DOCSLIB.ORG

Comparative Genomics of Closely Related Thermococcus Isolates, a Genus of Hyperthermophilic Archaea

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Comparative Genomics of Closely Related Thermococcus Isolates, a Genus of Hyperthermophilic Archaea Thèse&préparée&à&l'Université&de&Bretagne&Occidentale& pour obtenir le diplôme de DOCTEUR&délivré&de&façon&partagée&par& présentée par L'Université&de&Bretagne&Occidentale&et&l'Université&de&Bretagne&Loire& ! Damien Courtine Spécialité):)Microbiologie) ) Préparée au Laboratoire de Microbiologie des École!Doctorale!Sciences!de!la!Mer!et!du!Littoral! Environnements Extrêmes (LM2E) UMR6197, UBO – Ifremer – CNRS – Génomique comparative Thèse!soutenue!le!19!Décembre!2017! devant le jury composé de : d'isolats Anna?Louise!REYSENBACH!! Professeur, Université de Portland (USA) / Rapporteur) phylogénétiquement Simonetta!GRIBALDO! proches appartenant au Directrice de Recherche, Institut Pasteur / Rapporteur) genre Thermococcus, une Dominique!LAVENIER!! Directeur de Recherche, CNRS Rennes / Examinateur) archée hyperthermophile Karine!ALAIN!! Chargée de recherche, CNRS Brest / Directrice)de)thèse) Loïs!MAIGNIEN! Maître de Conférence, Université de Bretagne Occidentale / Co9 encadrant) A.!Murat!EREN! Maître de conférence, Université de Chicago (USA) / Co9encadrant) Yann!MOALIC! Enseignant Chercheur, Université de Bretagne Occidentale / Invité Acknowledgements This thesis work was carried out at the Laboratoire de Microbiologie des Environnements Extrêmes (LM2E) at the Institut Universitaire Européen de la Mer (IUEM). It was financed by the Région Bretagne (Brittany Region) and Labex MER. I thank Mohamed Jebbar, Anne Godfroy and Didier Flament for welcoming me in this laboratory. First of all, I would like to sincerely thank the members of the jury who agreed to evaluate this work. I would like to thank Anna-Louise Reysenbach, Professor at the Portland University, and Simoneta Gribaldo, Research director at the Institut Pasteur, for agreeing to review this thesis. I would also like to thank DominiQue Lavenier, Research Director at the CNRS, and Yann Moalic, Researcher at the Université de Bretagne Occidentale, for reviewing this work. I would like to thank Karine Alain for her support, availability and kindness. Many thanks to Lois Maignien, for his guidance; this work could not have taken place without his advices and its availability. I would also like to thank A. Murat Eren (aka Meren) for its advices, for allowing me to sequence more genomes in this project, and also for hosted me for 1 month in his lab at the University of Chicago. This visit was a very enriching experience. donner accès à des données génomiques supplémentaires, et égalem leUn séQuençage merci particulier de génomes à Patrick via Forterre, Jacques Oberto et Violette Da Cunha de mavoir ent davoir finalisé Je remercie Myriam Georges pourlERC toute EVOMOB)L. son aide apportée lors des manips de bio-mol et pour tous les autres moments. e, et des Thermococcales. MerciUn merci Stéphanie, également pour tonà Nadège aide et taBienvenu bienveillance pour aulutilisation quotidien. de la souchothèqu MerciStéphane à toutes L(aridon les personnes pour ses ayantnombreux participé conseils de près en culture ou de loin à ce travail. du LM2E pour leur disponibilité et leur gentillesse. UnMerci remerciement à lensemble particulierdes membres à la team EcoGenomics, Florian, Clarisse et la nouvelle recrue Blandine, pour toutes les discussions, les réunions du lundi, merci pour ces moments. des thésards, passés, présents, futurs, pour toutes les discussions, soutiens, et bons moments passés ensemble, en commençant par les anciens,Également Gaëlle, à lensemble Sandrine, Matthieu, Simon, Coraline; la génération 2014: Mélanie, Charlène, Vincent, Gwenn et Tiphaine; Les prochains sur la liste: Sébastien, Yang, Caroline, Clarisse, et Florian (encore toi?!); les « jeunes »: Sarah, Jordan, Pierre et les derniers arrivés, Marc, Blandine et David. Je souhaite adresser un sincère merci au FEIRI, et plus particulièrement à Sandy, Frédéric de informatiQue apportée : les debugs de Penduick, Quand . et Emmanuel, pour toute lai Margane, bien Quele mactu sois ne veutpartie plus du démarrer…labo peu après Merci mon arrivée, un grand merci pour tous les bons moments ! Je voudr faire cette thèse. ais également adresser un merci à )van, qui ma longuement aidé et poussé à Enfin je voudrais remercier ma famille, Maman, Papa, Steph, Brigitte, Mathis, Mémé, À ma moitié, pour avoir enduré mes crises et être à mes côtés tous les jours, dans les bonsdavoir et crules autresen moi, moments, je nen serais je ne pas te remercierai là sans vous. jamais assez. Table of contents Acknowledgements List of figures List of tables List of abbreviations Chapter I: Introduction.......................................................................................... 1 I) Introduction of deep-sea hydrothermal vents .................................................... 1 1) Generalities about deep-sea hydrothermal vents ........................................................... 1 2) Deep-sea hydrothermal vent ecology .................................................................................. 4 3) Extremophiles ............................................................................................................................... 7 II) The third domain of life: Archaea ........................................................................... 9 1) Generalities .................................................................................................................................... 9 2) The order Thermococcales ..................................................................................................... 11 III) Ordering microbial diversity in cohesive units ............................................. 17 1) The necessity to classify microorganisms ........................................................................ 17 a) Historical motivations ..................................................................................................... 17 b) Classification of living beings ....................................................................................... 17 2) The actual definition of a microbial species .................................................................... 19 a) The definition ..................................................................................................................... 19 b) How are species delineated? ........................................................................................ 19 i) Sequence similarity .................................................................................................. 19 x DNA-DNA sequence similarity ....................................................................... 19 x Average Nucleotide Identity ........................................................................... 22 ii) Phenotype ................................................................................................................... 23 iii) Additional methods ............................................................................................... 23 c) The lacking parameters: Ecology ................................................................................ 24 i) Species as a group of ecologically coherent isolates ................................... 24 d) Why species definition is still the same? ................................................................. 24 3) What about a new species definition in the genomic era? ......................................... 25 a) Currently, definition does not integrate ecology .................................................. 25 b) How incorporate ecology and genomic data in a more cohesive model? ... 25 4) Instead of thinking species, think population ................................................................. 26 a) Definition of a population .............................................................................................. 26 b) Genomic units: how to cluster genomes? ................................................................ 26 i) Sequence similarity .................................................................................................. 26 ii) Genetic units .............................................................................................................. 27 c) A population is not static ................................................................................................ 27 d) Different models exist ..................................................................................................... 28 i) Based on recombination/selection ratio ......................................................... 28 5) Examples of natural populations ......................................................................................... 31 a) Vibrio ...................................................................................................................................... 31 b) Sulfolobus ............................................................................................................................. 32 IV) Objectives of the thesis ............................................................................................ 33 Chapter II: Materials and Methods .................................................................. 34 I) The LM2E culture collection: UBOCC .................................................................... 34 1) Culture of hyperthermophilic and anaerobic isolates ................................................. 34 a) Preparation of culture media ....................................................................................... 35 b) Sterilization steps ............................................................................................................
Load more

Recommended publications
  • Extremozymes of the Hot and Salty Halothermothrix Orenii
    Extremozymes of the Hot and Salty Halothermothrix orenii Author Kori, Lokesh D Published 2012 Thesis Type Thesis (PhD Doctorate) School School of Biomolecular and Physical Sciences DOI https://doi.org/10.25904/1912/2191 Copyright Statement The author owns the copyright in this thesis, unless stated otherwise. Downloaded from http://hdl.handle.net/10072/366220 Griffith Research Online https://research-repository.griffith.edu.au Extremozymes of the hot and salty Halothermothrix orenii LOKESH D. KORI (M.Sc. Biotechnology) School of Biomolecular and Physical Sciences Science, Environment, Engineering and Technology Griffith University, Australia Submitted in fulfillment of the requirements of the degree of Doctor of Philosophy December 2011 STATEMENT OF ORIGINALITY STATEMENT OF ORIGINALITY This work has not previously been submitted for a degree or diploma in any university. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made in the thesis itself. LOKESH DULICHAND KORI II ACKNOWLEDGEMENTS ACKNOWLEDGEMENTS I owe my deepest gratitude to my supervisor Prof. Bharat Patel, for offering me an opportunity for being his postgraduate. His boundless knowledge motivates me for keep going and enjoy the essence of science. Without his guidance, great patience and advice, I could not finish my PhD program successfully. I take this opportunity to give my heartiest thanks to Assoc. Prof. Andreas Hofmann, (Structural Chemistry, Eskitis Institute for Cell & Molecular Therapies, Griffith University) for his support and encouragement for crystallographic work. I am grateful to him for teaching me about the protein structures, in silico analysis and their hidden chemistry.
    [Show full text]
  • 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.
    [Show full text]
  • The Status of Natural Resources on the High-Seas
    The status of natural resources on the high-seas Part 1: An environmental perspective Part 2: Legal and political considerations An independent study conducted by: The Southampton Oceanography Centre & Dr. A. Charlotte de Fontaubert The status of natural resources on the high-seas i The status of natural resources on the high-seas Published May 2001 by WWF-World Wide Fund for Nature (Formerly World Wildlife Fund) Gland, Switzerland. Any reproduction in full or in part of this publication must mention the title and credit the above mentioned publisher as the copyright owner. The designation of geographical entities in this book, and the presentation of the material, do not imply the expression of any opinion whatsoever on the part of WWF or IUCN concerning the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries. The views expressed in this publication do not necessarily reflect those of WWF or IUCN. Published by: WWF International, Gland, Switzerland IUCN, Gland, Switzerland and Cambridge, UK. Copyright: © text 2001 WWF © 2000 International Union for Conservation of Nature and Natural Resources © All photographs copyright Southampton Oceanography Centre Reproduction of this publication for educational or other non-commercial purposes is authorized without prior written permission from the copyright holder provided the source is fully acknowledged. Reproduction of this publication for resale or other commercial purposes is prohibited without prior written permission of the copyright holder. Citation: WWF/IUCN (2001). The status of natural resources on the high-seas. WWF/IUCN, Gland, Switzerland. Baker, C.M., Bett, B.J., Billett, D.S.M and Rogers, A.D.
    [Show full text]
  • 18Th EANA Conference European Astrobiology Network Association
    18th EANA Conference European Astrobiology Network Association 24-28 September 2018 Freie Universität Berlin, Germany Sponsors: Scientific Organizing Committee (EANA Council): Daniela Billi, Italy Oleg Kotsyurbenko, Russia Alexis Brandeker, Sweden Helmut Lammer, Austria John Brucato, Italy Harry Lehto, Finland Barbara Cavalazzi, Italy Kirsi Lehto, Finland Elias Chatzitheodoridis, Greece Zita Martins, Portugal Charles Cockell, UK Nigel Mason, UK Hervé Cottin, France Ralf Möller, Germany Rosa De la Torre, Spain Christine Moissl-Eichinger, Austria Jean-Pierre De Vera, Germany Lena Noack, Germany René Demets, ESA Karen Olsson-Francis, UK Cristina Dobrota, Romania François Raulin, France Pascale Ehrenfreund, The Netherlands Petra Rettberg, Germany Franco Ferrari, Poland Séverine Robert, Belgium Kai Finster, Denmark Gyorgyi Ronto, Hungary Muriel Gargaud, France Dirk Schulze-Makuch, Germany Beda Hofmann, Switzerland Alan Schwartz, The Netherlands Nils Holm, Sweden Ewa Szuszkiewicz, Poland Jan Jehlicka, Czech Republic Ruth-Sophie Taubner, Austria Jean-Luc Josset, Switzerland Jorge Vago, The Netherlands Kensei Kobayashi, Japan Frances Westall, France Local Organizing Committee: Lena Noack (FU) Lutz Hecht (MfN, FU) Jean-Pierre de Vera (DLR, DAbG) Jacob Heinz (TU) Dirk Schulze-Makuch (TU, DAbG) Dennis Höning (VU Amsterdam) Alessandro Airo (TU) Deborah Maus (TU) Felix Arens (FU) Ralf Möller (DLR) Alexander Balduin Carolin Rabethge (FU) Mickael Baqué (DLR) Heike Rauer (DLR, TU, FU) Doris Breuer
    [Show full text]
  • Sulfur Metabolism Pathways in Sulfobacillus Acidophilus TPY, a Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 18 November 2016 doi: 10.3389/fmicb.2016.01861 Sulfur Metabolism Pathways in Sulfobacillus acidophilus TPY, A Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent Wenbin Guo 1, Huijun Zhang 1, 2, Wengen Zhou 1, 2, Yuguang Wang 1, Hongbo Zhou 2 and Xinhua Chen 1, 3* 1 Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China, 2 Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, China, 3 Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory forMarine Science and Technology, Qingdao, China Sulfobacillus acidophilus TPY, isolated from a hydrothermal vent in the Pacific Ocean, is a moderately thermoacidophilic Gram-positive bacterium that can oxidize ferrous iron or Edited by: sulfur compounds to obtain energy. In this study, comparative transcriptomic analyses of Jake Bailey, University of Minnesota, USA S. acidophilus TPY were performed under different redox conditions. Based on these Reviewed by: results, pathways involved in sulfur metabolism were proposed. Additional evidence M. J. L. Coolen, was obtained by analyzing mRNA abundance of selected genes involved in the sulfur Curtin University, Australia Karen Elizabeth Rossmassler, metabolism of sulfur oxygenase reductase (SOR)-overexpressed S. acidophilus TPY Colorado State University, USA recombinant under different redox conditions. Comparative transcriptomic analyses of *Correspondence: S. acidophilus TPY cultured in the presence of ferrous sulfate (FeSO4) or elemental Xinhua Chen sulfur (S0) were employed to detect differentially transcribed genes and operons involved [email protected] in sulfur metabolism.
    [Show full text]
  • Thermodynamics of DNA Binding by DNA Polymerase I and Reca
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2014 Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans Jaycob Dalton Warfel Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Warfel, Jaycob Dalton, "Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans" (2014). LSU Doctoral Dissertations. 2382. https://digitalcommons.lsu.edu/gradschool_dissertations/2382 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THERMODYNAMICS OF DNA BINDING BY DNA POLYMERASE I AND RECA RECOMBINASE FROM DEINOCOCCUS RADIODURANS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Jaycob Dalton Warfel B.S. Louisiana State University, 2006 May 2015 ACKNOWLEDGEMENTS I would like to express my utmost gratitude to the myriad of individuals who have lent their support during the time it has taken to complete this dissertation. First and foremost is due glory to God, The Father, The Son and The Holy Spirit, through whom all is accomplished. It is with extreme thankfulness for the blessings bestowed upon me, and with vast appreciation for the beauty of God’s creation that I have pursued a scientific education.
    [Show full text]
  • Extremely Thermophilic Microorganisms As Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals
    REVIEW published: 05 November 2015 doi: 10.3389/fmicb.2015.01209 Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals Benjamin M. Zeldes 1, Matthew W. Keller 2, Andrew J. Loder 1, Christopher T. Straub 1, Michael W. W. Adams 2 and Robert M. Kelly 1* 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point Edited by: that the use of these microorganisms as metabolic engineering platforms has become Bettina Siebers, University of Duisburg-Essen, possible. While in its early days, complex metabolic pathways have been altered or Germany engineered into recombinant extreme thermophiles, such that the production of fuels and Reviewed by: chemicals at elevated temperatures has become possible. Not only does this expand the Haruyuki Atomi, thermal range for industrial biotechnology, it also potentially provides biodiverse options Kyoto University, Japan Phillip Craig Wright, for specific biotransformations unique to these microorganisms. The list of extreme University of Sheffield, UK thermophiles growing optimally between 70 and 100◦C with genetic toolkits currently *Correspondence: available includes archaea and bacteria, aerobes and anaerobes, coming from genera Robert M.
    [Show full text]
  • Access to Electronic Thesis
    Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield.
    [Show full text]
  • Functionalized Membrane Domains: an Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger
    Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger To cite this version: Maxime Tourte, Philippe Schaeffer, Vincent Grossi, Phil Oger. Functionalized Membrane Domains: An Ancestral Feature of Archaea?. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.526. 10.3389/fmicb.2020.00526. hal-02553764 HAL Id: hal-02553764 https://hal.archives-ouvertes.fr/hal-02553764 Submitted on 20 May 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. fmicb-11-00526 March 30, 2020 Time: 21:44 # 1 ORIGINAL RESEARCH published: 31 March 2020 doi: 10.3389/fmicb.2020.00526 Functionalized Membrane Domains: An Ancestral Feature of Archaea? Maxime Tourte1†, Philippe Schaeffer2†, Vincent Grossi3† and Phil M. Oger1*† 1 Université de Lyon, INSA Lyon, CNRS, MAP UMR 5240, Villeurbanne, France, 2 Université de Strasbourg-CNRS, UMR 7177, Laboratoire de Biogéochimie Moléculaire, Strasbourg, France, 3 Université de Lyon, ENS Lyon, CNRS, Laboratoire de Géologie de Lyon, UMR 5276, Villeurbanne, France Bacteria and Eukarya organize their plasma membrane spatially into domains of distinct functions. Due to the uniqueness of their lipids, membrane functionalization in Archaea remains a debated area.
    [Show full text]
  • And Thermo-Adaptation in Hyperthermophilic Archaea: Identification of Compatible Solutes, Accumulation Profiles, and Biosynthetic Routes in Archaeoglobus Spp
    Universidade Nova de Lisboa Osmo- andInstituto thermo de Tecnologia-adaptation Química e Biológica in hyperthermophilic Archaea: Subtitle Subtitle Luís Pedro Gafeira Gonçalves Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. OH OH OH CDP c c c - CMP O O - PPi O3P P CTP O O O OH OH OH OH OH OH O- C C C O P O O P i Dissertation presented to obtain the Ph.D degree in BiochemistryO O- Instituto de Tecnologia Química e Biológica | Universidade Nova de LisboaP OH O O OH OH OH Oeiras, Luís Pedro Gafeira Gonçalves January, 2008 2008 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica Osmo- and thermo-adaptation in hyperthermophilic Archaea: identification of compatible solutes, accumulation profiles, and biosynthetic routes in Archaeoglobus spp. This dissertation was presented to obtain a Ph. D. degree in Biochemistry at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa. By Luís Pedro Gafeira Gonçalves Supervised by Prof. Dr. Helena Santos Oeiras, January, 2008 Apoio financeiro da Fundação para a Ciência e Tecnologia (POCI 2010 – Formação Avançada para a Ciência – Medida IV.3) e FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH / BD / 5076 / 2001. ii ACKNOWNLEDGMENTS The work presented in this thesis, would not have been possible without the help, in terms of time and knowledge, of many people, to whom I am extremely grateful. Firstly and mostly, I need to thank my supervisor, Prof. Helena Santos, for her way of thinking science, her knowledge, her rigorous criticism, and her commitment to science.
    [Show full text]
  • Representatives of a Novel Archaeal Phylum Or a Fast-Evolving
    Open Access Research2005BrochieretVolume al. 6, Issue 5, Article R42 Nanoarchaea: representatives of a novel archaeal phylum or a comment fast-evolving euryarchaeal lineage related to Thermococcales? Celine Brochier*, Simonetta Gribaldo†, Yvan Zivanovic‡, Fabrice Confalonieri‡ and Patrick Forterre†‡ Addresses: *EA EGEE (Evolution, Génomique, Environnement) Université Aix-Marseille I, Centre Saint-Charles, 3 Place Victor Hugo, 13331 Marseille, Cedex 3, France. †Unite Biologie Moléculaire du Gène chez les Extremophiles, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex ‡ 15, France. Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Celine Brochier. E-mail: [email protected]. Simonetta Gribaldo. E-mail: [email protected] Published: 14 April 2005 Received: 3 December 2004 Revised: 10 February 2005 Genome Biology 2005, 6:R42 (doi:10.1186/gb-2005-6-5-r42) Accepted: 9 March 2005 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/5/R42 reports © 2005 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Placement<p>Anteins from analysis 25of Nanoarcheumarchaeal of the positiongenomes equitans of suggests Nanoarcheum in the that archaeal N. equitans phylogeny inis likethe lyarchaeal to be the phylogeny representative using aof large a fast-evolving dataset of concatenatedeuryarchaeal ribosomalineage.</p>l pro- deposited research Abstract Background: Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis.
    [Show full text]
  • Different Proteins Mediate Step-Wise Chromosome Architectures in 2 Thermoplasma Acidophilum and Pyrobaculum Calidifontis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.982959; this version posted May 4, 2020. 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 Different Proteins Mediate Step-wise Chromosome Architectures in 2 Thermoplasma acidophilum and Pyrobaculum calidifontis 3 4 5 Hugo Maruyama1†*, Eloise I. Prieto2†, Takayuki Nambu1, Chiho Mashimo1, Kosuke 6 Kashiwagi3, Toshinori Okinaga1, Haruyuki Atomi4, Kunio Takeyasu5 7 8 1 Department of Bacteriology, Osaka Dental University, Hirakata, Japan 9 2 National Institute of Molecular Biology and Biotechnology, University of the Philippines 10 Diliman, Quezon City, Philippines 11 3 Department of Fixed Prosthodontics, Osaka Dental University, Hirakata, Japan 12 4 Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, 13 Kyoto University, Kyoto, Japan 14 5 Graduate School of Biostudies, Kyoto University, Kyoto, Japan 15 † These authors have contributed equally to this work 16 17 * Correspondence: 18 Hugo Maruyama 19 [email protected]; [email protected] 20 21 Keywords: archaea, higher-order chromosome structure, nucleoid, chromatin, HTa, histone, 22 transcriptional regulator, horizontal gene transfer 23 Running Title: Step-wise chromosome architecture in Archaea 24 Manuscript length: 6955 words 25 Number of Figures: 7 26 Number of Tables: 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.13.982959; this version posted May 4, 2020. 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.
    [Show full text]