A Proposal to Rename the Hyperthermophile Pyrococcus Woesei As Pyrococcus Furiosus Subsp
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Methanothermus Fervidus Type Strain (V24S)
UC Davis UC Davis Previously Published Works Title Complete genome sequence of Methanothermus fervidus type strain (V24S). Permalink https://escholarship.org/uc/item/9367m39j Journal Standards in genomic sciences, 3(3) ISSN 1944-3277 Authors Anderson, Iain Djao, Olivier Duplex Ngatchou Misra, Monica et al. Publication Date 2010-11-20 DOI 10.4056/sigs.1283367 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:315-324 DOI:10.4056/sigs.1283367 Complete genome sequence of Methanothermus fervidus type strain (V24ST) Iain Anderson1, Olivier Duplex Ngatchou Djao2, Monica Misra1,3, Olga Chertkov1,3, Matt Nolan1, Susan Lucas1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxanne Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Evelyne Brambilla4, Amy Chen5, Krishna Palaniappan5, Miriam Land1,6, Loren Hauser1,6, Yun-Juan Chang1,6, Cynthia D. Jeffries1,6, Johannes Sikorski4, Stefan Spring4, Manfred Rohde2, Konrad Eichinger7, Harald Huber7, Reinhard Wirth7, Markus Göker4, John C. Detter1, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,8, Victor Markowitz5, Philip Hugenholtz1, Hans-Peter Klenk4, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 5 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 6 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 7 University of Regensburg, Archaeenzentrum, Regensburg, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. -
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. -
A Proposal to Rename the Hyperthermophile Pyrococcus Woesei As Pyrococcus Furiosus Subsp
Archaea 1, 277–283 © 2004 Heron Publishing—Victoria, Canada A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei WIROJNE KANOKSILAPATHAM,1 JUAN M. GONZÁLEZ,1,2 DENNIS L. MAEDER,1 1,3 1,4 JOCELYNE DIRUGGIERO and FRANK T. ROBB 1 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA 2 Present address: IRNAS-CSIC, P.O. Box 1052, 41080 Sevilla, Spain 3 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20274, USA 4 Corresponding author ([email protected]) Received April 8, 2004; accepted July 28, 2004; published online August 31, 2004 Summary Pyrococcus species are hyperthermophilic mem- relatively rapidly at temperatures above 90 °C and produce ° bers of the order Thermococcales, with optimal growth tem- H2S from elemental sulfur (S ) (Zillig et al. 1987). Two Pyro- peratures approaching 100 °C. All species grow heterotrophic- coccus species, P. furiosus (Fiala and Stetter 1986) and ° ally and produce H2 or, in the presence of elemental sulfur (S ), P. woesei (Zillig et al. 1987), were isolated from marine sedi- H2S. Pyrococcus woesei and P.furiosus were isolated from ma- ments at a Vulcano Island beach site in Italy. They have similar rine sediments at the same Vulcano Island beach site and share morphological and physiological characteristics: both species many morphological and physiological characteristics. We re- are cocci and move by means of a tuft of polar flagella. They port here that the rDNA operons of these strains have identical are heterotrophic and grow optimally at 95–100 °C, utilizing sequences, including their intergenic spacer regions and part of peptides as major carbon and nitrogen sources. -
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. -
Ana Maria Da Silva Esteves Dissertation Presented to Obtain The
Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus Ana Maria da Silva Esteves Dissertation presented to obtain the Ph.D. degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, February, 2015 Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus Ana Maria da Silva Esteves Supervisor: Professora Helena Santos Co-supervisor: Dr. Nuno Borges Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, February, 2015 From left to right: Prof. Volker Müller, Dr. Emmanouil Matzapetakis, Dr. Nuno Borges (Co-supervisor), Ana M. Esteves, Prof. Helena Santos (Supervisor), Prof. Pedro Moradas Ferreira, Prof. Beate Averhoff, Prof. Hermínia de Lencastre. Oeiras, 9th of February 2015. Apoio financeiro da Fundação para a Ciência e Tecnologia e do FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH/BD/61742/2009. In loving memory of my grandmother Elisa iv Acknowledgements First, I would like to thank Prof. Helena Santos, my supervisor, for accepting me as a Ph.D. student in her laboratory. Also, I want to express my appreciation to Prof. Helena Santos for being an excellent team leader, and for her constant effort to put together the resources and expertise her students need to carry out their projects with success. Her guidance, rigor, patience and enthusiasm for science definitely contributed to my development as a young scientist. I want to thank Dr. -
Hyperthermophilic Archae- and Eubacteria Occurring Within Indonesian Hydrothermal Areas
Mitt. Geol.-Paläont. Inst. Univ. Hamburg The Sea off Mount Tambora S. 161-172 Hamburg Heft 70 October 1992 Hyperthermophilic Archae- and Eubacteria occurring within Indonesian Hydrothermal Areas by G. HUBER, R. HUBER, B. JONES G. LAUERER, A. NEUNER, A. SEGERER, K. O. STETTER & E. T. DEGENS*) With 3 Figures and 6 Tables Contents Abstract 162 1. Introduction ^2 2. Results and Discussion 163 2.1 Sampling 163 2.2 Archaebacterial Isolates from Sea Sediments and Sea Water Samples from the Sumbawa and Komodo-Rinja Areas 164 2.3 Hyperthermophilic Archaebacterial and Eubacterial Isolates from the Shallow Submarine Hot Springs at the Beach of Sangeang Island 165 2.4 Methanogenic Isolates from the Toye Bungkah Hot Springs, Bali 167 2.5 Hyperthermophilic and Thermophilic Archae- and Eubacteria Isolated from Solfatara Fields at the Dieng Plateau and Tangkuban Prahu, Java 167 3. Acknowledgements 17C References 171 *) Addresses of the authors: B. JONES, Gist-Brocades, Delft, The Netherlands; G. HUBER, R. HUBER, G. LAUERER, A. NEUNER, A. SEGERER, Prof. Dr. K. O. STETTER, University of Regensburg, Institute of Microbiology, Universitätsstr. 31, D-8400 Regensburg, Federal Republic of Germany; Prof. Dr. E. T. DEGENS, SCOPE/UNEP International Carbon Unit, Institute of Biogeochemistry and Marine Chemistry, University of Hamburg, Bundesstraße 55, D-2000 Hamburg 13, Federal Republic of Germany. Abstract From 85 samples taken during cruise 45B of the R/V SONNE within the Sunda Arc subduction zone and from solfatara fields in Java, thermophilic and hyperthermophilic archae- and eubacteria were isolated. The archaebacteria belong to the genera Methanobacterium, Methanolobus, Methanosarcina, Acidianus, Thermoproteus, Desulfurococcus, Thermoplasma and to two up to now unknown genera of hyperthermophilic marine heterotrophs and continental metal mobilizers. -
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus Solfataricus
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis committee Thesis supervisors Prof. dr. J. van der Oost Personal chair at the laboratory of Microbiology Wageningen University Prof. dr. W. M. de Vos Professor of Microbiology Wageningen University Other members Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. V.A.F. Martins dos Santos Wageningen University Dr. T.J.G. Ettema Uppsala University, Sweden Dr. S.V. Albers Max Planck Institute for Terrestrial Microbiology, Marburg, Germany This research was conducted under the auspices of the Graduate School VLAG Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 23 January 2012 at 11 a.m. in the Aula. Jasper Walther Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus, 164 pages. Thesis, Wageningen University, Wageningen, NL (2012) With references, with summaries in Dutch and English ISBN 978-94-6173-203-3 Table of contents Chapter 1 Introduction 1 Chapter 2 Hot Transcriptomics 17 Chapter 3 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis 45 Chapter 4 Identification of the Missing -
Thermococcus Celer Genome Would Encode a Product Closely
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 4180-4184, May 1994 Evolution Transcription factor IID in the Archaea: Sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes (tancription inilaion/molecular evolution/gene duplcation/maximum likelihood and parsimony/least-squares didance) TERRY L. MARSH, CLAUDIA I. REICH, ROBERT B. WHITELOCK*, AND GARY J. OLSENt Department of Microbiology, University of Illinois, Urbana, IL 61801 Communicated by Carl R. Woese, January 7, 1994 ABSTRACT The first step in transcription initiation in the Bacteria. If this were true, then it is expected that there eukaryotes is mediated by the TATA-binding protein, a subunit will be biological innovations shared by the Eucarya and the of the transcription factor IID complex. We have cloned and Archaea but not present in the Bacteria. This is a testable sequenced the gene for a presumptive homolog of this eukary- hypothesis. otic protein from Thermococcus celer, a member ofthe Archaea Ouzounis and Sander (8) reported that the genome of the (formerly archaebacteria). The protein encoded by the ar- archaeon Pyrococcus woesei includes sequences that would chaeal gene is a tandem repeat of a conserved domain, corre- encode a protein similar to transcription factor IIB (TFIIB) of sponding to the repeated domain in its eukaryotic counterparts. eukaryotes. This fact, combined with previous observations Molecular phylogenetic analyses ofthe two halves ofthe repeat that archaeal gene promoters include sequences similar to the are consistent with the duplication occurring before the diver- TATA box of eukaryotic promoters (9), led them to suggest gence of the archaeal and eukaryotic domains. -
Ep 0949930 B1
Europäisches Patentamt *EP000949930B1* (19) European Patent Office Office européen des brevets (11) EP 0 949 930 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.7: A61K 38/46, C07H 19/00, of the grant of the patent: C07H 21/02, C07H 21/04, 06.10.2004 Bulletin 2004/41 C12N 9/14, C12N 1/20, (21) Application number: 97933154.3 C12N 15/00 (22) Date of filing: 19.06.1997 (86) International application number: PCT/US1997/010784 (87) International publication number: WO 1997/048416 (24.12.1997 Gazette 1997/55) (54) THERMOSTABLE PHOSPHATASES THERMOSTABILEN PHOSPHATASEN PHOSPHATASES THERMOSTABLES (84) Designated Contracting States: • EMBL DATABASE Accession no D83525 AT BE CH DE DK ES FI FR GB GR IE IT LI LU MC Sequence identity PSCS 29 February 1996 NL PT SE RAHAMAN N ET AL: "Gene cloning and sequence ananlysis of cobyric acid synthase (30) Priority: 19.06.1996 US 33752 P and cobalamin (5’-phosphate) synthase from hyperthermophilic archaeon Pyrococcus spec." (43) Date of publication of application: XP002151693 20.10.1999 Bulletin 1999/42 • BULT CAROL J ET AL: "Complete genome sequence of the methanogenic archaeon, (73) Proprietor: Diversa Corporation Methanococcus jannaschii." SCIENCE San Diego, CA 92121 (US) (WASHINGTON D C), vol. 273, no. 5278, 23 August 1996 (1996-08-23), pages 1058-1073, (72) Inventors: XP002151692 ISSN: 0036-8075 -& EMBL • MATHUR, Eric, J. DATABASE Accession no U67505 Sequence Carlsbad, CA 92009 (US) identitity MJU67505 26 August 1996 • LEE, Edd XP002151694 La Jolla, CA 92037 (US) • EMBL DATABASE Accession no AA080579, • BYLINA, Edward Sequence identity SSAA80579 16 October 1996 Andalusia, PA 19020 (US) CARSON D ET AL: "Sugercane cDNA from leaf roll tissue" XP002151695 (74) Representative: VOSSIUS & PARTNER • CLINICAL CHEMISTRY, December 1992, Vol. -
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Letter A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History Vincent Daubin1, Manolo Gouy, and Guy Perrie`re Laboratoire de Biome´trie et Biologie E´volutive, Unite´Mixte de Recherche Centre National de la Recherche Scientifique, Universite´ Claude Bernard –Lyon 1, 69622 Villeurbanne Cedex, France It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the fewgenes that are shared amo ng all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria. Though it seems sensible to consider that genes remain asso- base a reference prokaryotic phylogeny on evidence derived ciated in genomes for long periods in Eukaryotes, recent data from a large number of genes. -
Thermal Stability of the Ribosomal Protein L30e From
Thermal Stability of the Ribosomal Protein L30e from Hyperthermophilic Archaeon Thermococcus celer by Protein Engineering LEUNG Tak Yuen B.Sc. (Hon.), CUHK A Thesis Submitted in Partial Fulfillment of the Requirement For The Degree of Master of Philosophy in Biochemistry July 2003 The Chinese University of Hong Kong The Chinese University of Hong Kong holds the copyright of this thesis. Any person(s) intending to use a part or whole of the materials in the thesis in a proposed publication must seek copyright release from the Dean of the Graduate School /;/輕塑\ \ L; :^ \ U^VE^ /, / ^O^LIBRARY SYSTEMX./ Table of Contents Acknowledgments { Abstract “ Abbreviations 衍 Abbreviations of amino acids iv Abbreviations of nucleotides iv Naming system for TRP mutants v Chapter 1 I ntroduction 1 • 1 Hyperthermophile and hyperthermophilic proteins 1 1.2 Hyperthermophilic proteina are highly similar to their mesophilic 2 homologues 1.3 Hyperthermophilic proteins and free energy of stabilization 3 1.4 Mechanisms of protein stabilization 4 1.5 The difference in protein stability between mesophilic protein and 4 hyperthermophilic protein 1.6 Ribosomal protein L30e from T. celer can be used as a model 9 system to study thermostability 1.7 Protein engineering of TRP 10 1.8 Purpose of the present study 12 Chapter 2 Materials and Methods 2.1 Bacterial strains 13 2.2 Plasmids 13 2.3 Bacterial culture media and solutions 13 2.4 Antibiotic solutions 13 2.5 Restriction endonucleases and other enzymes 14 2.6 M9ZB medium 14 2.7 SDS-PAGE 14 2.8 Alkaline phosphatase -
Genome Analysis and Genome-Wide Proteomics
Open Access Research2009ZivanovicetVolume al. 10, Issue 6, Article R70 Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea Yvan Zivanovic¤*, Jean Armengaud¤†, Arnaud Lagorce*, Christophe Leplat*, Philippe Guérin†, Murielle Dutertre*, Véronique Anthouard‡, Patrick Forterre§, Patrick Wincker‡ and Fabrice Confalonieri* Addresses: *Laboratoire de Génomique des Archae, Université Paris-Sud 11, CNRS, UMR8621, Bât400 F-91405 Orsay, France. †CEA, DSV, IBEB Laboratoire de Biochimie des Systèmes Perturbés, Bagnols-sur-Cèze, F-30207, France. ‡CEA, DSV, Institut de Génomique, Genoscope, rue Gaston Crémieux CP5706, F-91057 Evry Cedex, France. §Laboratoire de Biologie moléculaire du gène chez les extrêmophiles, Université Paris-Sud 11, CNRS, UMR8621, Bât 409, F-91405 Orsay, France. ¤ These authors contributed equally to this work. Correspondence: Fabrice Confalonieri. Email: [email protected] Published: 26 June 2009 Received: 24 March 2009 Revised: 29 May 2009 Genome Biology 2009, 10:R70 (doi:10.1186/gb-2009-10-6-r70) Accepted: 26 June 2009 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2009/10/6/R70 © 2009 Zivanovic 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. Thermococcus<p>Theoresistance genome may gammatole besequence due to ransunknownof Thermococcus proteogenomics DNA repair gammatolerans, enzymes.</p> a radioresistant archaeon, is described; a proteomic analysis reveals that radi- Abstract Background: Thermococcus gammatolerans was isolated from samples collected from hydrothermal chimneys.