Microorganisms in the Environment − Unique Adaptations, Basic Metabolism, and Evolution
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A Virus That Infects a Hyperthermophile Encapsidates A-Form
RESEARCH | REPORTS we observe sets of regulatory sites that exhibit Illumina, Inc. One or more embodiments of one or more patents SUPPLEMENTARY MATERIALS patterns of coordinated regulation (e.g., LYN, and patent applications filed by Illumina may encompass the www.sciencemag.org/content/348/6237/910/suppl/DC1 encoding a tyrosine kinase involved in B cell methods, reagents, and data disclosed in this manuscript. All Materials and Methods methods for making the transposase complexes are described in signaling) (Fig. 4B), although reproducibility of Figs. S1 to S22 (18); however, Illumina will provide transposase complexes in Tables S1 and S2 these patterns across biological replicates was response to reasonable requests from the scientific community References (24–39) modest (fig. S22). Given the sparsity of the data, subject to a material transfer agreement. Some work in this study identifying pairs of coaccessible DNA elements is related to technology described in patent applications 19 March 2015; accepted 24 April 2015 WO2014142850, 2014/0194324, 2010/0120098, 2011/0287435, Published online 7 May 2015; within individual loci is statistically challenging 2013/0196860, and 2012/0208705. 10.1126/science.aab1601 and merits further development. We report chromatin accessibility maps for >15,000 single cells. Our combinatorial cellular indexing scheme could feasibly be scaled to col- VIROLOGY lect data from ~17,280 cells per experiment by using 384-by-384 barcoding and sorting 100 nu- clei per well (assuming similar cell recovery and A virus that infects a collision rates) (fig. S1) (19). Particularly as large- scale efforts to build a human cell atlas are con- templated (23), it is worth noting that because hyperthermophile encapsidates DNA is at uniform copy number, single-cell chro- matin accessibility mapping may require far fewer A-form DNA reads per single cell to define cell types, relative to single-cell RNA-seq. -
Extremely Thermophilic Microorganisms As Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals
REVIEW published: 05 November 2015 doi: 10.3389/fmicb.2015.01209 Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals Benjamin M. Zeldes 1, Matthew W. Keller 2, Andrew J. Loder 1, Christopher T. Straub 1, Michael W. W. Adams 2 and Robert M. Kelly 1* 1 Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point Edited by: that the use of these microorganisms as metabolic engineering platforms has become Bettina Siebers, University of Duisburg-Essen, possible. While in its early days, complex metabolic pathways have been altered or Germany engineered into recombinant extreme thermophiles, such that the production of fuels and Reviewed by: chemicals at elevated temperatures has become possible. Not only does this expand the Haruyuki Atomi, thermal range for industrial biotechnology, it also potentially provides biodiverse options Kyoto University, Japan Phillip Craig Wright, for specific biotransformations unique to these microorganisms. The list of extreme University of Sheffield, UK thermophiles growing optimally between 70 and 100◦C with genetic toolkits currently *Correspondence: available includes archaea and bacteria, aerobes and anaerobes, coming from genera Robert M. -
2003 Archaea: Ecology, Metabolism and Molecular Biology
GORDON RESEARCH CONFERENCES frontiers of science P.O. Box 984, West Kingston, RI 02892-0984 Phone: 401 783-4011 Fax: 401 783-7644 E-Mail: [email protected] World Wide Web: http://www.grc.org founded in 1931 Nancy Ryan Gray, Ph.D. Director 2003 GORDON RESEARCH CONFERENCE on 2003 Archaea: Ecology, Metabolism and Molecular Biology FINAL PROGRESS REPORT DOE DE-FG02-03ER15432 The Gordon Research Conference (GRC) on 2003 Archaea: Ecology, Metabolism and Molecular Biology was held at Proctor Academy, Andover, NH from August 3-8, 2003. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, "free time" was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field. I want to personally thank you for your support of this Conference. As you know, in the interest of promoting the presentation of unpublished and frontier- breaking research, Gordon Research Conferences does not permit publication of meeting proceedings. -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
A Korarchaeal Genome Reveals Insights Into the Evolution of the Archaea
A korarchaeal genome reveals insights into the evolution of the Archaea James G. Elkinsa,b, Mircea Podarc, David E. Grahamd, Kira S. Makarovae, Yuri Wolfe, Lennart Randauf, Brian P. Hedlundg, Ce´ line Brochier-Armaneth, Victor Kunini, Iain Andersoni, Alla Lapidusi, Eugene Goltsmani, Kerrie Barryi, Eugene V. Koonine, Phil Hugenholtzi, Nikos Kyrpidesi, Gerhard Wannerj, Paul Richardsoni, Martin Kellerc, and Karl O. Stettera,k,l aLehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, D-93053 Regensburg, Germany; cBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831; dDepartment of Chemistry and Biochemistry, University of Texas, Austin, TX 78712; eNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; fDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; gSchool of Life Sciences, University of Nevada, Las Vegas, NV 89154; hLaboratoire de Chimie Bacte´rienne, Unite´ Propre de Recherche 9043, Centre National de la Recherche Scientifique, Universite´de Provence Aix-Marseille I, 13331 Marseille Cedex 3, France; iU.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; jInstitute of Botany, Ludwig Maximilians University of Munich, D-80638 Munich, Germany; and kInstitute of Geophysics and Planetary Physics, University of California, Los Angeles, CA 90095 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, April 2, 2008 (received for review January 7, 2008) The candidate division Korarchaeota comprises a group of uncul- and sediment samples from Obsidian Pool as an inoculum. The tivated microorganisms that, by their small subunit rRNA phylog- cultivation system supported the stable growth of a mixed commu- eny, may have diverged early from the major archaeal phyla nity of hyperthermophilic bacteria and archaea including an or- Crenarchaeota and Euryarchaeota. -
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. -
Do Ultrastable Proteins from Hyperthermophiles Have High Or Low Conformational Rigidity?
Commentary Do ultrastable proteins from hyperthermophiles have high or low conformational rigidity? Rainer Jaenicke* Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany ife on earth has an unbelievable adaptive parisons of their protein inventories with Lcapacity. Except for centers of volcanic those of suitable mesophilic counterparts, a activity, the entire surface of our planet is a wealth of data has been accumulated that biosphere. In this context, the most surpris- indicated that stabilization involves all levels ing discovery in our lifetime was the expan- of the hierarchy of protein structure, i.e., sion from the anthropocentrically defined secondary, supersecondary, tertiary, and ‘‘normal temperature’’ of mesophiles quaternary interactions. The common con- (Ͻ40°C) to the optimum temperature range clusion from model studies was that the of hyperthermophiles around and above the stability of proteins from extremophiles is boiling point of water. That in this class of optimized to maintain corresponding func- microorganisms high temperature is re- tional states under a given set of environ- quired for growth rather than tolerated im- mental conditions. For the standard state at plies that the whole repertoire of their bi- 25°C, enhanced thermal stability of hyper- omolecules must be sufficiently stable to thermophile proteins would then be the allow the cellular microcosm to work. The result of enhanced conformational rigidity Fig. 1. Three-dimensional structure of rubre- strategies nature has used to stabilize the in their folded native state (5). doxin from P. furiosus. Numbered residues mark inventory of the cell, especially proteins, Evidence from recent amide hydrogen the most slowly exchanging hydrogens, close to under extreme conditions are still enig- exchange experiments reported in this is- the two cysteine knuckles (7–9). -
Bhattacharya.1999.Thermophiles.Pdf
THE PHYLOGENY OF THERMOPHILES AND HYPERTHERMOPHILES AND THE THREE DOMAINS OF LIFE The Phylogeny of Thermophiles DEBASHISH BHATTACHARYA University of Iowa Department of Biological Sciences Biology Building, Iowa City, Iowa 52242-1324 United States THOMAS FRIEDL Department of Biology, General Botany University of Kaiserslautern P.O. Box 3049, D-67653 Kaiserslautern, Germany HEIKO SCHMIDT Deutsches Krebsforschungszentrum Theoretische Bioinformatik Im Neuenheimer Feld 280 , D-69120 Heidelberg, Germany 1. Introduction The nature of the first cells and the environment in which they lived are two of the most interesting problems in evolutionary biology. All living things are descendents of these primordial cells and are divided into three fundamental lineages or domains, Archaea (formerly known as Archaebacteria), Bacteria (formerly known as Eubacteria), and the Eucarya (formerly known as Eukaryotes, Woese et al. 1990). The Archaea and Bacteria are prokaryotic domains whereas the Eucarya includes all other living things that have a nucleus (i.e., the genetic material is separated from the cytoplasm by a nuclear envelope). The observation of the three primary domains, first made on the basis of small subunit (i.e., 16S, 18S) ribosomal DNA (rDNA) sequence comparisons (Woese 1987), has created a framework with which the nature of the last common ancestor (LCA) can be addressed. In this review we present phylogenies of the prokaryotic domains to understand the origin and distribution of the thermophiles (organisms able to grow in temperatures > 45°C) and the hyperthermophiles (organisms able to grow in temperatures > 80°C). Hyperthermophiles are limited to the Archaea and Bacteria. In addition, we inspect the distribution of extremophiles within the cyanobacteria. -
The Archaeal Concept and the World It Lives In: a Retrospective
Carl R. Woese (center) with His Majesty Carl XVI Gustaf of Sweden and Queen Silvia on the occassion of his receiving the 2003 Crafoord Prize, given by the Royal Swedish Academy of Sciences. Photo credit: Royal Swedish Academy of Sciences. Photosynthesis Research 80: 361–372, 2004. 363 © 2004 Kluwer Academic Publishers. Printed in the Netherlands. Personal perspective The archaeal concept and the world it lives in: a retrospective Carl R. Woese Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemical and Life Sciences Laboratory, 601 South Goodwin Ave, Urbana, IL 61801-3709, USA (e-mail: [email protected]; fax: +1-217-244-6697) Received 9 July 2003; accepted in revised form 30 August 2003 Key words: archaea, evolution, genomics, molecular phylogeny, phylogenetic reconstruction, ribosomal RNA Abstract The present retrospective concerns the discovery and development of the archaea, the so-called ‘third form of life’ that no one anticipated and many did not, and still do not want. In its birth pangs, which the archaea had a plenty, the concept encountered biology unmasked; for it ran up against some of the key struts in the 20th century biological edifice. Consequently, the history of the development of the archaeal concept provides an excellent window on certain of the weaknesses in the 20th century biology paradigm, weaknesses that have now led that paradigm to a conceptual dead end. On the other hand, the archaeal concept has also provided us one of the pillars on which a new holistic paradigm for biology can be built. So, it would seem of value to retrace some of the twists and turns in the history of the development of the archaeal concept. -
Chapter 6 of Discover the World of Microbes
Some like it hot I.A.L. Diamond and Billy Wilder Chapter 6 Life in b oiling w ater The press most likely did not highlight the report of Thomas Brock (Bloomington, Indiana; later Madison, Wisconsin, USA) in 1969 on the isolation of a bacterium from a pond in Yellowstone National Park. This bacterium, Thermus aquaticus, grows at 70 ° C (nearly 160 ° F). Every molecular biologist or microbiologist is famil- iar with the enzyme Taq polymerase, which was isolated from T. aquaticus and has proved essential for the PCR technique used for analysis of trace amounts of DNA (see Chapter 25 ). Growth at 70 ° C s ounds p retty e xciting, b ut i t ’ s f ar from the 100 ° C (212 ° F ) at w hich w ater b oils! Just wait a few minutes. Brock then isolated an organism that grows at 80 ° C, Sul- folobus acidocaldarius . Among microbiologists, these reports aroused an interest in microorganisms growing at high temperatures, so sites in the immediate vicinity of volcanoes or geysers, where it spits and sputters, became the hunting grounds of microbiologists. Two German microbiologists from Munich, Wolfgang Zillig (1925 – 2005) and Karl Otto Stetter, were especially eager to isolate and characterize microorganisms growing in boiling water. First, they studied the sulfur - oxidizing Sulfolobus species from the Solfatara volcanic crater near Naples, Italy, then they concentrated on hot springs in Iceland. It is no easy task to take samples at such hostile sites and to then demonstrate in the samples the presence of living organ- isms that can be grown in cultures and are able to yield a suffi cient cell mass for detailed studies. -
ATP Synthases from Archaea: the Beauty of a Molecular Motor
Biochimica et Biophysica Acta 1837 (2014) 940–952 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Review ATP synthases from archaea: The beauty of a molecular motor Gerhard Grüber a,⁎, Malathy Sony Subramanian Manimekalai a, Florian Mayer b, Volker Müller b,⁎ a School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore b Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany article info abstract Article history: Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot tem- Received 13 November 2013 peratures. How energy is conserved under such harsh environmental conditions is a major question in cellular Received in revised form 7 March 2014 bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class Accepted 11 March 2014 of ATP synthases distinct from the F F ATP synthase ATP synthase found in bacteria, mitochondria and chloro- Available online 17 March 2014 1 O plasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar- Keywords: like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase dur- ATPase ing rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic Na+ bioenergetics energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and Energy conservation subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this Methanogenesis unique class of ATP synthases. -
Extremophiles — Link Between Earth and Astrobiology
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Directory of Open Access Journals Zbornik Matice srpske za prirodne nauke / Proc. Nat. Sci, Matica Srpska Novi Sad, ¥ 114, 5—16, 2008 UDC 133.52:57 Dejan B. Stojanoviã1 , Oliver O. Fojkar2 , Aleksandra V. Drobac-Åik1 , Kristina O. Åajko3 , Tamara I. Duliã1 ,ZoricaB.Sviråev1 1 Faculty of Sciences, Department of Biology and Ecology, Trg Dositeja Obradoviãa 2, 21000 Novi Sad, Serbia 2 Institute for nature conservation of Serbia, Radniåka 20A, 21000 Novi Sad, Serbia 3 Faculty of Sciences, Department of Physics, Trg Dositeja Obradoviãa 4, 21000 Novi Sad, Serbia EXTREMOPHILES — LINK BETWEEN EARTH AND ASTROBIOLOGY ABSTRACT: Astrobiology studies the origin, evolution, distribution and future of life in the universe. The most promising worlds in Solar system, beyond Earth, which may har- bor life are Mars and Jovian moon Europa. Extremophiles are organisms that thrive on the edge of temperature, hypersalinity, pH extremes, pressure, dryness and so on. In this paper, some extremophile cyanobacteria have been discussed as possible life forms in a scale of astrobiology. Samples were taken from solenetz and solonchak types of soil from the Voj- vodina region. The main idea in this paper lies in the fact that high percentage of salt found in solonchak and solonetz gives the possibility of comparison these types of soil with “soil" on Mars, which is also rich in salt. KEYWORDS: Astrobiology, extremophiles, cyanobacteria, halophiles 1. INTRODUCTION 1.1. About astrobiology Astrobiology studies the origin, evolution, distribution and future of life in the universe.