Structure and Function of Archaeal Histones
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Microbial Community Dynamics During Composting Process of Animal Manure Analyzed by Molecular Biological Methods
Microbial Community Dynamics during Composting Process of Animal Manure Analyzed by Molecular Biological Methods 著者 Yamamoto Nozomi, Asano Ryoki, Otawa Kenichi, Oishi Ryu, Yoshii Hiroki, Tada Chika, Nakai Yutaka journal or Journal of Integrated Field Science publication title volume 11 page range 27-34 year 2014-03 URL http://hdl.handle.net/10097/57385 lIFS, 11 : 27 - 34 (2014) Symposium Mini Paper (Oral Session) Microbial Community Dynamics during Composting Process of Animal Manure Analyzed by Molecular Biological Methods Nozomi Yamamoto!, RyokiAsano2, Kenichi Otawa3, Ryu Oishi3, Hiroki YoshiP, Chika Tada3 and Yutaka NakaP IGraduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Japan, 2Department of Biotechnology, Faculty of Bioresource Sciences, Akita Prefectural University, Japan, 3Graduate School of Agricultural Science, Tohoku University, Japan Keywords: 16S rRNA gene, animal manure, archaea, bacteria, cloning, compost Abstract we revealed the pattern of changes in the prokaryotic Composting is a biological process involving sta communities involved in the compo sting process. bilization of animal manure and transformation into organic fertilizer. Microorganisms such as bacteria Introduction and archaea participate in the compo sting process. Cattle manure accounts for a large part of the total Because bacteria form huge communities in compost, animal waste generated in Japan (MAFF, 2013) and they are thought to play an important role as decom can cause environmental problems such as soil con posers of organic substances. However, only few tamination, air pollution, or offensive odor emission studies are tracking bacterial communities throughout without appropriate treatment (Bernal et aI., 2008). the composting process. The role of archaeal com Composting is the most effective technique for min munities in compo sting has not been also elucidated. -
Differences in Lateral Gene Transfer in Hypersaline Versus Thermal Environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1
Rhodes et al. BMC Evolutionary Biology 2011, 11:199 http://www.biomedcentral.com/1471-2148/11/199 RESEARCH ARTICLE Open Access Differences in lateral gene transfer in hypersaline versus thermal environments Matthew E Rhodes1*, John R Spear2, Aharon Oren3 and Christopher H House1 Abstract Background: The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these “long distance” LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles. Results: We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles. Conclusions: Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. -
Orthologs of the Small RPB8 Subunit of the Eukaryotic RNA Polymerases
Biology Direct BioMed Central Discovery notes Open Access Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota" Eugene V Koonin*1, Kira S Makarova1 and James G Elkins2 Address: 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 2Microbial Ecology and Physiology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Email: Eugene V Koonin* - [email protected]; Kira S Makarova - [email protected]; James G Elkins - [email protected] * Corresponding author Published: 14 December 2007 Received: 13 December 2007 Accepted: 14 December 2007 Biology Direct 2007, 2:38 doi:10.1186/1745-6150-2-38 This article is available from: http://www.biology-direct.com/content/2/1/38 © 2007 Koonin 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. Abstract : Although most of the key components of the transcription apparatus, and in particular, RNA polymerase (RNAP) subunits, are conserved between archaea and eukaryotes, no archaeal homologs of the small RPB8 subunit of eukaryotic RNAP have been detected. We report that orthologs of RPB8 are encoded in all sequenced genomes of hyperthermophilic Crenarchaeota and a recently sequenced "korarchaeal" genome, but not in Euryarchaeota or the mesophilic crenarchaeon Cenarchaeum symbiosum. These findings suggest that all 12 core subunits of eukaryotic RNAPs were already present in the last common ancestor of the extant archaea. -
Archaea and the Origin of Eukaryotes
REVIEWS Archaea and the origin of eukaryotes Laura Eme, Anja Spang, Jonathan Lombard, Courtney W. Stairs and Thijs J. G. Ettema Abstract | Woese and Fox’s 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor. Sister groups Two descendants that split The pioneering work by Carl Woese and colleagues In this Review, we discuss how culture- independent from the same node; the revealed that all cellular life could be divided into three genomics has transformed our understanding of descendants are each other’s major evolutionary lines (also called domains): the archaeal diversity and how this has influenced our closest relative. -
Phylogeny and Taxonomy of Archaea: a Comparison of the Whole-Genome-Based Cvtree Approach with 16S Rrna Sequence Analysis
Life 2015, 5, 949-968; doi:10.3390/life5010949 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Article Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis Guanghong Zuo 1, Zhao Xu 2 and Bailin Hao 1;* 1 T-Life Research Center and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China; E-Mail: [email protected] 2 Thermo Fisher Scientific, 200 Oyster Point Blvd, South San Francisco, CA 94080, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-21-6565-2305. Academic Editors: Roger A. Garrett, Hans-Peter Klenk and Michael W. W. Adams Received: 9 December 2014 / Accepted: 9 March 2015 / Published: 17 March 2015 Abstract: A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1) the whole-genome-based and alignment-free CVTree using 179 genomes; (2) the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3) the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation. -
Downloaded from Mage and Compared
bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. 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. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta Florian U. Moeller1, Nicole S. Webster2,3, Craig W. Herbold1, Faris Behnam1, Daryl Domman1, 5 Mads Albertsen4, Maria Mooshammer1, Stephanie Markert5,8, Dmitrij Turaev6, Dörte Becher7, Thomas Rattei6, Thomas Schweder5,8, Andreas Richter9, Margarete Watzka9, Per Halkjaer Nielsen4, and Michael Wagner1,* 1Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, 10 Austria. 2Australian Institute of Marine Science, Townsville, Queensland, Australia. 3 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of 15 Queensland, St Lucia, QLD, Australia 4Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark. 20 5Institute of Marine Biotechnology e.V., Greifswald, Germany 6Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Austria. 25 7Institute of Microbiology, Microbial Proteomics, University of Greifswald, Greifswald, Germany 8Institute of Pharmacy, Pharmaceutical Biotechnology, University of Greifswald, Greifswald, Germany 9Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, 30 University of Vienna, Austria. *Corresponding author: Michael Wagner, Department of Microbiology and Ecosystem Science, Althanstrasse 14, University of Vienna, 1090 Vienna, Austria. Email: wagner@microbial- ecology.net 1 bioRxiv preprint doi: https://doi.org/10.1101/527234; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
Expansion of Thaumarchaeota Habitat Range Is Correlated with Horizontal Transfer of Atpase Operons
Lawrence Berkeley National Laboratory Recent Work Title Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons. Permalink https://escholarship.org/uc/item/19h9369p Journal The ISME journal, 13(12) ISSN 1751-7362 Authors Wang, Baozhan Qin, Wei Ren, Yi et al. Publication Date 2019-12-01 DOI 10.1038/s41396-019-0493-x Peer reviewed eScholarship.org Powered by the California Digital Library University of California The ISME Journal (2019) 13:3067–3079 https://doi.org/10.1038/s41396-019-0493-x ARTICLE Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons 1,2 3 4 1 2 2 5,6 Baozhan Wang ● Wei Qin ● Yi Ren ● Xue Zhou ● Man-Young Jung ● Ping Han ● Emiley A. Eloe-Fadrosh ● 7 8 1 9 9 7 4 10 10 Meng Li ● Yue Zheng ● Lu Lu ● Xin Yan ● Junbin Ji ● Yang Liu ● Linmeng Liu ● Cheryl Heiner ● Richard Hall ● 11 2 12 5 13 Willm Martens-Habbena ● Craig W. Herbold ● Sung-keun Rhee ● Douglas H. Bartlett ● Li Huang ● 3 2,14 15 1 Anitra E. Ingalls ● Michael Wagner ● David A. Stahl ● Zhongjun Jia Received: 15 April 2019 / Revised: 1 July 2019 / Accepted: 29 July 2019 / Published online: 28 August 2019 © The Author(s) 2019. This article is published with open access Abstract Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. -
A Robust Nitrifying Community in a Bioreactor at 50&Thinsp;&Deg;C Opens up the Path for Thermophilic Nitrogen Removal
The ISME Journal (2016) 10, 2293–2303 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE A robust nitrifying community in a bioreactor at 50°C opens up the path for thermophilic nitrogen removal Emilie NP Courtens1, Eva Spieck2, Ramiro Vilchez-Vargas1, Samuel Bodé3, Pascal Boeckx3, Stefan Schouten4, Ruy Jauregui5, Dietmar H Pieper5, Siegfried E Vlaeminck1,6,7 and Nico Boon1,7 1Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Gent, Belgium; 2Biocenter Klein Flottbek and Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany; 3Isotope Bioscience Laboratory, Ghent University, Gent, Belgium; 4Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands; 5Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany and 6Research Group of Sustainable Energy, Air and Water Technology, University of Antwerp, Antwerpen, Belgium The increasing production of nitrogen-containing fertilizers is crucial to meet the global food demand, yet high losses of reactive nitrogen associated with the food production/consumption chain progressively deteriorate the natural environment. Currently, mesophilic nitrogen-removing microbes eliminate nitrogen from wastewaters. Although thermophilic nitrifiers have been separately enriched from natural environments, no bioreactors are described that couple these processes for the treatment of nitrogen in hot wastewaters. Samples from composting facilities were used as inoculum for the batch-wise enrichment of thermophilic nitrifiers (350 days). Subsequently, the enrichments were transferred to a bioreactor to obtain a stable, high-rate nitrifying process (560 days). The community contained up to 17% ammonia-oxidizing archaea (AOAs) closely related to ‘Candidatus Nitrososphaera gargensis’, and 25% nitrite-oxidizing bacteria (NOBs) related to Nitrospira calida. -
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. -
A Scientific Literature Review Comic by Lilja Strang
A scientific literature review comic by Lilja Strang In Norse mythology all of life is contained within nine realms. These realms are connected by Yggdrasil, or the World Tree. A similar concept exists in biology. It’s called the tree of life and it shows the evolutionary connections between all life on earth. These two trees have more in common than most people think. To begin our story, think back to your earliest biology class. You probably saw either the 1959 tree of life, organized into Carl Woese—1990 either 5 kingdoms, or the 1990 tree with 3 domains. The 5 kingdoms tree compared life on the basis of how things looked. Microscopic organisms were too small to see easily, and were excluded. Whittaker’s 5 Kingdom Tree (1959) Woese’s 3 Domain Tree (1990) Plantae Fungi Animalia Bacteria Archaea Eucarya Carl Woese’s tree Protista was based on the best DNA evidence Monera of his time. Here, the microscopic Bacteria and Archaea were front and center. In fact, Woese realized that the Archaea were Níðhöggr (Nidhogg) is the dragon that gnaws at the roots of Yggdrasil. very special. In the 1990s, Archaea were thought to only be extremophiles living in very Methanosarcina mazeii produces the methane gas in cow farts. hot/cold, acidic/basic, or There are no known methane otherwise unusual habitats. producing Bacteria, only Archaea. Sulfolobus live in the Geysers of Yellowstone at temperatures of 40–55°C (104–131°F). Methane producers are found in humans too. Ferroplasma acidiphilum live They’re similar to those in the toxic byproducts of found in cows. -
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. -
Oxidizing Archaeon Nitrososphaera Gargensis † ‡ § ∥ ⊥ § † Yujie Men,*, , Ping Han, Damian E
This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes. Article pubs.acs.org/est Biotransformation of Two Pharmaceuticals by the Ammonia- Oxidizing Archaeon Nitrososphaera gargensis † ‡ § ∥ ⊥ § † Yujie Men,*, , Ping Han, Damian E. Helbling, Nico Jehmlich, Craig Herbold, Rebekka Gulde, # # † § † ⊗ Annalisa Onnis-Hayden, April Z. Gu, David R. Johnson, Michael Wagner, and Kathrin Fenner , † Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland ‡ Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States § Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria ∥ School of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14853, United States ⊥ Department of Proteomics, Helmholtz-Centre for Environmental Research − UFZ, 04318 Leipzig, Germany # Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States ⊗ Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland *S Supporting Information ABSTRACT: The biotransformation of some micropollutants has previously been observed to be positively associated with ammonia oxidation activities and the transcript abundance of the