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A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L
JOURNAL OF BACTERIOLOGY, Feb. 1990, p. 756-761 Vol. 172, No. 2 0021-9193/90/020756-06$02.00/0 Copyright © 1990, American Society for Microbiology A Plasmid Vector with a Selectable Marker for Halophilic Archaebacteria MELISSA L. HOLMES* AND MICHAEL L. DYALL-SMITH Department of Microbiology, University of Melbourne, Parkville, Victoria 3052, Australia Received 25 May 1989/Accepted 10 November 1989 A mutant resistant to the gyrase inhibitor novobiocin was selected from a halophilic archaebacterium belonging to the genus Haloferax. Chromosomal DNA from this mutant was able to transform wild-type ceils to novobiocin resistance, and these transformants formed visible colonies in 3 to 4 days on selective plates. The resistance gene was isolated on a 6.7-kilobase DNA KpnI fragment, which was inserted into a cryptic multicopy plasmid (pHK2) derived from the same host strain. The recombinant plasmid transformed wild-type cells at a high efficiency (>106/pg), was stably maintained, and could readily be reisolated from transformants. It could also transform Halobacterium volcanii and appears to be a useful system for genetic analysis in halophilic archaebacteria. Archaebacteria are phylogenetically distinct from eubac- cle was the lack of selectable traits, such as antibiotic teria and eucaryotes and can be broadly divided into three resistance. groups: methanogens, sulfur-dependent thermoacidophiles, The aim of this study was to find a selectable marker for and extreme halophiles (for a review, see reference 22). use in constructing plasmid vectors suitable for isolating and Numerous halobacteria have been isolated from hypersaline studying genes in halobacteria. We report the successful environments around the world, but it is only recently that construction of such a vector by using a gene conferring their taxonomy has been analyzed in a rigorous and compre- resistance to novobiocin and a cryptic plasmid from Halo- hensive fashion. -
Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past. -
Characterization of the First Cultured Representative of Verrucomicrobia Subdivision 5 Indicates the Proposal of a Novel Phylum
The ISME Journal (2016) 10, 2801–2816 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum Stefan Spring1, Boyke Bunk2, Cathrin Spröer3, Peter Schumann3, Manfred Rohde4, Brian J Tindall1 and Hans-Peter Klenk1,5 1Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 2Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 3Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and 4Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. -
The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. -
Across the Tree of Life, Radiation Resistance Is Governed By
Across the tree of life, radiation resistance is PNAS PLUS + governed by antioxidant Mn2 , gauged by paramagnetic resonance Ajay Sharmaa,1, Elena K. Gaidamakovab,c,1, Olga Grichenkob,c, Vera Y. Matrosovab,c, Veronika Hoekea, Polina Klimenkovab,c, Isabel H. Conzeb,d, Robert P. Volpeb,c, Rok Tkavcb,c, Cene Gostincarˇ e, Nina Gunde-Cimermane, Jocelyne DiRuggierof, Igor Shuryakg, Andrew Ozarowskih, Brian M. Hoffmana,i,2, and Michael J. Dalyb,2 aDepartment of Chemistry, Northwestern University, Evanston, IL 60208; bDepartment of Pathology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814; cHenry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817; dDepartment of Biology, University of Bielefeld, Bielefeld, 33615, Germany; eDepartment of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, SI-1000, Slovenia; fDepartment of Biology, Johns Hopkins University, Baltimore, MD 21218; gCenter for Radiological Research, Columbia University, New York, NY 10032; hNational High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306; and iDepartment of Molecular Biosciences, Northwestern University, Evanston, IL 60208 Contributed by Brian M. Hoffman, September 15, 2017 (sent for review August 1, 2017; reviewed by Valeria Cizewski Culotta and Stefan Stoll) Despite concerted functional genomic efforts to understand the agents of cellular damage. In particular, irradiated cells rapidly form •− complex phenotype of ionizing radiation (IR) resistance, a genome superoxide (O2 ) ions by radiolytic reduction of both atmospheric sequence cannot predict whether a cell is IR-resistant or not. Instead, O2 and O2 released through the intracellular decomposition of IR- we report that absorption-display electron paramagnetic resonance generated H2O2 ascatalyzedbybothenzymaticandnonenzymatic (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR •− metal ions. -
Potential Biotechnological Applications of Cyanobacterial Exopolysaccharides
Vol.64: e21200401, 2021 https://doi.org/10.1590/1678-4324-2021200401 ISSN 1678-4324 Online Edition Review - Agriculture, Agribusiness and Biotechnology Potential Biotechnological Applications of Cyanobacterial Exopolysaccharides Laxmi Parwani1* https://orcid.org/0000-0001-7627-599X Medha Bhatt1 https://orcid.org/0000-0002-2411-8172 Jaspreet Singh2 https://orcid.org/0000-0003-2470-3280 1Banasthali Vidyapith, Department of Bioscience and Biotechnology, P.O. Banasthali, Rajasthan, India; 2 Jaipur National University, SIILAS Campus, School of Life Sciences, Jaipur, Rajasthan, India. Editor-in-Chief: Paulo Vitor Farago Associate Editor: Aline Alberti Received: 2020.06.24; Accepted: 2021.02.24. *Correspondence: [email protected]; Tel.: +91-9982216197 HIGHLIGHTS Illustration of various important fields of biotechnology where cyanobacterial exopolysaccharides are potentially useful. Discussion of research gaps and new opportunities to make the biomaterial suitable for industrial uses. Abstract: The cyanobacterial exopolysaccharides (EPSs) are considered as one of the important group of biopolymers having significant ecological, industrial, and biotechnological importance. Cyanobacteria are regarded as a very abundant source of structurally diverse, high molecular weight polysaccharides having variable composition and roles according to the organisms and the environmental conditions in which they are produced. Due to their structural complexity, versatility and valuable biological properties, they are now emerging as high-value compounds. -
Determination of Hydrolytic Enzyme Capabilities of Halophilic Archaea Isolated from Hides and Skins and Their Phenotypic and Phylogenetic Identification by S
33 DETERMinATION OF HYDROLYTic ENZYME CAPABILITIES OF HALOPHILIC ARCHAEA ISOLATED FROM HIDES AND SKins AND THEIR PHENOTYpic AND PHYLOGENETic IDENTIFicATION by S. T. B LG School of Health, Canakkale Onsekiz Mart University, Terzioglu Campus Canakkale, Turkey, 17100. and B. MER ÇL YaPiCi Biology Department, Faculty of Arts and Science, Canakkale ONSEKIZ MART UNIVERSITY, TERZIOGLU CAMPUS, Canakkale, Turkey, 17100. and İsmail Karaboz Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, İzmi r, Turkey, 35100. ABSTRACT INTRODUCTION This research aims to isolate extremely halophilic archaea The main constituent of the raw hide is protein, mainly from salted hides, to determine the capacities of their collagen (33% w/w), and remainder is moisture and fat. During hydrolytic enzymes, and to identify them by using phenotypic storage of raw hide, collagen’s excessive proteolysis by and molecular methods. Domestic and imported salted hide lysosomal autolysis or proteolytic bacterial enzymes can lead and skin samples obtained from eight different sources were to the disintegration of the structure of collagen fibers.1 used as the research material. 186 extremely halophilic Biodeterioration is among the major causes of impairment of microorganisms were isolated from salted raw hides and aesthetic, functional and other properties of leather and other skins. Some biochemical, antibiotic sensitivity, pH, NaCl, biopolymers or organic materials and the products made from temperature tolerance and quantitative and qualitative them. Due to the fact that prevention of biological degradation hydrolytic enzyme tests were performed on these isolates. In is very important in conservation and processing of leather, our study, taking into account the phenotypic findings of the great effort is being made for decontamination of these research, 34 of 186 isolates were selected. -
Characterization and Identification of an Isolate of Halobacterium from Soda Springs Mojave Desert
California State University, San Bernardino CSUSB ScholarWorks Theses Digitization Project John M. Pfau Library 1979 Characterization and identification of an isolate of halobacterium from Soda Springs Mojave Desert Abayomi Odubela Follow this and additional works at: https://scholarworks.lib.csusb.edu/etd-project Part of the Biology Commons, and the Desert Ecology Commons Recommended Citation Odubela, Abayomi, "Characterization and identification of an isolate of halobacterium from Soda Springs Mojave Desert" (1979). Theses Digitization Project. 67. https://scholarworks.lib.csusb.edu/etd-project/67 This Thesis is brought to you for free and open access by the John M. Pfau Library at CSUSB ScholarWorks. It has been accepted for inclusion in Theses Digitization Project by an authorized administrator of CSUSB ScholarWorks. For more information, please contact [email protected]. CHARAG'liERIZATION AND IDENT'IFICATION GF AN ISOLATl OF HALOBACTERIUM FROM SODA:SPRINGS. MOJAVE DESERT —, A Thesis Presented to the Faculty of California State Cblleges San Bernardino in Partial FulfilIment of the.Requirements for the .Degree Master of Science in: • . Biology hy . Abayomi Qdubela April 1979 CHARACTERIZATION AND IDENTIFICATION OF AN ISOLATE OF . HALOBACTERIUM FROM SODA SPRINGS MO J AYE 'DESERT A Thesis .. Preisented to the Faculty of California State College, San Bernardino by Abayomi Odubela April 1979 Approved bys Gh^i»arson Biol _ Date Graduate Committee Corama^tee Member Co mi itt Member Mayor Professor ■ . Representative of^he Graduate^ Dean ABSTRACT : : A strai|i of Halobacterium . isolated from a vond at the California State Universities and Colleges Desert . Studies Center |at, Soda Springs, Mojave Desert, California „ was studied in order to define its taxonomic placeuin the genus Halohactelrium. -
Natronococcus Arnylolyticus Sp. Nov., a Haloalkaliphilic Archaeon
INTERNATIONAL JOURNALOF SYSTEMATIC BACTERIOLOGY,OCt. 1995, p. 762-766 Vol. 45, No. 4 0020-7713/95/$04.00+O Copyright 0 1995, International Union of Microbiological Societies Natronococcus arnylolyticus sp. nov., a Haloalkaliphilic Archaeon HARUHIKO KANA1,l TETSUO KOBAYASHI,2* RIKIZO AONO,' AND TOSHIAKI KUDO2 Department of Bioengineering, Tokyo Institute of Technoloa, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 227 and Laboratory of Microbiology, Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako, Saitama 351-01,* Japan The a-amylase-producing haloalkaliphilic archaeon Natronococcus sp. strain Ah-36T (T = type strain) was isolated previously from a Kenyan soda lake, Lake Magadi. Most cells of strain Ah-3(iT occurred in irregular clusters, and the colonies were orange-red. The polar lipids of this organism were composed of CZ0,C,, and C,,, C,, derivatives of phosphatidylglycerol and phosphatidylglycerophosphate.Phosphatidylglycero-(cyclo-) phosphate, which is characteristic of Natronococcus occultus, was not detected. The complete nucleotide se- quence of the 16s rRNA gene revealed that the closest relative of strain Ah-3tiT is N. occultus ATCC43101T (level of similarity, 96.4%), an extremely halophilic archaeon. However, strain Ah-36T did not exhibit a significant level of DNA homology to N. occultus ATCC43101T, which represents the only previously described species in the genus Natronococcus. We describe a new species for strain Ah-36T, for which we propose the name Natronococcus arnylolyticus. The extremely halophilic archaea are currently placed in six scribe a new species for this organism, for which we propose validly described genera, including two genera of haloalkali- the name Natronococcus amylolyticus. philes, which are characterized by their alkaliphily and very low Mg2+ requirements (3). -
Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks
Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez M¨unchen, 2009 Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez Dissertation an der Fakult¨at f¨ur Mathematik, Informatik und Statistik der Ludwig-Maximilians-Universit¨at M¨unchen vorgelegt von Orland Gonzalez aus Manila M¨unchen, den 02.03.2009 Erstgutachter: Prof. Dr. Ralf Zimmer Zweitgutachter: Prof. Dr. Dieter Oesterhelt Tag der m¨undlichen Pr¨ufung: 21.01.2009 Contents Summary xiii Zusammenfassung xvi 1 Introduction 1 2 The Halophilic Archaea 9 2.1NaturalEnvironments............................. 9 2.2Taxonomy.................................... 11 2.3PhysiologyandMetabolism.......................... 14 2.3.1 Osmoadaptation............................ 14 2.3.2 NutritionandTransport........................ 16 2.3.3 Motility and Taxis ........................... 18 2.4CompletelySequencedGenomes........................ 19 2.5DynamicsofBlooms.............................. 20 2.6Motivation.................................... 21 3 The Metabolism of Halobacterium salinarum 23 3.1TheModelArchaeon.............................. 24 3.1.1 BacteriorhodopsinandOtherRetinalProteins............ 24 3.1.2 FlexibleBioenergetics......................... 26 3.1.3 Industrial Applications ......................... 27 3.2IntroductiontoMetabolicReconstructions.................. 27 3.2.1 MetabolismandMetabolicPathways................. 27 3.2.2 MetabolicReconstruction....................... 28 3.3Methods.................................... -
Protective Roles of Bacterioruberin and Intracellular Kcl in the Resistance of Halobacterium Salinarium Against DNA-Damaging Agents
Protective Roles of Bacterioruberin and Intracellular KCl in the Resistance of Halobacterium salinarium against DNA-damaging Agents HAMID REZA SHAHMOHAMMADI, EZAT ASGARANI, HIROAKI TERATO, TAKESHI SAITO, YOSHIHIKO OHYAMA, KUNIHIKO GEKKO, OSAMU YAMAMOTO and HIROSHI IDE* Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8 526, Japan (Received, March 16, 1998) (Revision received, October 15, 1998) (Accepted, October 30, 1998) Halobacterium salinarium/Bacterioruberin/Salt effect! Radiation/DNA-damage Halobacteriumm salinarium, a member of the extremely halophilic archaebacteria, contains a C50-caro tenoid namely bacterioruberin. We have previously reported the high resistance of this organism against the lethal actions of DNA-damaging agents including ionizing radiation and ultraviolet light (UV). In this study, we have examined whether bacterioruberin and the highly concentrated salts in this bacterium play protec tive roles against the lethal actions of ionizing radiation, UV, hydrogen peroxide, and mitomycin-C (MMC). The colourless mutant of H. salinarium deficient in bacterioruberin was more sensitive than the red-pigmented wild-type to all tested DNA-damaging agents except MMC. Circular dichroism (CD) spec tra of H. salinarium chromosomal DNA at various concentrations of KCI (0-3.5 M) were similar to that of B-DNA, indicating that no conformational changes occurred as a result of high salt concentrations. How ever, DNA strand-breaks induced by ionizing radiation were significantly reduced by the presence of either bacterioruberin or concentrated KCI, presumably due to scavenging of free radicals. These results suggest that bacterioruberin and intracellular KC1 of H. salinarium protect this organism against the lethal effects of oxidative DNA-damaging agents. -
Halobacterium Salinarum NRC-1
Hindawi Publishing Corporation Archaea Volume 2011, Article ID 716456, 13 pages doi:10.1155/2011/716456 Research Article Regulatory Multidimensionality of Gas Vesicle Biogenesis in Halobacterium salinarum NRC-1 Andrew I. Yao and Marc T. Facciotti Genome Center UC Davis, Department of Biomedical Engineering, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA Correspondence should be addressed to Marc T. Facciotti, [email protected] Received 18 June 2011; Accepted 7 August 2011 Academic Editor: Jerry Eichler Copyright © 2011 A. I. Yao and M. T. Facciotti. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. It is becoming clear that the regulation of gas vesicle biogenesis in Halobacterium salinarum NRC-1 is multifaceted and appears to integrate environmental and metabolic cues at both the transcriptional and posttranscriptional levels. The mechanistic details underlying this process, however, remain unclear. In this manuscript, we quantify the contribution of light scattering made by both intracellular and released gas vesicles isolated from Halobacterium salinarum NRC-1, demonstrating that each form can lead to distinct features in growth curves determined by optical density measured at 600 nm (OD600).Inthecourseofthestudy,we also demonstrate the sensitivity of gas vesicle accumulation in Halobacterium salinarum NRC-1 on small differences in growth conditions and reevaluate published works in the context of our results to present a hypothesis regarding the roles of the general transcription factor tbpD and the TCA cycle enzyme aconitase on the regulation of gas vesicle biogenesis.