Compatible Solutes of Organisms That Live in Hot Saline Environments
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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. -
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. -
A Proposal to Rename the Hyperthermophile Pyrococcus Woesei As Pyrococcus Furiosus Subsp
Archaea 1, 277–283 © 2004 Heron Publishing—Victoria, Canada A proposal to rename the hyperthermophile Pyrococcus woesei as Pyrococcus furiosus subsp. woesei WIROJNE KANOKSILAPATHAM,1 JUAN M. GONZÁLEZ,1,2 DENNIS L. MAEDER,1 1,3 1,4 JOCELYNE DIRUGGIERO and FRANK T. ROBB 1 Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA 2 Present address: IRNAS-CSIC, P.O. Box 1052, 41080 Sevilla, Spain 3 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20274, USA 4 Corresponding author ([email protected]) Received April 8, 2004; accepted July 28, 2004; published online August 31, 2004 Summary Pyrococcus species are hyperthermophilic mem- relatively rapidly at temperatures above 90 °C and produce ° bers of the order Thermococcales, with optimal growth tem- H2S from elemental sulfur (S ) (Zillig et al. 1987). Two Pyro- peratures approaching 100 °C. All species grow heterotrophic- coccus species, P. furiosus (Fiala and Stetter 1986) and ° ally and produce H2 or, in the presence of elemental sulfur (S ), P. woesei (Zillig et al. 1987), were isolated from marine sedi- H2S. Pyrococcus woesei and P.furiosus were isolated from ma- ments at a Vulcano Island beach site in Italy. They have similar rine sediments at the same Vulcano Island beach site and share morphological and physiological characteristics: both species many morphological and physiological characteristics. We re- are cocci and move by means of a tuft of polar flagella. They port here that the rDNA operons of these strains have identical are heterotrophic and grow optimally at 95–100 °C, utilizing sequences, including their intergenic spacer regions and part of peptides as major carbon and nitrogen sources. -
Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria)
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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 2 Genomic analysis of family UBA6911 (Group 18 3 Acidobacteria) expands the metabolic capacities of the 4 phylum and highlights adaptations to terrestrial habitats. 5 6 Archana Yadav1, Jenna C. Borrelli1, Mostafa S. Elshahed1, and Noha H. Youssef1* 7 8 1Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, 9 OK 10 *Correspondence: Noha H. Youssef: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.04.09.439258; this version posted April 10, 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. 11 Abstract 12 Approaches for recovering and analyzing genomes belonging to novel, hitherto unexplored 13 bacterial lineages have provided invaluable insights into the metabolic capabilities and 14 ecological roles of yet-uncultured taxa. The phylum Acidobacteria is one of the most prevalent 15 and ecologically successful lineages on earth yet, currently, multiple lineages within this phylum 16 remain unexplored. Here, we utilize genomes recovered from Zodletone spring, an anaerobic 17 sulfide and sulfur-rich spring in southwestern Oklahoma, as well as from multiple disparate soil 18 and non-soil habitats, to examine the metabolic capabilities and ecological role of members of 19 the family UBA6911 (group18) Acidobacteria. -
MIAMI UNIVERSITY the Graduate School Certificate for Approving The
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Qiuyuan Huang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director ________________________________________ Yildirim Dilek, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Chuanlun Zhang, External examiner ______________________________________ Annette Bollmann, Graduate School Representative ABSTRACT GEOMICROBIAL INVESTIGATIONS ON EXTREME ENVIRONMENTS: LINKING GEOCHEMISTRY TO MICROBIAL ECOLOGY IN TERRESTRIAL HOT SPRINGS AND SALINE LAKES by Qiuyuan Huang Terrestrial hot springs and saline lakes represent two extreme environments for microbial life and constitute an important part of global ecosystems that affect the biogeochemical cycling of life-essential elements. Despite the advances in our understanding of microbial ecology in the past decade, important questions remain regarding the link between microbial diversity and geochemical factors under these extreme conditions. This dissertation first investigates a series of hot springs with wide ranges of temperature (26-92oC) and pH (3.72-8.2) from the Tibetan Plateau in China and the Philippines. Within each region, microbial diversity and geochemical conditions were studied using an integrated approach with 16S rRNA molecular phylogeny and a suite of geochemical analyses. In Tibetan springs, the microbial community was dominated by archaeal phylum Thaumarchaeota -
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. -
Counts Metabolic Yr10.Pdf
Advanced Review Physiological, metabolic and biotechnological features of extremely thermophilic microorganisms James A. Counts,1 Benjamin M. Zeldes,1 Laura L. Lee,1 Christopher T. Straub,1 Michael W.W. Adams2 and Robert M. Kelly1* The current upper thermal limit for life as we know it is approximately 120C. Microorganisms that grow optimally at temperatures of 75C and above are usu- ally referred to as ‘extreme thermophiles’ and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, hetero- trophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs— basically, anywhere there is hot water. Initial efforts to study extreme thermo- philes faced challenges with their isolation from difficult to access locales, pro- blems with their cultivation in laboratories, and lack of molecular tools. Fortunately, because of their relatively small genomes, many extreme thermo- philes were among the first organisms to be sequenced, thereby opening up the application of systems biology-based methods to probe their unique physiologi- cal, metabolic and biotechnological features. The bacterial genera Caldicellulosir- uptor, Thermotoga and Thermus, and the archaea belonging to the orders Thermococcales and Sulfolobales, are among the most studied extreme thermo- philes to date. The recent emergence of genetic tools for many of these organ- isms provides the opportunity to move beyond basic discovery and manipulation to biotechnologically relevant applications of metabolic engineering. -
Ts2631 Endolysin from the Extremophilic Thermus Scotoductus Bacteriophage Vb Tsc2631 As an Antimicrobial Agent Against Gram-Negative Multidrug-Resistant Bacteria
viruses Article Ts2631 Endolysin from the Extremophilic Thermus scotoductus Bacteriophage vB_Tsc2631 as an Antimicrobial Agent against Gram-Negative Multidrug-Resistant Bacteria Magdalena Plotka 1,* , Malgorzata Kapusta 2, Sebastian Dorawa 1, Anna-Karina Kaczorowska 3 and Tadeusz Kaczorowski 1,* 1 Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland 2 Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland 3 Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland * Correspondence: [email protected] (M.P.); [email protected] (T.K.); Tel.: +48-58-523-60-75 (M.P.); +48-58-523-60-67 (T.K.) Received: 5 June 2019; Accepted: 15 July 2019; Published: 18 July 2019 Abstract: Bacteria that thrive in extreme conditions and the bacteriophages that infect them are sources of valuable enzymes resistant to denaturation at high temperatures. Many of these heat-stable proteins are useful for biotechnological applications; nevertheless, none have been utilized as antibacterial agents. Here, we demonstrate the bactericidal potential of Ts2631 endolysin from the extremophilic bacteriophage vB_Tsc2631, which infects Thermus scotoductus, against the alarming multidrug-resistant clinical strains of Acinetobacter baumannii, Pseudomonas aeruginosa and pathogens from the Enterobacteriaceae family. A 2–3.7 log reduction in the bacterial load was observed in antibacterial tests against A. baumannii and P. aeruginosa after 1.5 h. The Ts2631 activity was further enhanced by ethylenediaminetetraacetic acid (EDTA), a metal ion chelator (4.2 log reduction in carbapenem-resistant A. baumannii) and, to a lesser extent, by malic acid and citric acid (2.9 and 3.3 log reductions, respectively). -
Ana Maria Da Silva Esteves Dissertation Presented to Obtain The
Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus Ana Maria da Silva Esteves Dissertation presented to obtain the Ph.D. degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, February, 2015 Insights into the biochemical strategies of adaptation to heat stress in the hyperthermophilic archaeon Pyrococcus furiosus Ana Maria da Silva Esteves Supervisor: Professora Helena Santos Co-supervisor: Dr. Nuno Borges Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica António Xavier | Universidade Nova de Lisboa Oeiras, February, 2015 From left to right: Prof. Volker Müller, Dr. Emmanouil Matzapetakis, Dr. Nuno Borges (Co-supervisor), Ana M. Esteves, Prof. Helena Santos (Supervisor), Prof. Pedro Moradas Ferreira, Prof. Beate Averhoff, Prof. Hermínia de Lencastre. Oeiras, 9th of February 2015. Apoio financeiro da Fundação para a Ciência e Tecnologia e do FSE no âmbito do Quadro Comunitário de apoio, Bolsa de Doutoramento com a referência SFRH/BD/61742/2009. In loving memory of my grandmother Elisa iv Acknowledgements First, I would like to thank Prof. Helena Santos, my supervisor, for accepting me as a Ph.D. student in her laboratory. Also, I want to express my appreciation to Prof. Helena Santos for being an excellent team leader, and for her constant effort to put together the resources and expertise her students need to carry out their projects with success. Her guidance, rigor, patience and enthusiasm for science definitely contributed to my development as a young scientist. I want to thank Dr. -
BIOGEOCHEMICAL INTERACTIONS in FLOODED UNDERGROUND MINES Renee Schmidt Montana Tech
Montana Tech Library Digital Commons @ Montana Tech Graduate Theses & Non-Theses Student Scholarship Summer 2017 BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES Renee Schmidt Montana Tech Follow this and additional works at: http://digitalcommons.mtech.edu/grad_rsch Part of the Geochemistry Commons Recommended Citation Schmidt, Renee, "BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES" (2017). Graduate Theses & Non-Theses. 129. http://digitalcommons.mtech.edu/grad_rsch/129 This Thesis is brought to you for free and open access by the Student Scholarship at Digital Commons @ Montana Tech. It has been accepted for inclusion in Graduate Theses & Non-Theses by an authorized administrator of Digital Commons @ Montana Tech. For more information, please contact [email protected]. BIOGEOCHEMICAL INTERACTIONS IN FLOODED UNDERGROUND MINES by Renée Schmidt A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Geoscience: Geochemistry Option Montana Tech 2017 ii Abstract This study presents a biogeochemical analysis of microbial communities in flooded underground mines in Butte, Montana, USA. Samples were collected from nine mineshafts representing three distinct geochemical zones. These zones consist of the East, West, and Outer Camp mines. The East Camp mines, bordering the Berkeley Pit Superfund site, have the highest concentrations of dissolved metals and the most acidic pH values. Dissolved metal concentrations in the West Camp are one to three orders of magnitude lower than in the East Camp and have nearly neutral pH values. The Outer Camp mines have similar metal concentrations to the West Camp but are neutral to alkaline in pH. Sulfide levels also differ between the zones. In the East Camp, sulfide levels were below detection limits, whereas the West and Outer Camp mines had sulfide -6 -4 18 concentrations ranging from 10 to 10 mol/L. -
Ionizing Radiation Resistance in Deinococcus Radiodurans
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by CSCanada.net: E-Journals (Canadian Academy of Oriental and Occidental Culture,... ISSN 1715-7862 [PRINT] Advances in Natural Science ISSN 1715-7870 [ONLINE] Vol. 7, No. 2, 2014, pp. 6-14 www.cscanada.net DOI: 10.3968/5058 www.cscanada.org Ionizing Radiation Resistance in Deinococcus Radiodurans LI Wei[a]; MA Yun[a]; XIAO Fangzhu[a]; HE Shuya[a],* [a]Institute of Biochemistry and Molecular Biology, University of South Treatment of D. radiodurans with an acute dose of 5,000 China, Hengyang, China. Gy of ionizing radiation with almost no loss of viability, *Corresponding author. and an acute dose of 15,000 Gy with 37% viability (Daly, Supported by the National Natural Science Foundation of China 2009; Ito, Watanabe, Takeshia, & Iizuka, 1983; Moseley (81272993). & Mattingly, 1971). In contrast, 5 Gy of ionizing radiation can kill a human, 200-800 Gy of ionizing radiation will Received 12 March 2014; accepted 2 June 2014 Published online 26 June 2014 kill E. coli, and more than 4,000 Gy of ionizing radiation will kill the radiation-resistant tardigrade. D. radiodurans can survive 5,000 to 30,000 Gy of ionizing radiation, Abstract which breaks its genome into hundreds of fragments (Daly Deinococcus radiodurans is unmatched among all known & Minton, 1995; Minton, 1994; Slade & Radman, 2011). species in its ability to resist ionizing radiation and other Surprisingly, the genome is reassembled accurately before DNA-damaging factors. It is considered a model organism beginning of the next cycle of cell division.