Extremophiles and Their Biocatalytic Potential Anuj Sharma1, Rimpy Sharma2, Tishu Devi3 1,2Department of Biotechnology, Govt
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Life at Low Water Activity
Published online 12 July 2004 Life at low water activity W. D. Grant Department of Infection, Immunity and Inflammation, University of Leicester, Maurice Shock Building, University Road, Leicester LE1 9HN, UK ([email protected]) Two major types of environment provide habitats for the most xerophilic organisms known: foods pre- served by some form of dehydration or enhanced sugar levels, and hypersaline sites where water availability is limited by a high concentration of salts (usually NaCl). These environments are essentially microbial habitats, with high-sugar foods being dominated by xerophilic (sometimes called osmophilic) filamentous fungi and yeasts, some of which are capable of growth at a water activity (aw) of 0.61, the lowest aw value for growth recorded to date. By contrast, high-salt environments are almost exclusively populated by prokaryotes, notably the haloarchaea, capable of growing in saturated NaCl (aw 0.75). Different strategies are employed for combating the osmotic stress imposed by high levels of solutes in the environment. Eukaryotes and most prokaryotes synthesize or accumulate organic so-called ‘compatible solutes’ (osmolytes) that have counterbalancing osmotic potential. A restricted range of bacteria and the haloar- chaea counterbalance osmotic stress imposed by NaCl by accumulating equivalent amounts of KCl. Haloarchaea become entrapped and survive for long periods inside halite (NaCl) crystals. They are also found in ancient subterranean halite (NaCl) deposits, leading to speculation about survival over geological time periods. Keywords: xerophiles; halophiles; haloarchaea; hypersaline lakes; osmoadaptation; microbial longevity 1. INTRODUCTION aw = P/P0 = n1/n1 ϩ n2, There are two major types of environment in which water where n is moles of solvent (water); n is moles of solute; availability can become limiting for an organism. -
Marine Extremophiles: a Source of Hydrolases for Biotechnological Applications
Mar. Drugs 2015, 13, 1925-1965; doi:10.3390/md13041925 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications Gabriel Zamith Leal Dalmaso 1,2, Davis Ferreira 3 and Alane Beatriz Vermelho 1,* 1 BIOINOVAR—Biotechnology laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] 2 Graduate Program in Plant Biotechnology, Health and Science Centre, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil 3 BIOINOVAR—Biotechnology Laboratories: Virus-Cell Interaction, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-(21)-3936-6743; Fax: +55-(21)-2560-8344. Academic Editor: Kirk Gustafson Received: 1 December 2014 / Accepted: 25 March 2015 / Published: 3 April 2015 Abstract: The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. -
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. -
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. -
Mesohaline Responses to Cycles of “Famine Or Feast” in Layered Brines
Int. Assoc. Sedimentol. Spec. Publ. (2011) 43, 315–392 Evaporitic source rocks: mesohaline responses to cycles of “famine or feast” in layered brines JOHN K. WARREN International Master Program in Petroleum Geoscience, Department of Geology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand. Formerly: Shell Professor in Carbonate Studies, Oil and Gas Research Centre, Sultan Qaboos University, Muscat, Oman (E-mail: [email protected]) ABSTRACT Organic matter in modern saline systems tends to accumulate in bottom sediments beneath a density-stratified mass of saline water where layered hydrologies are subject to oscillations in salinity and brine level. Organic matter is not produced at a constant rate in such systems; rather, it is generated in pulses by a halotolerant community in response to relatively short times of less stressful conditions (brackish to mesohaline) that occur in the upper part of the layered hydrology. Accumulations of organic matter can occur in any layered brine lake or epeiric seaway when an upper less-saline water mass forms on top of nutrient-rich brines, or in wet mudflats wherever waters freshen in and above the uppermost few millimetres of a microbial mat. A flourishing community of halotolerant algae, bacteria and archaeal photosynthesizers drives the resulting biomass bloom. Brine freshening is a time of “feast” characterized by very high levels of organic productivity. In a stratified brine column (oligotrophic and meromictic) the typical producers are planktonic algal or cyanobacterial communities inhabiting the upper mesohaline portion of the stratified water mass. In mesohaline holomictic waters, where light penetrates to the water bottom, the organic-producing layer is typically the upper algal and bacterial portion of a benthic laminated microbialite characterized by elevated numbers of cyanobacteria. -
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus Solfataricus
Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis committee Thesis supervisors Prof. dr. J. van der Oost Personal chair at the laboratory of Microbiology Wageningen University Prof. dr. W. M. de Vos Professor of Microbiology Wageningen University Other members Prof. dr. W.J.H. van Berkel Wageningen University Prof. dr. V.A.F. Martins dos Santos Wageningen University Dr. T.J.G. Ettema Uppsala University, Sweden Dr. S.V. Albers Max Planck Institute for Terrestrial Microbiology, Marburg, Germany This research was conducted under the auspices of the Graduate School VLAG Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus Jasper Walther Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Monday 23 January 2012 at 11 a.m. in the Aula. Jasper Walther Post-Genomic Characterization of Metabolic Pathways in Sulfolobus solfataricus, 164 pages. Thesis, Wageningen University, Wageningen, NL (2012) With references, with summaries in Dutch and English ISBN 978-94-6173-203-3 Table of contents Chapter 1 Introduction 1 Chapter 2 Hot Transcriptomics 17 Chapter 3 Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis 45 Chapter 4 Identification of the Missing -
Chapter 1 Introduction
VU Research Portal A step towards the molecular detection of life on Mars Oliveira Lebre Direito, M.S. 2012 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Oliveira Lebre Direito, M. S. (2012). A step towards the molecular detection of life on Mars. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 30. Sep. 2021 Chapter 1 Introduction 9 Chapter 1. Introduction The chemistry of life. What is life? One of the current definitions of life states that life is a self-replicating system capable of evolution (Pace, 2001). Others require a living entity to be able to maintain itself vis-a-vis substantial challenges and to rebuild itself after incurring damage, all of this in substantial autonomy (Westerhoff and Hofmeyr, 2005). -
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Downloaded from genome.cshlp.org on September 27, 2021 - Published by Cold Spring Harbor Laboratory Press Letter A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History Vincent Daubin1, Manolo Gouy, and Guy Perrie`re Laboratoire de Biome´trie et Biologie E´volutive, Unite´Mixte de Recherche Centre National de la Recherche Scientifique, Universite´ Claude Bernard –Lyon 1, 69622 Villeurbanne Cedex, France It has been claimed that complete genome sequences would clarify phylogenetic relationships between organisms, but up to now, no satisfying approach has been proposed to use efficiently these data. For instance, if the coding of presence or absence of genes in complete genomes gives interesting results, it does not take into account the phylogenetic information contained in sequences and ignores hidden paralogies by using a BLAST reciprocal best hit definition of orthology. In addition, concatenation of sequences of different genes as well as building of consensus trees only consider the fewgenes that are shared amo ng all organisms. Here we present an attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny. This led us to perform a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny. We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria. Though it seems sensible to consider that genes remain asso- base a reference prokaryotic phylogeny on evidence derived ciated in genomes for long periods in Eukaryotes, recent data from a large number of genes. -
The Genus Wallemia—From Contamination of Food to Health Threat
microorganisms Review The Genus Wallemia—From Contamination of Food to Health Threat Janja Zajc 1,2 and Nina Gunde-Cimerman 2,* 1 National Institute of Biology, Veˇcnapot 111, SI-1000 Ljubljana, Slovenia; [email protected] 2 Biology Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia * Correspondence: [email protected]; Tel: +386-1-3203400 Received: 11 April 2018; Accepted: 18 May 2018; Published: 21 May 2018 Abstract: The fungal genus Wallemia of the order Wallemiales (Wallemiomycotina, Basidiomycota) comprises the most xerotolerant, xerophilic and also halophilic species worldwide. Wallemia spp. are found in various osmotically challenged environments, such as dry, salted, or highly sugared foods, dry feed, hypersaline waters of solar salterns, salt crystals, indoor and outdoor air, and agriculture aerosols. Recently, eight species were recognized for the genus Wallemia, among which four are commonly associated with foods: W. sebi, W. mellicola, W. muriae and W. ichthyophaga. To date, only strains of W. sebi, W. mellicola and W. muriae have been reported to be related to human health problems, as either allergological conditions (e.g., farmer’s lung disease) or rare subcutaneous/cutaneous infections. Therefore, this allergological and infective potential, together with the toxins that the majority of Wallemia spp. produce even under saline conditions, defines these fungi as filamentous food-borne pathogenic fungi. Keywords: Wallemia; food; air; pathogen; xerophile; halophile; mycotoxin; farmer’s lung disease; subcutaneous infection 1. Introduction Low availability of water is one of the most life-limiting factors, and only specially adapted organisms can cope with such stress in their environment. -
BMC Genetics Biomed Central
BMC Genetics BioMed Central Research article Open Access Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA James A Coker* and Shiladitya DasSarma Address: University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202, USA Email: James A Coker* - [email protected]; Shiladitya DasSarma - [email protected] * Corresponding author Published: 24 September 2007 Received: 15 February 2007 Accepted: 24 September 2007 BMC Genetics 2007, 8:61 doi:10.1186/1471-2156-8-61 This article is available from: http://www.biomedcentral.com/1471-2156/8/61 © 2007 Coker and DasSarma; 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 Background: Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including Halobacterium sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters. Results: We attempted to knock out all six TBP and seven TFB genes in Halobacterium sp. NRC- 1 using the ura3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, tbpCDF and tfbACG, indicating that they are not essential for cell viability under standard conditions.