (by up to 13.9 fold) in the presence of elemental sulfur. Palaeococcus pacificus cultured with elemental sulfur promoted the following: the induction of membrane-bound hydrogenase (MBX), NADH:polysulfide oxidoreductase (NPSOR), NAD(P)H sulfur oxidoreductase (Nsr), sulfide dehydrogenase (SuDH), connected to the sulfur-reducing process, the upregulation of iron and nickel/cobalt transfer, iron–sulfur cluster-carrying proteins (NBP35), and some iron–sulfur cluster-containing proteins (SipA, SAM, CobQ, etc.). The accumulation of metal ions might further impact on regulators, e.g., SurR and TrmB. -
Pyrococcus CH1, an Obligate Piezophilic Hyperthermophile: Extending the Upper Pressure-Temperature Limits for Life
The ISME Journal (2009) 3, 873–876 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej SHORT COMMUNICATION Pyrococcus CH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life Xiang Zeng1,3,6, Jean-Louis Birrien1, Yves Fouquet2, Georgy Cherkashov4, Mohamed Jebbar1, Joe¨l Querellou1, Philippe Oger5, Marie-Anne Cambon-Bonavita1, Xiang Xiao3 and Daniel Prieur1 1Laboratoire de Microbiologie des Environnements Extreˆmes, CNRS, Universite´ de Bretagne Occidentale, Ifremer, IUEM, Technopole Brest-Iroise, Plouzane´, France; 2De´partement Ge´osciences Marines, Ifremer, Centre de Brest, Plouzane´, France; 33rd Institute of Oceanography, SOA, Xiamen, PR China; 4VNIIOkeangeologia 1, Angliysky Prospect, St Petersburg, Russia; 5Laboratoire des Sciences de la Terre, Universite´ de Lyon, ENS, Lyon, France and 6School of life science, Xiamen University, Xiamen, PR China 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-hydro- static 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 1C and a pressure range of 20 to 120 MPa, with optima for 98 1C and 52 MPa respectively. Pyrococcus CH1 represents the first obligate piezophilic hyperthermophilic microorganism known so far. -
H2-Dependent Formate Production by Hyperthermophilic Thermococcales: an Alternative to Sulfur Reduction for Reducing- Equivalents Disposal
The ISME Journal https://doi.org/10.1038/s41396-021-01020-x ARTICLE H2-dependent formate production by hyperthermophilic Thermococcales: an alternative to sulfur reduction for reducing- equivalents disposal 1 1 1 1 1 Sébastien Le Guellec ● Elodie Leroy ● Damien Courtine ● Anne Godfroy ● Erwan G. Roussel Received: 24 November 2020 / Revised: 13 May 2021 / Accepted: 20 May 2021 © The Author(s), under exclusive licence to International Society for Microbial Ecology 2021 Abstract Removal of reducing equivalents is an essential catabolic process for all microorganisms to maintain their internal redox balance. The electron disposal by chemoorganotrophic Thermococcales generates H2 by proton reduction or H2S in presence 0 0 of S . Although in the absence of S growth of these (hyper)thermopiles was previously described to be H2-limited, it 0 remains unclear how Thermococcales could be present in H2-rich S -depleted habitats. Here, we report that 12 of the 0 47 strains tested, distributed among all three orders of Thermococcales, could grow without S at 0.8 mM dissolved H2 and that tolerance to H2 was always associated with formate production. Two conserved gene clusters coding for a formate 1234567890();,: 1234567890();,: hydrogenlyase (FHL) and a putative formate dehydrogenase-NAD(P)H-oxidoreductase were only present in H2-dependent formate producers, and were both systematically associated with a formate dehydrogenase and a formate transporter. As the reaction involved in this alternative pathway for disposal of reducing equivalents was close to thermodynamic equilibrium, it was strongly controlled by the substrates–products concentration ratio even in the presence of S0. Moreover, experimental data and thermodynamic modelling also demonstrated that H2-dependent CO2 reduction to formate could occur within a large temperature range in contrasted hydrothermal systems, suggesting it could also provide an adaptive advantage. -
Biogeography and Evolution of Thermococcus Isolates from Hydrothermal Vent Systems of the Pacific
Western Washington University Western CEDAR WWU Graduate School Collection WWU Graduate and Undergraduate Scholarship 2013 Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific Mark T. (Mark Thomas) Price Western Washington University Follow this and additional works at: https://cedar.wwu.edu/wwuet Part of the Biology Commons Recommended Citation Price, Mark T. (Mark Thomas), "Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific" (2013). WWU Graduate School Collection. 293. https://cedar.wwu.edu/wwuet/293 This Masters Thesis is brought to you for free and open access by the WWU Graduate and Undergraduate Scholarship at Western CEDAR. It has been accepted for inclusion in WWU Graduate School Collection by an authorized administrator of Western CEDAR. For more information, please contact [email protected]. BIOGEOGRAPHY AND EVOLUTION OF THERMOCOCCUS ISOLATES FROM HYDROTHERMAL VENT SYSTEMS OF THE PACIFIC By Mark T. Price Accepted in Partial Completion Of the Requirements for the Degree Master of Science Kathleen L. Kitto, Dean of the Graduate School ADVISORY COMMITTEE Chair, Dr. Craig Moyer Dr. David Leaf Dr. Jeff Young Dr. Dietmar Schwarz MASTER’S THESIS In presenting this thesis in partial fulfillment of the requirements for a master’s degree at Western Washington University, I grant to Western Washington University the non‐ exclusive royalty‐free right to archive, reproduce, distribute, and display the thesis in any and all forms, including electronic format, via any digital library mechanisms maintained by WWU. I represent and warrant this is my original work, and does not infringe or violate any rights of others.