Evidence for Associated Horizontal Gene Transfer in Pyrococcus Furiosus
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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. -
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. -
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. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
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. -
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. -
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. -
Methanocaldococcus Jannaschii Mja Methanococci Methanococcales
Table S2 List of the archaeal species used for evaluation of physiological and metabolic potential by MAPLE system Species Species ID Class Order [Euryarchaeota: 53 species] Methanocaldococcus jannaschii mja Methanococci Methanococcales Methanotorris igneus mig Methanococci Methanococcales Methanococcus vannielii mvn Methanococci Methanococcales Methanothermococcus okinawensis mok Methanococci Methanococcales Methanosarcina barkeri mba Methanomicrobia Methanosarcinales Methanococcoides burtonii mbu Methanomicrobia Methanosarcinales Methanohalophilus mahii mmh Methanomicrobia Methanosarcinales Methanohalobium evestigatum mev Methanomicrobia Methanosarcinales Methanosalsum zhilinae mzh Methanomicrobia Methanosarcinales Methanolobus psychrophilus mpy Methanomicrobia Methanosarcinales Methanomethylovorans hollandica mhz Methanomicrobia Methanosarcinales Methanosaeta concilii mcj Methanomicrobia Methanosarcinales Methanospirillum hungatei mhu Methanomicrobia Methanomicrobiales Methanocorpusculum labreanum mla Methanomicrobia Methanomicrobiales Methanoculleus bourgensis mbg Methanomicrobia Methanomicrobiales Methanoplanus petrolearius mpi Methanomicrobia Methanomicrobiales Methanoregula boonei mbn Methanomicrobia Methanomicrobiales Candidatus Methanosphaerula palustris mpl Methanomicrobia Methanomicrobiales Methanocella paludicola mpd Methanomicrobia Methanocellales Methanomassiliicoccus sp. Mx1-Issoire mer Methanomicrobia Unclassified Methanothermobacter thermautotrophicus mth Methanobacteria Methanobacteriales Methanosphaera stadtmanae mst -
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. -
Pyrococcus Glycovorans Sp. Nov., a Hyperthermophilic Archaeon Isolated from the East Pacific Rise
International Journal of Systematic Bacteriology (1 999), 49, 1829-1 837 Printed in Great Britain Pyrococcus glycovorans sp. nov., a hyperthermophilic archaeon isolated from the East Pacific Rise Georges Barbier,' Anne Godfroy,' Jean-Roch Meunier,'t Joel Querellou,' Marie-Anne Cambon,' Franqoise Lesongeur,' Patrick A. D. Grimont' and Gerard Raguenes' Author for correspondence: Georges Barbier. Tel: + 33 2 98 22 45 21. Fax: +33 2 98 22 45 45. e-mail: gbarbier(difremer.fr 1 Laboratoire de A hyperthermophilic archaeon, strain AL585T, was isolated from a deep-sea Caracterisation des Micro- hydrothermal vent located on the East Pacific Rise at latitude 13 O N and a organismes Marins, IFREMER, Centre de Brest, depth of 2650 m. The isolate was a strictly anaerobic coccus with a mean cell BP 70, 29280 Plouzane, diameter of 1 pm. The optimum temperature, pH and concentration of sea salt France for growth were 95 "C, 7.5 and 30 g I-'. Under these conditions, the doubling 2 Unite des Enterobacteries, time and cell yield were 0.5 h and 5 x lo8cells ml-l. Strain AL585T grew lnstitut Pasteur, 75724 preferentially in media containing complex proteinaceous carbon sources, Paris cedex 15, France glucose and elemental sulfur. The G+C content of the DNA was 47 molo/o. Sequencing of the 165 rDNA gene showed that strain AL585T belonged to the genus Pyrococcus and was probably a new species. This was confirmed by total DNA hybridization. Consequently, this strain is described as a new species, Pyrococcus glycovorans sp. nov. Keywords: archaea, Pyrococcus, hyperthermophile, deep-sea, hydrothermal vent ~ ~ ~ INTRODUCTION woesei are subjective synonyms (Erauso et al., 1993) and their 16s rDNA and DNA polymerases sequences From the beginning of the last decade, the scientific are identical (5. -
Random Mutagenesis of the Hyperthermophilic Archaeon
www.nature.com/scientificreports OPEN Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro Received: 01 August 2016 Accepted: 19 October 2016 mariner transposition and natural Published: 08 November 2016 transformation Natalia Guschinskaya1,2,3, Romain Brunel1,2, Maxime Tourte3,4, Gina L. Lipscomb5, Michael W. W. Adams5, Philippe Oger3,4 & Xavier Charpentier1,2 Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon- mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes. It is now well established that Archaea represent a taxonomic domain distinct from Bacteria, their prokary- otic counterpart.