Extremophiles
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The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
SUPPLEMENTARY INFORMATIONARTICLES https://doi.org/10.1038/s41559-020-1221-7 In the format provided by the authors and unedited. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. -
Extreme Organisms on Earth Show Us Just How Weird Life Elsewhere Could Be. by Chris Impey Astrobiology
Astrobiology Extreme organisms on Earth show us just how weird life elsewhere could be. by Chris Impey How life could thrive on hostile worlds Humans have left their mark all over Earth. We’re proud of our role as nature’s generalists — perhaps not as swift as the gazelle or as strong as the gorilla, but still pretty good at most things. Alone among all species, technology has given us dominion over the planet. Humans are endlessly plucky and adaptable; it seems we can do anything. Strain 121 Yet in truth, we’re frail. From our safe living rooms, we may admire the people who conquer Everest or cross deserts. But without technology, we couldn’t live beyond Earth’s temperate zones. We cannot survive for long in temperatures below freezing or above 104° Fahrenheit (40° Celsius). We can stay underwater only as long as we can hold our breath. Without water to drink we’d die in 3 days. Microbes, on the other hand, are hardy. And within the microbial world lies a band of extremists, organisms that thrive in conditions that would cook, crush, smother, and dissolve most other forms of life. Collectively, they are known as extremophiles, which means, literally, “lovers of extremes.” Extremophiles are found at temperatures above the boiling point and below the freezing point of water, in high salinity, and in strongly acidic conditions. Some can live deep inside rock, and others can go into a freeze-dried “wait state” for tens of thousands of years. Some of these microbes harvest energy from meth- ane, sulfur, and even iron. -
A DNA Ligase from the Psychrophile Pseudoalteromonas Haloplanktis Gives Insights Into the Adaptation of Proteins to Low Temperatures
Eur. J. Biochem. 267, 3502±3512 (2000) q FEBS 2000 A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures D. Georlette1,Z.O.JoÂnsson2,3, F. Van Petegem4, J.-P. Chessa1, J. Van Beeumen4,U.HuÈ bscher2 and C. Gerday1 1Laboratory of Biochemistry, Institute of Chemistry, B6a Universite de LieÁge, Sart-Tilman, Belgium; 2Institute of Veterinary Biochemistry, UniversitaÈtZuÈrich-Irchel, ZuÈrich, Switzerland; 3Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA; 4Laboratory for Protein Biochemistry and Protein Engineering, Department of Biochemistry Physiology and Microbiology, Gent, Belgium The cloning, overexpression and characterization of a cold-adapted DNA ligase from the Antarctic sea water bacterium Pseudoalteromonas haloplanktis are described. Protein sequence analysis revealed that the cold- adapted Ph DNA ligase shows a significant level of sequence similarity to other NAD1-dependent DNA ligases and contains several previously described sequence motifs. Also, a decreased level of arginine and proline residues in Ph DNA ligase could be involved in the cold-adaptation strategy. Moreover, 3D modelling of the N-terminal domain of Ph DNA ligase clearly indicates that this domain is destabilized compared with its thermophilic homologue. The recombinant Ph DNA ligase was overexpressed in Escherichia coli and purified to homogeneity. Mass spectroscopy experiments indicated that the purified enzyme is mainly in an adenylated form with a molecular mass of 74 593 Da. Ph DNA ligase shows similar overall catalytic properties to other NAD1-dependent DNA ligases but is a cold-adapted enzyme as its catalytic efficiency (kcat/Km) at low and moderate temperatures is higher than that of its mesophilic counterpart E. -
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. -
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. -
Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. -
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. -
The Thermal Limits to Life on Earth
International Journal of Astrobiology 13 (2): 141–154 (2014) doi:10.1017/S1473550413000438 © Cambridge University Press 2014. The online version of this article is published within an Open Access environment subject to the conditions of the Creative Commons Attribution licence http://creativecommons.org/licenses/by/3.0/. The thermal limits to life on Earth Andrew Clarke1,2 1British Antarctic Survey, Cambridge, UK 2School of Environmental Sciences, University of East Anglia, Norwich, UK e-mail: [email protected] Abstract: Living organisms on Earth are characterized by three necessary features: a set of internal instructions encoded in DNA (software), a suite of proteins and associated macromolecules providing a boundary and internal structure (hardware), and a flux of energy. In addition, they replicate themselves through reproduction, a process that renders evolutionary change inevitable in a resource-limited world. Temperature has a profound effect on all of these features, and yet life is sufficiently adaptable to be found almost everywhere water is liquid. The thermal limits to survival are well documented for many types of organisms, but the thermal limits to completion of the life cycle are much more difficult to establish, especially for organisms that inhabit thermally variable environments. Current data suggest that the thermal limits to completion of the life cycle differ between the three major domains of life, bacteria, archaea and eukaryotes. At the very highest temperatures only archaea are found with the current high-temperature limit for growth being 122 °C. Bacteria can grow up to 100 °C, but no eukaryote appears to be able to complete its life cycle above *60 °C and most not above 40 °C. -
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. -
Chapter 02282
Psychrophiles and Psychrotrophs$ Craig L Moyer, Western Washington University, Bellingham, WA, United States R Eric Collins, University of Alaska Fairbanks, Fairbanks, AK, United States Richard Y Morita, Oregon State University, Corvallis, OR, United States r 2017 Elsevier Inc. All rights reserved. Glossary Cryophiles Cold-loving eukaryotes. Barophiles (also known as piezophiles) Pressure-loving Homeophasic adaptation The ability of the cell bacteria and archaea. membrane to maintain a relatively constant viscosity Cryobiosis A temporary state of reduced metabolism in (fluidity) throughout the growth temperature range. which metabolic activity is absent or undetectable due to Membrane fluidity The ability of the cell membrane to freezing. To initiate cryobiosis, the organism freezes all of remain fluid in order to modulate the activity of the the water within its cell(s). This allows the organism to intrinsic proteins which perform functions such as electron endure the freezing temperatures until more transport, ion pumping, and nutrient uptake. hospitable conditions return. Studies have shown that the Psychrophiles Cold-loving bacteria and archaea. longer an organism remains in cryobiosis, the longer it takes Psychrotrophs Cold-tolerant bacteria and archaea. for the organism to come out of cryobiosis. This is because Thermocline In the stratification of warm surface water the organism must use its own energy to come out of over cold deeper water, the transition zone of rapid cryobiosis, and the longer it stays in cryobiosis the less temperature decline between two layers. energy it will retain. Introduction Psychrophiles are cold-loving bacteria or archaea, whereas cryophiles are cold-loving higher biological forms (e.g., polar fish). -
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.