Genomic Collections According to Their Metabolic Machinery
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Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline
Phylogenetics of Archaeal Lipids Amy Kelly 9/27/2006 Outline • Phlogenetics of Archaea • Phlogenetics of archaeal lipids • Papers Phyla • Two? main phyla – Euryarchaeota • Methanogens • Extreme halophiles • Extreme thermophiles • Sulfate-reducing – Crenarchaeota • Extreme thermophiles – Korarchaeota? • Hyperthermophiles • indicated only by environmental DNA sequences – Nanoarchaeum? • N. equitans a fast evolving euryarchaeal lineage, not novel, early diverging archaeal phylum – Ancient archael group? • In deepest brances of Crenarchaea? Euryarchaea? Archaeal Lipids • Methanogens – Di- and tetra-ethers of glycerol and isoprenoid alcohols – Core mostly archaeol or caldarchaeol – Core sometimes sn-2- or Images removed due to sn-3-hydroxyarchaeol or copyright considerations. macrocyclic archaeol –PMI • Halophiles – Similar to methanogens – Exclusively synthesize bacterioruberin • Marine Crenarchaea Depositional Archaeal Lipids Biological Origin Environment Crocetane methanotrophs? methane seeps? methanogens, PMI (2,6,10,15,19-pentamethylicosane) methanotrophs hypersaline, anoxic Squalane hypersaline? C31-C40 head-to-head isoprenoids Smit & Mushegian • “Lost” enzymes of MVA pathway must exist – Phosphomevalonate kinase (PMK) – Diphosphomevalonate decarboxylase – Isopentenyl diphosphate isomerase (IPPI) Kaneda et al. 2001 Rohdich et al. 2001 Boucher et al. • Isoprenoid biosynthesis of archaea evolved through a combination of processes – Co-option of ancestral enzymes – Modification of enzymatic specificity – Orthologous and non-orthologous gene -
Template for Taxonomic Proposal to the ICTV Executive Committee to Create a New Family
Template for Taxonomic Proposal to the ICTV Executive Committee To create a new Family Code† 2005.088B.04 To create a new family* Code† 2005.089B.04 To name the new family* Ampullaviridae † Code 2005.090B.04 To designate the following genera as part of the new family*: Ampullavirus † Assigned by ICTV officers ° Leave blank is not appropriate * repeat these lines and the corresponding arguments for each genus created in the family Author(s) with email address(es) of the Taxonomic Proposal David Prangishvili [email protected] Old Taxonomic Order Order Family Genus Ampullavirus Type Species Acidianus bottle-shaped virus Species in the Genus Acidianus bottle-shaped virus Tentative Species in the Genus none Unassigned Species in the family none New Taxonomic Order Order Family Ampullaviridae Genus Ampullavirus Type Species Acidianus bottle-shaped virus Species in the Genus Acidianus bottle-shaped virus Tentative Species in the Genus none Unassigned Species in the family none ICTV-EC comments and response of the SG Argumentation to create a new family: We propose classifying the Acidianus bottle-shaped virus as a first representative of a new family because of the unique bottle-shaped morphology of the virion which, to our knowledge, has not previously been observed in the viral world. Moreover, the complex asymmetric virion, lacking elements with icosahedral or regular helical symmetry, with two completely different structures at each end and an envelope encasing a funnel-shaped core represents, as far as we can judge, represents a principally novel type of virus particle. The funnel-shaped core of the enveloped virion consists of three distinct structural units: the “stopper”, the nucleoprotein cone, consisting of double-stranded DNA and DNA-binding proteins, and the inner core. -
Archaeoglobus Profundus Type Strain (AV18T)
Standards in Genomic Sciences (2010) 2:327-346 DOI:10.4056/sigs.942153 Complete genome sequence of Archaeoglobus profundus type strain (AV18T) Mathias von Jan1, Alla Lapidus2, Tijana Glavina Del Rio2, Alex Copeland2, Hope Tice2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, Lynne Goodwin2,3, Cliff Han2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinnikova2, Olga Chertkov2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Elizabeth Saunders2, Thomas Brettin2,3, John C. Detter2,3, Patrick Chain2,4, Konrad Eichinger6, Harald Huber6, Ste- fan Spring1, Manfred Rohde7, Markus Göker1, Reinhard Wirth6, Tanja Woyke2, Jim Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophilic, marine, strictly anaerobic, sulfate respiration, hydrogen utili- zation, hydrothermal systems, Archaeoglobaceae, GEBA Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the eu- ryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeog- lobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no va- lidly published name. -
Specific Enrichment of Hyperthermophilic Electroactive Archaea From
bioRxiv preprint doi: https://doi.org/10.1101/272039; this version posted February 27, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Specific enrichment of hyperthermophilic electroactive Archaea from 2 deep-sea hydrothermal vent on electrically conductive support. 3 4 Guillaume Pillot1, Eléonore Frouin1, Emilie Pasero1, Anne Godfroy2, Yannick Combet-Blanc1, 5 Sylvain Davidson1 & Pierre-Pol Liebgott1* 6 1 Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France. 7 2 Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197 IFREMER, CNRS, 8 UBO Centre de Brest–CS10070/IUEM, Plouzané, France. 9 *Corresponding author: [email protected]; Mediterranean Institute of 10 Oceanography, Campus de Luminy, Bâtiment OCEANOMED, 13288 Marseille Cedex 09. 11 Abstract 12 While more and more investigations are done to isolate hyperthermophilic exoelectrogenic 13 communities from environments, none have been performed yet on deep-sea hydrothermal vent. 14 Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have 15 been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic 16 (80°C) condition. Two enrichments have been performed: one from direct inoculation of crushed 17 chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both 18 experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode 19 potential of +0.05 vs SHE. Taxonomic affiliation of the exoelectrogen communities obtained 20 exhibited a specific enrichment of Archaea from Thermococcales and Archeoglobales orders on the 21 electrode, even when both inocula were dominated by Bacteria. -
Spindle Shaped Virus (SSV) : Mutants and Their Infectivity
Portland State University PDXScholar University Honors Theses University Honors College 2014 Spindle Shaped Virus (SSV) : Mutants and Their Infectivity Thien Hoang Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/honorstheses Let us know how access to this document benefits ou.y Recommended Citation Hoang, Thien, "Spindle Shaped Virus (SSV) : Mutants and Their Infectivity" (2014). University Honors Theses. Paper 231. https://doi.org/10.15760/honors.56 This Thesis is brought to you for free and open access. It has been accepted for inclusion in University Honors Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Spindle Shaped Virus (SSV): Mutants and Their Infectivity by Thien Hoang An undergraduate honors thesis submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in University Honors and Biology: Micro/molecular biology Thesis Adviser Dr. Kenneth Stedman Portland State University 2014 Abstract: SSV1 is an archaeal virus that infects the thermoacidophile Sulfolobus residing in hot springs. The lemon shaped/spindle-shaped fuselloviruses (SSV) that infect Sulfolobus solfataricus is quite morphologically different from almost all other viruses. Because these archaeal viruses live in hot springs with high temperatures and low pH, their genomes and structures have adapted to withstand such harsh conditions. Little research has been done on these extreme viruses, and of the little research, SSV has been the most prominent. Not much is known about the genes that the genome encodes and so I have inserted transposons randomly into genome to determine functionality. -
Sp. Nov. and Acidianus Brierleyi Comb
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1986, p. 559-564 Vol. 36, No. 4 0020-7713/86/040559-06$02.OO/O Copyright 0 1986, International Union of Microbiological Societies Acidianus infernus gen. nov.? sp. nov. and Acidianus brierleyi comb. nov. : Facultatively Aerobic, Extremely Acidophilic Thermophilic Sulfur-Metabolizing Archaebacteria ANDREAS SEGERER,l ANNEMARIE NEUNER,I JAKOB K. KRISTJANSSON,2 AND KARL 0. STETTER1* Lehrstuhl fur Mikrobiologie, Universitat, 8400 Regensburg, Federal Republic of Germany' and Institute of Biology, University of Iceland, Reykjavik, Icelana A new genus, Acidianus, is characterized from studies of 26 isolates of thermoacidophilic archaebacteria from different solfatara fields and marine hydrothermal systems; these isolates grow as facultative aerobes by lithotrophic oxidation and reduction of So, respectively, and are therefore different from the strictly aerobic Sulfolobus species. The Acidianus isolates have a deoxyribonucleic acid guanine-plus-cytosinecontent of 31 mol%. In contrast, two of three Sulfolobus species, including the type species, have a guanine-plus-cytosine content of 37 mol%; Sulfolobus brierleyi is the exception, with a guanine-plus-cytosine content of 31 mol%. In contrast to its earlier descriptions, S. brierleyi is able to grow strictly anaerobically by hydrogen-sulfur autotrophy. Therefore, it is described here as a member of the genus Acidiunus. The following species are assigned to the genus Acidiunus: Acidiunus infernus sp. nov. (type strain, strain DSM 3191) and Acidiunus brierleyi comb. nov. (type strain, strain DSM 1651). The following two major groups of extremely thermophilic MATERIALS AND METHODS So-metabolizing archaebacteria (12) that thrive within acidic solfatara fields have been described previously: (i) the genus Bacterial strains. -
Lipids of Sulfolobus Spp. | Encyclopedia
Lipids of Sulfolobus spp. Subjects: Biophysics | Biotechnology Contributors: Kerstin Rastaedter , David J. Wurm Submitted by: Kerstin Rastaedter Definition Archaea, and thereby, Sulfolobus spp. exhibit a unique lipid composition of ether lipids, which are altered in regard to the ratio of diether to tetraether lipids, number of cyclopentane rings and type of head groups, as a coping mechanism against environmental changes. Sulfolobales mainly consist of C40-40 tetraether lipids (caldarchaeol) and partly of C20-20 diether lipids (archaeol). A variant of caldarchaeol called glycerol dialkylnonitol tetraether (GDNT) has only been found in Sulfolobus and other members of the Creanarchaeota phylum so far. Altering the numbers of incorporated cyclopentane rings or the the diether to tetraether ratio results in more tightly packed membranes or vice versa. 1. The Cell Membrane and Lipids of Sulfolobus spp. The thermoacidophilic genus Sulfolobus belongs to the phylum Crenarchaeota and is a promising player for biotechnology [1], since it harbors a couple of valuable products, such as extremozymes[ 2], trehalose [3], archaeocins [4] and lipids for producing archaeosomes [5]. Genetic tools for this genus have rapidly advanced in recent years[ 6], generating new possibilities in basic science and for biotechnological applications alike. The cultivation conditions are preferably at around 80 °C and pH 3 [7]. Sulfolobus species are able to grow aerobically and can be readily cultivated on a laboratory scale. These organisms became a model organism for Crenarchaeota and for adaption processes to extreme environments [8][9][10][11][12][13]. Sulfolobus species were found in solfataric fields all over the world[ 14]. A major drawback of cultivating this organism was the lack of a defined cultivation medium. -
Extremophiles-Basic Concepts
CONTENTS CONTENTS EXTREMOPHILES Extremophiles - Volume 1 No. of Pages: 396 ISBN: 978-1-905839-93-3 (eBook) ISBN: 978-1-84826-993-4 (Print Volume) Extremophiles - Volume 2 No. of Pages: 392 ISBN: 978-1-905839-94-0 (eBook) ISBN: 978-1-84826-994-1 (Print Volume) Extremophiles - Volume 3 No. of Pages: 364 ISBN: 978-1-905839-95-7 (eBook) ISBN: 978-1-84826-995-8 (Print Volume) For more information of e-book and Print Volume(s) order, please click here Or contact : [email protected] ©Encyclopedia of Life Support Systems (EOLSS) EXTREMOPHILES CONTENTS VOLUME I Extremophiles: Basic Concepts 1 Charles Gerday, Laboratory of Biochemistry, University of Liège, Belgium 1. Introduction 2. Effects of Extreme Conditions on Cellular Components 2.1. Membrane Structure 2.2. Nucleic Acids 2.2.1. Introduction 2.2.2. Desoxyribonucleic Acids 2.2.3. Ribonucleic Acids 2.3. Proteins 2.3.1. Introduction 2.3.2. Thermophilic Proteins 2.3.2.1. Enthalpically Driven Stabilization Factors: 2.3.2.2. Entropically Driven Stabilization Factors: 2.3.3. Psychrophilic Proteins 2.3.4. Halophilic Proteins 2.3.5. Piezophilic Proteins 2.3.5.1. Interaction with Other Proteins and Ligands: 2.3.5.2. Substrate Binding and Catalytic Efficiency: 2.3.6. Alkaliphilic Proteins 2.3.7. Acidophilic Proteins 3. Conclusions Extremophiles: Overview of the Biotopes 43 Michael Gross, University of London, London, UK 1. Introduction 2. Extreme Temperatures 2.1. Terrestrial Hot Springs 2.2. Hot Springs on the Ocean Floor and Black Smokers 2.3. Life at Low Temperatures 3. High Pressure 3.1. -
4 Metabolic and Taxonomic Diversification in Continental Magmatic Hydrothermal Systems
Maximiliano J. Amenabar, Matthew R. Urschel, and Eric S. Boyd 4 Metabolic and taxonomic diversification in continental magmatic hydrothermal systems 4.1 Introduction Hydrothermal systems integrate geological processes from the deep crust to the Earth’s surface yielding an extensive array of spring types with an extraordinary diversity of geochemical compositions. Such geochemical diversity selects for unique metabolic properties expressed through novel enzymes and functional characteristics that are tailored to the specific conditions of their local environment. This dynamic interaction between geochemical variation and biology has played out over evolu- tionary time to engender tightly coupled and efficient biogeochemical cycles. The timescales by which these evolutionary events took place, however, are typically in- accessible for direct observation. This inaccessibility impedes experimentation aimed at understanding the causative principles of linked biological and geological change unless alternative approaches are used. A successful approach that is commonly used in geological studies involves comparative analysis of spatial variations to test ideas about temporal changes that occur over inaccessible (i.e. geological) timescales. The same approach can be used to examine the links between biology and environment with the aim of reconstructing the sequence of evolutionary events that resulted in the diversity of organisms that inhabit modern day hydrothermal environments and the mechanisms by which this sequence of events occurred. By combining molecu- lar biological and geochemical analyses with robust phylogenetic frameworks using approaches commonly referred to as phylogenetic ecology [1, 2], it is now possible to take advantage of variation within the present – the distribution of biodiversity and metabolic strategies across geochemical gradients – to recognize the extent of diversity and the reasons that it exists. -
Electrical Current Generation in Microbial Electrolysis Cells by Hyperthermophilic Archaea Ferroglobus Placidus and Geoglobus Ahangari
Bioelectrochemistry 119 (2018) 142–149 Contents lists available at ScienceDirect Bioelectrochemistry journal homepage: www.elsevier.com/locate/bioelechem Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari Yasemin D. Yilmazel a,b,⁎, Xiuping Zhu b,c,Kyoung-YeolKimb,DawnE.Holmesd, Bruce E. Logan b a Department of Chemical Engineering, Rochester Institute of Technology, Rochester, NY, USA b Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA c Department of Civil and Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA d Department of Biology, Western New England University, Springfield, MA, USA article info abstract Article history: Few microorganisms have been examined for current generation under thermophilic (40–65 °C) or hyperther- Received 5 May 2017 mophilic temperatures (≥80 °C) in microbial electrochemical systems. Two iron-reducing archaea from the fam- Received in revised form 27 September 2017 ily Archaeoglobaceae, Ferroglobus placidus and Geoglobus ahangari, showed electro-active behavior leading to Accepted 28 September 2017 current generation at hyperthermophilic temperatures in single-chamber microbial electrolysis cells (MECs). A Available online 02 October 2017 current density (j) of 0.68 ± 0.11 A/m2 was attained in F. placidus MECs at 85 °C, and 0.57 ± 0.10 A/m2 in G. ahangari MECs at 80 °C, with an applied voltage of 0.7 V. Cyclic voltammetry (CV) showed that both strains pro- Keywords: − − Hyperthermophilic archaea duced a sigmoidal catalytic wave, with a mid-point potential of 0.39 V (vs. Ag/AgCl) for F. placidus and 0.37 V Ferroglobus placidus for G. -
International Code of Nomenclature of Prokaryotes
2019, volume 69, issue 1A, pages S1–S111 International Code of Nomenclature of Prokaryotes Prokaryotic Code (2008 Revision) Charles T. Parker1, Brian J. Tindall2 and George M. Garrity3 (Editors) 1NamesforLife, LLC (East Lansing, Michigan, United States) 2Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig, Germany) 3Michigan State University (East Lansing, Michigan, United States) Corresponding Author: George M. Garrity ([email protected]) Table of Contents 1. Foreword to the First Edition S1–S1 2. Preface to the First Edition S2–S2 3. Preface to the 1975 Edition S3–S4 4. Preface to the 1990 Edition S5–S6 5. Preface to the Current Edition S7–S8 6. Memorial to Professor R. E. Buchanan S9–S12 7. Chapter 1. General Considerations S13–S14 8. Chapter 2. Principles S15–S16 9. Chapter 3. Rules of Nomenclature with Recommendations S17–S40 10. Chapter 4. Advisory Notes S41–S42 11. References S43–S44 12. Appendix 1. Codes of Nomenclature S45–S48 13. Appendix 2. Approved Lists of Bacterial Names S49–S49 14. Appendix 3. Published Sources for Names of Prokaryotic, Algal, Protozoal, Fungal, and Viral Taxa S50–S51 15. Appendix 4. Conserved and Rejected Names of Prokaryotic Taxa S52–S57 16. Appendix 5. Opinions Relating to the Nomenclature of Prokaryotes S58–S77 17. Appendix 6. Published Sources for Recommended Minimal Descriptions S78–S78 18. Appendix 7. Publication of a New Name S79–S80 19. Appendix 8. Preparation of a Request for an Opinion S81–S81 20. Appendix 9. Orthography S82–S89 21. Appendix 10. Infrasubspecific Subdivisions S90–S91 22. Appendix 11. The Provisional Status of Candidatus S92–S93 23. -
The Oligomeric State of the Active Vps4 AAA Atpase
NIH Public Access Author Manuscript J Mol Biol. Author manuscript; available in PMC 2015 February 06. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: J Mol Biol. 2014 February 6; 426(3): 510–525. doi:10.1016/j.jmb.2013.09.043. The oligomeric state of the active Vps4 AAA ATPase Nicole Monroe1, Han Han1, Malgorzata D. Gonciarz1,2, Debra M. Eckert1, Mary Anne Karren1, Frank G. Whitby1, Wesley I. Sundquist1,*, and Christopher P. Hill1,* 1Department of Biochemistry, University of Utah School of Medicine, 15 N Medical Drive East RM 4100, Salt Lake City, UT 84112-5650, USA Abstract The cellular ESCRT pathway drives membrane constriction toward the cytosol and effects membrane fission during cytokinesis, endosomal sorting, and the release of many enveloped viruses, including HIV. A component of this pathway, the AAA ATPase Vps4, provides energy for pathway progression. Although it is established that Vps4 functions as an oligomer, subunit stoichiometry and other fundamental features of the functional enzyme are unclear. Higher-order oligomers have thus far only been characterized for a Walker B mutant of Vps4 in the presence of ATP. Here, we report that although some mutant Vps4 proteins form dodecameric assemblies, active wild-type S. cerevisiae and S. solfataricus Vps4 enzymes can form hexamers in the presence of ATP and ADP, as assayed by size exclusion chromatography and equilibrium analytical ultracentifugation. The Vta1p activator binds hexameric yeast Vps4p without changing the oligomeric state of Vps4p, implying that the active Vta1p:Vps4p complex also contains a single hexameric ring.