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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. -
Histone Variants in Archaea and the Evolution of Combinatorial Chromatin Complexity
Histone variants in archaea and the evolution of combinatorial chromatin complexity Kathryn M. Stevensa,b, Jacob B. Swadlinga,b, Antoine Hochera,b, Corinna Bangc,d, Simonetta Gribaldoe, Ruth A. Schmitzc, and Tobias Warneckea,b,1 aMolecular Systems Group, Quantitative Biology Section, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom; bInstitute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom; cInstitute for General Microbiology, University of Kiel, 24118 Kiel, Germany; dInstitute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany; and eDepartment of Microbiology, Unit “Evolutionary Biology of the Microbial Cell,” Institut Pasteur, 75015 Paris, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved October 28, 2020 (received for review April 14, 2020) Nucleosomes in eukaryotes act as platforms for the dynamic inte- additional histone dimers can be taggedontothistetramertoyield gration of epigenetic information. Posttranslational modifications oligomers of increasing length that wrap correspondingly more DNA are reversibly added or removed and core histones exchanged for (3, 6–9). Almost all archaeal histones lack tails and PTMs have yet to paralogous variants, in concert with changing demands on tran- be reported. Many archaea do, however, encode multiple histone scription and genome accessibility. Histones are also common in paralogs (8, 10) that can flexibly homo- and heterodimerize in -
Implantation Du Microbiote Et Mise En Place Des Fonctions Du Rumen Chez Le Veau De Race Laitière Et Effet De La Supplémentation En Levures Vivantes
En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par : Institut National Polytechnique de Toulouse (INP Toulouse) Discipline ou spécialité : Pathologie, Toxicologie, Génétique et Nutrition Présentée et soutenue par : Mickael Rey Le : 15 novembre 2012 Titre : Implantation du microbiote et mise en place des fonctions du rumen chez le veau de race laitière et effet de la supplémentation en levures vivantes Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : UMR 1289 INRA-INP/ENSAT-ENVT ‘TANDEM’ Directeur(s) de Thèse : Valérie Monteils Francis Enjalbert Rapporteurs : Evelyne Forano Véronique Julliand Membre(s) du jury: Evelyne Forano Véronique Julliand Gérard Fonty Valérie Monteils Francis Enjalbert 1 2 REMERCIEMENTS Ce manuscrit de thèse vient clôturer une belle expérience scientifique et humaine qui a été réalisée au sein de l’UMR 1289 TANDEM (Tissus Animaux, Nutrition, Digestion, Ecosystème, Métabolisme). Pour cela, je souhaiterai remercier toutes les personnes ayant contribué de près ou de loin à l’aboutissement de ce projet. Je tiens à remercier les personnes qui ont accepté de participer à mon jury de thèse : Evelyne Forano (Unité de Microbiologie, INRA, Clermont-Ferrand-Theix), Véronique Julliand (AgroSup Dijon, D2A2E, URANIE-USC INRA Nutrition du cheval athlète, Dijon), pour m’avoir fait l’honneur d’être rapporteurs de cette thèse. Mais aussi Gérard Fonty (Microorganismes : Génome et Environnement, CNRS, Aubière Cedex. France) pour avoir accepté de participer à ce jury et m’avoir fait l’honneur d’en être le président. Je tiens à remercier mes directeurs de thèse, Francis Enjalbert et Valérie Monteils pour leurs encadrements et leurs qualités scientifiques et pédagogiques qui m’ont permis de structurer mon travail au cours de ces trois années. -
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. -
Biotechnology of Archaea- Costanzo Bertoldo and Garabed Antranikian
BIOTECHNOLOGY– Vol. IX – Biotechnology Of Archaea- Costanzo Bertoldo and Garabed Antranikian BIOTECHNOLOGY OF ARCHAEA Costanzo Bertoldo and Garabed Antranikian Technical University Hamburg-Harburg, Germany Keywords: Archaea, extremophiles, enzymes Contents 1. Introduction 2. Cultivation of Extremophilic Archaea 3. Molecular Basis of Heat Resistance 4. Screening Strategies for the Detection of Novel Enzymes from Archaea 5. Starch Processing Enzymes 6. Cellulose and Hemicellulose Hydrolyzing Enzymes 7. Chitin Degradation 8. Proteolytic Enzymes 9. Alcohol Dehydrogenases and Esterases 10. DNA Processing Enzymes 11. Archaeal Inteins 12. Conclusions Glossary Bibliography Biographical Sketches Summary Archaea are unique microorganisms that are adapted to survive in ecological niches such as high temperatures, extremes of pH, high salt concentrations and high pressure. They produce novel organic compounds and stable biocatalysts that function under extreme conditions comparable to those prevailing in various industrial processes. Some of the enzymes from Archaea have already been purified and their genes successfully cloned in mesophilic hosts. Enzymes such as amylases, pullulanases, cyclodextrin glycosyltransferases, cellulases, xylanases, chitinases, proteases, alcohol dehydrogenase,UNESCO esterases, and DNA-modifying – enzymesEOLSS are of potential use in various biotechnological processes including in the food, chemical and pharmaceutical industries. 1. Introduction SAMPLE CHAPTERS The industrial application of biocatalysts began in 1915 with the introduction of the first detergent enzyme by Dr. Röhm. Since that time enzymes have found wider application in various industrial processes and production (see Enzyme Production). The most important fields of enzyme application are nutrition, pharmaceuticals, diagnostics, detergents, textile and leather industries. There are more than 3000 enzymes known to date that catalyze different biochemical reactions among the estimated total of 7000; only 100 enzymes are being used industrially. -
S-Layer and Cytoplasmic Membrane – Exceptions from the Typical Archaeal Cell Wall with a Focus on Double Membranes
MINI REVIEW ARTICLE published: 25 November 2014 doi: 10.3389/fmicb.2014.00624 S-layer and cytoplasmic membrane – exceptions from the typical archaeal cell wall with a focus on double membranes Andreas Klingl* Plant Development, Department of Biology, Biocenter LMU Munich – Botany, Ludwig Maximilian University Munich, Munich, Germany Edited by: The common idea of typical cell wall architecture in archaea consists of a pseudo-crystalline Sonja-Verena Albers, University of proteinaceous surface layer (S-layer), situated upon the cytoplasmic membrane.This is true Freiburg, Germany for the majority of described archaea, hitherto. Within the crenarchaea, the S-layer often Reviewed by: represents the only cell wall component, but there are various exceptions from this wall Jerry Eichler, Ben-Gurion University of the Negev, Israel architecture. Beside (glycosylated) S-layers in (hyper)thermophilic cren- and euryarchaea Benjamin Harry Meyer, University of as well as halophilic archaea, one can find a great variety of other cell wall structures like Freiburg, Germany proteoglycan-like S-layers (Halobacteria), glutaminylglycan (Natronococci), methanochon- *Correspondence: droitin (Methanosarcina) or double layered cell walls with pseudomurein (Methanothermus Andreas Klingl, Plant Development, and Methanopyrus). The presence of an outermost cellular membrane in the crenarchaeal Department of Biology, Biocenter LMU Munich – Botany, Ludwig species Ignicoccus hospitalis already gave indications for an outer membrane similar to Maximilian University Munich, Gram-negative bacteria. Although there is just limited data concerning their biochemistry Grosshaderner Street 2–4, and ultrastructure, recent studies on the euryarchaeal methanogen Methanomassiliicoccus Planegg-Martinsried 82152, Munich, Germany luminyensis, cells of the ARMAN group, and the SM1 euryarchaeon delivered further e-mail: andreas.klingl@biologie. -
Taxonomy and Ecology of Methanogens
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Horizon / Pleins textes FEMS Microbiology Reviews 87 (1990) 297-308 297 Pubfished by Elsevier FEMSRE 00180 Taxonomy and ecology of methanogens J.L. Garcia Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France Key words: Methanogens; Archaebacteria; Taxonomy; Ecology 1. INTRODUCTION methane from CO2 using alcohols as hydrogen donors; 2-propanol is oxidized to acetone, and More fhan nine reviews on taxonomy of 2-butanol to 2-butanone. Carbon monoxide may methanogens have been published during the last also be converted into methane; most hydro- decade [l-91, after the discovery of the unique genotrophic species (60%) will also use formate. biochemical and genetic properties of these Some aceticlastic species are incapable of oxidiz- organisms led to the concept of Archaebacteria at ing H,. The aceticlastic species of the genus the end of the seventies. Moreover, important Methanosurcina are the most metabolically diverse economic factors have ,placed these bacteria in the methanogens, whereas the obligate aceticlastic limelight [5], including the need to develop alter- Methanosaeta (Methanothrix) can use only acetate. native forms of energy, xenobiotic pollution con- The taxonomy of the methanogenic bacteria trol, the enhancement of meat yields in the cattle has been extensively revised in the light of new industry, the distinction between biological and information based on comparative studies of 16 S thermocatalytic petroleum generation, and the rRNA oligonucleotide sequences, membrane lipid global distribution of methane in the earth's atmo- composition, and antigenic fingerprinting data. sphere. The phenotypic characteristics often do not pro- vide a sufficient means of distinguishing among taxa or determining the phylogenetic position of a 2. -
Hydrogen Stress and Syntrophy of Hyperthermophilic Heterotrophs and Methanogens
University of Massachusetts Amherst ScholarWorks@UMass Amherst Doctoral Dissertations Dissertations and Theses July 2018 HYDROGEN STRESS AND SYNTROPHY OF HYPERTHERMOPHILIC HETEROTROPHS AND METHANOGENS Begum Topcuoglu University of Massachusetts Amherst Follow this and additional works at: https://scholarworks.umass.edu/dissertations_2 Part of the Environmental Microbiology and Microbial Ecology Commons, and the Microbial Physiology Commons Recommended Citation Topcuoglu, Begum, "HYDROGEN STRESS AND SYNTROPHY OF HYPERTHERMOPHILIC HETEROTROPHS AND METHANOGENS" (2018). Doctoral Dissertations. 1299. https://doi.org/10.7275/11912692.0 https://scholarworks.umass.edu/dissertations_2/1299 This Open Access Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. HYDROGEN STRESS AND SYNTROPHY OF HYPERTHERMOPHILIC HETEROTROPHS AND METHANOGENS A Dissertation Presented by BEGÜM D. TOPÇUOĞLU Submitted to the Graduate School of the University of Massachusetts Amherst in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY May 2018 Microbiology © Copyright by Begüm Topçuoğlu 2018 All Rights Reserved HYDROGEN STRESS AND SYNTROPHY OF HYPERTHERMOPHILIC HETEROTROPHS AND METHANOGENS A Dissertation Presented by BEGÜM D. TOPÇUOĞLU Approved as to style and content by: ____________________________________ -
Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB List No
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY, OCt. 1986, p. 573-576 Vol. 36, No. 4 0020-7713/86/040573-04$~2.OO/O Copyright 0 1986, International Union of Microbiological Societies Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB List No. 22t The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedufe described previously (Int. J. Syst. Bacteriol. 27(3):iv, 1977). Authors and other individuals wishing to have new names and/or combinations included in future lists should send the pertinent reprint or a photocopy thereof to the IJSB for confirmation that all of the other requirements for valid publication have been met. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, arid these authors’ names will be included in the author index of the present issue and in the volume author index in this issue of the IJSB. Inclusion of a name on these lists validates the name and thereby makes it available in bacteriological nomenclature. The, inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organism may be transferred to another genus, thus necessitating the creation of a new combination. -
Phylogenetic- and Genome-Derived Insight Into the Evolution of N-Glycosylation in Archaea ⇑ Lina Kaminski A, Mor N
Molecular Phylogenetics and Evolution 68 (2013) 327–339 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea ⇑ Lina Kaminski a, Mor N. Lurie-Weinberger b, Thorsten Allers c, Uri Gophna b, Jerry Eichler a, a Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel b Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel c School of Biology, University of Nottingham, Nottingham NG7 2UH, UK article info abstract Article history: N-glycosylation, the covalent attachment of oligosaccharides to target protein Asn residues, is a post- Received 25 January 2013 translational modification that occurs in all three domains of life. In Archaea, the N-linked glycans that Revised 23 March 2013 decorate experimentally characterized glycoproteins reveal a diversity in composition and content Accepted 26 March 2013 unequaled by their bacterial or eukaryal counterparts. At the same time, relatively little is known of Available online 6 April 2013 archaeal N-glycosylation pathways outside of a handful of model strains. To gain insight into the distri- bution and evolutionary history of the archaeal version of this universal protein-processing event, 168 Keywords: archaeal genome sequences were scanned for the presence of aglB, encoding the known archaeal oli- Archaea gosaccharyltransferase, an enzyme key to N-glycosylation. Such analysis predicts the presence of AglB N-glycosylation Oligosaccharyltransferase in 166 species, with some species seemingly containing multiple versions of the protein. Phylogenetic analysis reveals that the events leading to aglB duplication occurred at various points during archaeal evolution. -
Hyperthermophilic Microorganisms
FEMS Microbiology Reviews 75 (1990) 117-124 Published by Elsevier FEMSRE 00133 Hyperthermophilic microorganisms K.O. Steuer, G. Fiala, G. Huber, R. Huber and A. Segerer Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, F.R.G. Key words: Hyperthermophiles; Taxonomy 1. INTRODUCTION 7 to 9) rich in NaCl. Also man-made hot environ• ments such as the boiling outflows of geothermal The most extremely thermophilic living beings power plants are suitable environments for hyper• known to date are bacteria growing at tempera• thermophiles [9]. Submarine hydrothermal systems tures between 80 and 110 °C [1-3]. Some of them are slightly acidic to alkaline (pH 5 to 8.5) and are so well adapted to the high temperatures that normally contain high amounts of NaCl and SO4 ~ they do not even grow below 80 ° C [4]. As a rule, due to the presence of sea water (Table 1). Due to non of these hyperthermophilic bacteria are able the low solubility of oxygen at high temperatures to grow at 60 ° C or below. Hyperthermophiles are and the presence of reducing gases, most biotopes occurring mainly within the archaebacterial king• of hyperthermophiles are anaerobic. Within con• dom [5]; some of them are also present within the tinental solfataric fields, oxygen is only present eubacteria [6,7]. Due to their existence within within the upper acidic layer which appears phylogenetically highly divergent groups, the lack ochre-coloured due to the existence of ferric iron of closely related mesophiles, and their biotopes [8]. existing already since the Archean age, hyperther• Although not growing below 60 °C, hyperther• mophiles may have adapted to the hot environ• mophiles are able to survive at low temperatures ment already billions of years ago.