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CRISPR Loci Reveal Networks of Gene Exchange in Archaea Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna*
Brodt et al. Biology Direct 2011, 6:65 http://www.biology-direct.com/content/6/1/65 RESEARCH Open Access CRISPR loci reveal networks of gene exchange in archaea Avital Brodt, Mor N Lurie-Weinberger and Uri Gophna* Abstract Background: CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past “infection history” of the organism. Results: Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions: CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti- plasmid defense. Open peer review: This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. -
Efficient Genome Editing of an Extreme Thermophile, Thermus
www.nature.com/scientificreports OPEN Efcient genome editing of an extreme thermophile, Thermus thermophilus, using a thermostable Cas9 variant Bjorn Thor Adalsteinsson1*, Thordis Kristjansdottir1,2, William Merre3, Alexandra Helleux4, Julia Dusaucy5, Mathilde Tourigny4, Olafur Fridjonsson1 & Gudmundur Oli Hreggvidsson1,2 Thermophilic organisms are extensively studied in industrial biotechnology, for exploration of the limits of life, and in other contexts. Their optimal growth at high temperatures presents a challenge for the development of genetic tools for their genome editing, since genetic markers and selection substrates are often thermolabile. We sought to develop a thermostable CRISPR-Cas9 based system for genome editing of thermophiles. We identifed CaldoCas9 and designed an associated guide RNA and showed that the pair have targetable nuclease activity in vitro at temperatures up to 65 °C. We performed a detailed characterization of the protospacer adjacent motif specifcity of CaldoCas9, which revealed a preference for 5′-NNNNGNMA. We constructed a plasmid vector for the delivery and use of the CaldoCas9 based genome editing system in the extreme thermophile Thermus thermophilus at 65 °C. Using the vector, we generated gene knock-out mutants of T. thermophilus, targeting genes on the bacterial chromosome and megaplasmid. Mutants were obtained at a frequency of about 90%. We demonstrated that the vector can be cured from mutants for a subsequent round of genome editing. CRISPR-Cas9 based genome editing has not been reported previously in the extreme thermophile T. thermophilus. These results may facilitate development of genome editing tools for other extreme thermophiles and to that end, the vector has been made available via the plasmid repository Addgene. -
The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
The Isolation of Viruses Infecting Archaea
Portland State University PDXScholar Biology Faculty Publications and Presentations Biology 2010 The Isolation of Viruses Infecting Archaea Kenneth M. Stedman Portland State University Kate Porter Mike L. Dyall-Smith Follow this and additional works at: https://pdxscholar.library.pdx.edu/bio_fac Part of the Bacteria Commons, Biology Commons, and the Viruses Commons Let us know how access to this document benefits ou.y Citation Details Stedman, Kenneth M., Kate Porter, and Mike L. Dyall-Smith. "The isolation of viruses infecting Archaea." Manual of aquatic viral ecology. American Society for Limnology and Oceanography (ASLO) (2010): 57-64. This Article is brought to you for free and open access. It has been accepted for inclusion in Biology Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. MANUAL of MAVE Chapter 6, 2010, 57–64 AQUATIC VIRAL ECOLOGY © 2010, by the American Society of Limnology and Oceanography, Inc. The isolation of viruses infecting Archaea Kenneth M. Stedman1, Kate Porter2, and Mike L. Dyall-Smith3 1Department of Biology, Center for Life in Extreme Environments, Portland State University, P.O. Box 751, Portland, OR 97207, USA 2Biota Holdings Limited, 10/585 Blackburn Road, Notting Hill Victoria 3168, Australia 3Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Abstract A mere 50 viruses of Archaea have been reported to date; these have been investigated mostly by adapting methods used to isolate bacteriophages to the unique growth conditions of their archaeal hosts. The most numer- ous are viruses of thermophilic Archaea. -
The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales. Microorganisms 2021, 9
microorganisms Article The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales Alejandra Recalde 1,2 , Marleen van Wolferen 2 , Shamphavi Sivabalasarma 2 , Sonja-Verena Albers 2, Claudio A. Navarro 1 and Carlos A. Jerez 1,* 1 Laboratory of Molecular Microbiology and Biotechnology, Department of Biology, Faculty of Sciences, University of Chile, Santiago 8320000, Chile; [email protected] (A.R.); [email protected] (C.A.N.) 2 Laboratory of Molecular Biology of Archaea, Institute of Biology II-Microbiology, University of Freiburg, 79085 Freiburg, Germany; [email protected] (M.v.W.); [email protected] (S.S.); [email protected] (S.-V.A.) * Correspondence: [email protected] Abstract: Polyphosphates (polyP) are polymers of orthophosphate residues linked by high-energy phosphoanhydride bonds that are important in all domains of life and function in many different processes, including biofilm development. To study the effect of polyP in archaeal biofilm formation, our previously described Sa. solfataricus polyP (−) strain and a new polyP (−) S. acidocaldarius strain generated in this report were used. These two strains lack the polymer due to the overexpression of their respective exopolyphosphatase gene (ppx). Both strains showed a reduction in biofilm formation, decreased motility on semi-solid plates and a diminished adherence to glass surfaces as seen by DAPI (40,6-diamidino-2-phenylindole) staining using fluorescence microscopy. Even though arlB (encoding the archaellum subunit) was highly upregulated in S. acidocardarius polyP (−), no archaellated cells were observed. These results suggest that polyP might be involved in the regulation of the expression of archaellum components and their assembly, possibly by affecting energy availability, phosphorylation or other phenomena. -
Fermentation of Biodegradable Organic Waste by the Family Thermotogaceae
resources Review Fermentation of Biodegradable Organic Waste by the Family Thermotogaceae Nunzia Esercizio 1 , Mariamichela Lanzilli 1 , Marco Vastano 1 , Simone Landi 2 , Zhaohui Xu 3 , Carmela Gallo 1 , Genoveffa Nuzzo 1 , Emiliano Manzo 1 , Angelo Fontana 1,2 and Giuliana d’Ippolito 1,* 1 Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Italy; [email protected] (N.E.); [email protected] (M.L.); [email protected] (M.V.); [email protected] (C.G.); [email protected] (G.N.); [email protected] (E.M.); [email protected] (A.F.) 2 Department of Biology, University of Naples “Federico II”, Via Cinthia, I-80126 Napoli, Italy; [email protected] 3 Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA; [email protected] * Correspondence: [email protected] Abstract: The abundance of organic waste generated from agro-industrial processes throughout the world has become an environmental concern that requires immediate action in order to make the global economy sustainable and circular. Great attention has been paid to convert such nutrient- rich organic waste into useful materials for sustainable agricultural practices. Instead of being an environmental hazard, biodegradable organic waste represents a promising resource for the Citation: Esercizio, N.; Lanzilli, M.; production of high value-added products such as bioenergy, biofertilizers, and biopolymers. The Vastano, M.; Landi, S.; Xu, Z.; Gallo, ability of some hyperthermophilic bacteria, e.g., the genera Thermotoga and Pseudothermotoga, to C.; Nuzzo, G.; Manzo, E.; Fontana, A.; anaerobically ferment waste with the concomitant formation of bioproducts has generated great d’Ippolito, G. -
Resolution of Carbon Metabolism and Sulfur-Oxidation Pathways of Metallosphaera Cuprina Ar-4 Via Comparative Proteomics
JOURNAL OF PROTEOMICS 109 (2014) 276– 289 Available online at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/jprot Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics Cheng-Ying Jianga, Li-Jun Liua, Xu Guoa, Xiao-Yan Youa, Shuang-Jiang Liua,c,⁎, Ansgar Poetschb,⁎⁎ aState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China bPlant Biochemistry, Ruhr University Bochum, Bochum, Germany cEnvrionmental Microbiology and Biotechnology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China ARTICLE INFO ABSTRACT Article history: Metallosphaera cuprina is able to grow either heterotrophically on organics or autotrophically Received 16 March 2014 on CO2 with reduced sulfur compounds as electron donor. These traits endowed the species Accepted 6 July 2014 desirable for application in biomining. In order to obtain a global overview of physiological Available online 14 July 2014 adaptations on the proteome level, proteomes of cytoplasmic and membrane fractions from cells grown autotrophically on CO2 plus sulfur or heterotrophically on yeast extract Keywords: were compared. 169 proteins were found to change their abundance depending on growth Quantitative proteomics condition. The proteins with increased abundance under autotrophic growth displayed Bioleaching candidate enzymes/proteins of M. cuprina for fixing CO2 through the previously identified Autotrophy 3-hydroxypropionate/4-hydroxybutyrate cycle and for oxidizing elemental sulfur as energy Heterotrophy source. The main enzymes/proteins involved in semi- and non-phosphorylating Entner– Industrial microbiology Doudoroff (ED) pathway and TCA cycle were less abundant under autotrophic growth. Also Extremophile some transporter proteins and proteins of amino acid metabolism changed their abundances, suggesting pivotal roles for growth under the respective conditions. -
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. -
The Crystal Structure of Pyrococcus Furiosus Ornithine Carbamoyltransferase Reveals a Key Role for Oligomerization in Enzyme Stability at Extremely High Temperatures
Proc. Natl. Acad. Sci. USA Vol. 95, pp. 2801–2806, March 1998 Biochemistry The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures VINCENT VILLERET*, BERNARD CLANTIN†,CATHERINE TRICOT‡,CHRISTIANNE LEGRAIN‡,MARTINE ROOVERS§¶, i VICTOR STALON†,NICOLAS GLANSDORFF‡§¶, AND JOZEF VAN BEEUMEN* *Laboratorium voor Eiwitbiochemie en Eiwitengineering, Universiteit Gent, Ledeganckstraat 35, B-9000 Gent, Belgium; and †Laboratoire de Microbiologie, Universite´Libre de Bruxelles, ‡Institut de Recherches du Centre d’Enseignement et de Recherches des Industries Alimentaires, Commission de la Communaute´ Franc¸aise de Belgique, Re´gionBruxelles Capitale, §Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, and ¶Vlaams Interuniversitair Instituut voor Biotechnologie, avenue E. Gryson 1, B-1070 Brussels, Belgium Edited by Max F. Perutz, Medical Research Council, Cambridge, United Kingdom, and approved January 5, 1998 (received for review September 8, 1997) ABSTRACT The Pyrococcus furiosus (PF) ornithine car- lating agent (8). The involvement of such a thermolabile bamoyltransferase (OTCase; EC 2.1.3.3) is an extremely heat- intermediate in the metabolism of extreme thermophilic mi- stable enzyme that maintains about 50% of its activity after croorganisms raises the question of which mechanisms protect heat treatment for 60 min at 100°C. To understand the it from decomposition at elevated growth temperatures. Re- molecular basis of thermostability of this enzyme, we have cent results suggest that in Thermus aquaticus and Pyrococcus determined its three-dimensional structure at a resolution of furiosus (PF), CP is protected from the bulk of the aqueous 2.7 Å and compared it with the previously reported structures phase by channeling between carbamoylphosphate synthetase of OTCases isolated from mesophilic bacteria. -
Life at High Temperatures Biotechnology in Yellowstone
Life at High Temperatures by Thomas D. Brock Biotechnology in Yellowstone © 1994 Yellowstone Association for Natural Science, History & Education, Inc. Yellowstone National Park, Wyoming 82190. The thermophilic bacteria that live in the Yellowstone hot springs have been the foundation of impressive developments in medicine and biotechnology. The unique thermostable enzymes of these bacteria are finding wide industrial and medical use, and have become the basis of a multimillion dollar industry! When researchers began to study the biology of Yellowstone hot springs in the 1960s, the presence of these hyperthermophilic bacteria was not suspected. The upper temperature limit for life was thought to be around 73 degrees C (163 degrees F), which was actually the limit for photosynthetic organisms such as cyanobacteria. The preferred temperature for thermophilic bacteria was considered even lower, around 55 degrees C (131 degrees F). Because of the known effects of heat on biological structures such as proteins and DNA, it was thought that life at higher temperatures would be impossible. In fact, biochemists have known for over 100 years that enzymes (key cellular proteins) are destroyed by boiling. However, field observations in Yellowstone showed that in certain springs bacteria existed at much higher temperatures. Although these springs were rather small and not especially conspicuous among the impressive geysers and giant hot pools of the Yellowstone thermal basins, they were impressive microbial culture systems and turned out to be of great scientific and intellectual interest. It turns out that the enzymes of Yellowstone thermophiles are very tolerant of heat and are active even at boiling water temperatures. -
Potential Contamination of Yellowstone Hot Springs by Human Activity
Western North American Naturalist Volume 62 Number 1 Article 6 2-19-2002 Invisible invasion: potential contamination of Yellowstone hot springs by human activity Robert F. Lindstrom National Park Service, Yellowstone National Park, Wyoming Robert F. Ramaley University of Nebraska Medical Center, Omaha, Nebraska Richard L. Weiss Bizzoco San Diego University, San Diego, California Follow this and additional works at: https://scholarsarchive.byu.edu/wnan Recommended Citation Lindstrom, Robert F.; Ramaley, Robert F.; and Weiss Bizzoco, Richard L. (2002) "Invisible invasion: potential contamination of Yellowstone hot springs by human activity," Western North American Naturalist: Vol. 62 : No. 1 , Article 6. Available at: https://scholarsarchive.byu.edu/wnan/vol62/iss1/6 This Article is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Western North American Naturalist by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Western North American Naturalist 62(1), © 2002, pp. 44–58 INVISIBLE INVASION: POTENTIAL CONTAMINATION OF YELLOWSTONE HOT SPRINGS BY HUMAN ACTIVITY1 Robert F. Lindstrom2, Robert F. Ramaley3, and Richard L. Weiss Bizzoco4 ABSTRACT.—This report establishes a baseline inventory of microorganisms in acidic hot springs of Yellowstone National Park (YNP). The analysis is based on observations carried out over the past 25 years using light microscopy, DNA staining, and electron microscopy of environmental samples. The inventory, while incomplete in that not all organ- isms have been cultured or examined using genetic approaches, represents a study of several solfatara (acid sulfate) geyser basins in YNP. -
Towards a Congruent Reclassification And
Towards a congruent reclassification and nomenclature of the thermophilic species of the genus Pseudothermotoga within the order Thermotogales Hassiba Belahbib, Zarath Summers, Marie-Laure Fardeau, Manon Joseph, Christian Tamburini, Alain Dolla, Bernard Ollivier, Fabrice Armougom To cite this version: Hassiba Belahbib, Zarath Summers, Marie-Laure Fardeau, Manon Joseph, Christian Tamburini, et al.. Towards a congruent reclassification and nomenclature of the thermophilic species of thegenus Pseudothermotoga within the order Thermotogales. Systematic and Applied Microbiology, Elsevier, 2018, 41 (6), pp.555-563. 10.1016/J.SYAPM.2018.04.007. hal-01975970 HAL Id: hal-01975970 https://hal.archives-ouvertes.fr/hal-01975970 Submitted on 9 Jan 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Towards a congruent reclassification and nomenclature of the thermophilic species of the genus Pseudothermotoga within the order Thermotogales a b a a Hassiba Belahbib , Zarath M. Summers , Marie-Laure Fardeau , Manon Joseph , a c a a,∗ Christian Tamburini , Alain Dolla , Bernard Ollivier , Fabrice Armougom a Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France b ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, NJ 08801, United States c Aix Marseille Univ, CNRS, LCB, Marseille, France a r t i c l e i n f o a b s t r a c t Article history: The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic Received 15 December 2017 anaerobic bacteria that are mostly originated from geothermally heated environments.