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. -
High-Fidelity Amplification Using a Thermostable DNA Polymerase Isolated from P’~Ococcusfuriosus
Gette, 108 (1991) 1-6 8 1991 Elsevier Science Publishers B.V. All rights reserved. 0378-l 119/91/SO3.50 GENE 06172 High-fidelity amplification using a thermostable DNA polymerase isolated from P’~OCOCCUSfuriosus (Polymerase chain reaction; mutation frequency; lack; proofreading; 3’40-5 exonuclease; recombinant DNA; archaebacteria) Kelly S. Lundberg”, Dan D. Shoemaker*, Michael W.W. Adamsb, Jay M. Short”, Joseph A. Serge* and Eric J. Mathur” “ Division of Research and Development, Stratagene, Inc., La Jolla, CA 92037 (U.S.A.), and h Centerfor Metalloen~~vme Studies, University of Georgia, Athens, GA 30602 (U.S.A.) Tel. (404/542-2060 Received by M. Salas: 16 May 1991 Revised/Accepted: 11 August/l3 August 1991 Received at publishers: 17 September 1991 -.-- SUMMARY A thermostable DNA polymerase which possesses an associated 3’-to-5’ exonuclease (proofreading) activity has been isolated from the hyperthermophilic archaebacterium, Pyrococcus furiosus (Pfu). To test its fidelity, we have utilized a genetic assay that directly measures DNA polymerase fidelity in vitro during the polymerase chain reaction (PCR). Our results indicate that PCR performed with the DNA polymerase purified from P. furiosus yields amplification products containing less than 10s.~ of the number of mutations obtained from similar amplifications performed with Tuq DNA polymerase. The PCR fidelity assay is based on the ampli~cation and cloning of lad, lac0 and IacZor gene sequences (IcrcIOZa) using either ffil or 7ii~irqDNA poIymerase. Certain mutations within the lucf gene inactivate the Lac repressor protein and permit the expression of /?Gal. When plated on a chromogenic substrate, these Lacl - mutants exhibit a blue-plaque phenotype. -
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. -
Evidence for Associated Horizontal Gene Transfer in Pyrococcus Furiosus
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC J Appl Genet 50(4), 2009, pp. 421–430 Original article CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer in Pyrococcus furiosus M.C. Portillo, J.M. Gonzalez Institute for Natural Resources and Agrobiology, IRNAS-CSIC, Sevilla, Spain Abstract. The presence and distribution of CRISPR (clustered regularly interspaced short palindrome repeat)el- ements in the archaeal order Thermococcales were analyzed. Four complete genome sequences from the species Pyrococcus abyssi, P. furiosus, P. horikoshii, and Thermococcus kodakaraensis were studied. A fragment of the genome of P. furiosus was flanked by CRISPR elements upstream and by a single element downstream. The composition of the gene sequences contained in this genome fragment (positions 699013 to 855319) showed sig- nificant differences from the other genes in the P. furiosus genome. Differences were observed in the GC content at the third codon positions and the frequency of codon usage between the genes located in the analyzed fragment and the other genes in the P. furiosus genome. These results represent the first evidence suggesting that repeated CRISPR elements can be involved in horizontal gene transfer and genomic differentiation of hyperthermophilic Archaea. Keywords: CRISPR, gene transfer, genome, hyperthermophilic Archaea, Pyrococcus furiosus. Introduction spacers and repetitive elements modified the phage-resistance phenotype of bacteria Genomic regions consisting of tandem repeat (Barrangou et al. 2007). The incorporation of short DNA elements, typically of 21–47 base pairs (bp) fragments of foreign DNA into the genome of in length, separated by nonrepetitive spacer se- prokaryotes at CRISPR loci has been reported quences of approximately similar length, have (Bolotin et al. -
Gene Cloning and Characterization of NADH Oxidase from Thermococcus Kodakarensis
African Journal of Biotechnology Vol. 10(78), pp. 17916-17924, 7 December, 2011 Available online at http://www.academicjournals.org/AJB DOI: 10.5897/AJB11.989 ISSN 1684–5315 © 2011 Academic Journals Full Length Research Paper Gene cloning and characterization of NADH oxidase from Thermococcus kodakarensis Naeem Rashid 1*, Saira Hameed 2, Masood Ahmed Siddiqui 3 and Ikram-ul-Haq 2 1School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan. 2Institute of Industrial Biotechnology, GC University, Lahore, Pakistan. 3Department of Chemistry, University of Balochistan, Quetta, Pakistan. Accepted 12 October, 2011 The genome search of Thermococcus kodakarensis revealed three open reading frames, Tk0304, Tk1299 and Tk1392 annotated as nicotinamide adenine dinucleotide (NADH) oxidases. This study deals with cloning, and characterization of Tk0304. The gene, composed of 1320 nucleotides, encodes a protein of 439 amino acids with a molecular weight of 48 kDa. Expression of the gene in Escherichia coli resulted in the production of Tk0304 in soluble form which was purified by heat treatment at 80°C followed by ion exchange chromatography. Enzyme activity of Tk0304 was enhanced about 50% in the presence of 30 µM flavin adenine dinucleotide (FAD) when assay was conducted at 60°C. Surprisingly the activity of the enzyme was not affected by FAD when the assay was conducted at 75°C or at higher temperatures. Tk0304 displayed highest activity at pH 9 and 80°C. The enzyme was highly thermostable displaying 50% of the original activity even after an incubation of 80 min in boiling water. Among the potent inhibitors of NADH oxidases, silver nitrate and potassium cyanide did not show any significant inhibitory effect at a final concentration of 100 µM. -
Tackling the Methanopyrus Kandleri Paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo†
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Open Access Research2004BrochieretVolume al. 5, Issue 3, Article R17 Archaeal phylogeny based on proteins of the transcription and comment translation machineries: tackling the Methanopyrus kandleri paradox Céline Brochier*, Patrick Forterre† and Simonetta Gribaldo† Addresses: *Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France. †Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, 91405 Orsay, France. reviews Correspondence: Céline Brochier. E-mail: [email protected] Published: 26 February 2004 Received: 14 November 2003 Revised: 5 January 2004 Genome Biology 2004, 5:R17 Accepted: 21 January 2004 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2004/5/3/R17 reports © 2004 Brochier et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. ArchaealPhylogeneticsequencedusingrespectively). two phylogeny concatenated genomes, analysis based it of is datasetsthe now on Archaea proteinspossible consisting has ofto been thetest of transcription alternative mainly14 proteins established approach involv and translationed byes in 16S bytranscription rRNAusing machineries: largesequence andsequence 53comparison.tackling ribosomal datasets. the Methanopyrus Withproteins We theanalyzed accumulation(3,275 archaealkandleri and 6,377 of phyparadox comp positions,logenyletely Abstract deposited research Background: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. -
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 -
Pyrococcus Horikoshii Rada Intein Site Selection
Murray State's Digital Commons Honors College Theses Honors College Fall 11-12-2020 Pyrococcus horikoshii RadA Intein Site Selection Noah Stallins Follow this and additional works at: https://digitalcommons.murraystate.edu/honorstheses Part of the Biology Commons Recommended Citation Stallins, Noah, "Pyrococcus horikoshii RadA Intein Site Selection" (2020). Honors College Theses. 61. https://digitalcommons.murraystate.edu/honorstheses/61 This Thesis is brought to you for free and open access by the Honors College at Murray State's Digital Commons. It has been accepted for inclusion in Honors College Theses by an authorized administrator of Murray State's Digital Commons. For more information, please contact [email protected]. Murray State University Honors College HONORS THESIS Certificate of Approval Pyrococcus horikoshii RadA Intein Site Selection Noah Reed Stallins November 2020 Approved to fulfill the requirements of HON 437 __________________________________________ Professor Dr. Christopher Lennon, Assistant Professor Biology Approved to fulfill the Honors Thesis requirement __________________________________________ Of the Murray State Honors Dr. Warren Edminster, Executive Director College Honors College Examination Approval Page Author: Noah Reed Stallins Project Title: Pyrococcus horikoshii RadA Intein Site Selection Department: Biology Date of Defense: 11/12/2020 Approval by Examining Committee: _____________________________ ________ (Dr. Christopher Lennon, Advisor) (Date) ________________________________ ________ (Dr. Gary ZeRuth, Committee Member) (Date) _____________________________ ________ (Dr. Terry Derting, Committee Member) (Date) Pyrococcus horikoshii RadA Intein Site Selection Submitted in partial fulfillment Of the requirements Of the Murray State University Honors Diploma Noah Reed Stallins November 2020 ABSTRACT Inteins are protein segments interrupting polypeptides with the unique ability to excise from the host protein and link flanking protein fragments (exteins) to form a functional protein. -
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. -
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. -
Discovery of Pyrobaculum Small RNA Families with Atypical Pseudouridine Guide RNA Features
Downloaded from rnajournal.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press REPORT Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features DAVID L. BERNICK,1 PATRICK P. DENNIS,2 MATTHIAS HO¨ CHSMANN,1 and TODD M. LOWE1,3 1Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA 2Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA ABSTRACT In the Eukarya and Archaea, small RNA-guided pseudouridine modification is believed to be an essential step in ribosomal RNA maturation. While readily modeled and identified by computational methods in eukaryotic species, these guide RNAs have not been found in most archaeal genomes. Using high-throughput transcriptome sequencing and comparative genomics, we have identified ten novel small RNA families that appear to function as H/ACA pseudouridylation guide sRNAs, yet surprisingly lack several expected canonical features. The new RNA genes are transcribed and highly conserved across at least six species in the archaeal hyperthermophilic genus Pyrobaculum. The sRNAs exhibit a single hairpin structure interrupted by a conserved kink- turn motif, yet only two of ten families contain the complete canonical structure found in all other H/ACA sRNAs. Half of the sRNAs lack the conserved 39-terminal ACA sequence, and many contain only a single 39 guide region rather than the canonical 59 and 39 bipartite guides. The predicted sRNA structures contain guide sequences that exhibit strong complementarity to ribosomal RNA or transfer RNA. Most of the predicted targets of pseudouridine modification are structurally equivalent to those known in other species.