DMSO Reductase Family: Phylogenetics and Applications of Extremophiles
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Resolving Electron Transport Pathways in the Selenate Respiring Bacterium Thauera Selenatis
RESOLVING ELECTRON TRANSPORT PATHWAYS IN THE SELENATE RESPIRING BACTERIUM THAUERA SELENATIS. Submitted by Elisabeth Clare Lowe To the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Sciences, July 2008. This thesis is available for Library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Elisabeth Clare Lowe Acknowledgements I would like to thank Clive Butler for all his help, support, encouragement and enthusiasm, especially during the move to Exeter and my last few months in the lab. Thanks to Ian Singleton for help and enthusiasm during my time in Newcastle. I also owe huge thanks to everyone in Team Butler, past and present, Carys Watts for helping me get started and all the help with the Thauera preps, Auntie Helen for being brilliant, Jim Leaver for rugby, beer, tea-offs and 30 hour growth curves and Lizzy Dridge for being a great friend and scientific team member, in and out of the lab. Thanks also to everyone in M3013 at the start of my PhD and everyone in the Biocat at the end, for lots of help, borrowing of equipment and most importantly, tea. Thanks to AFP for help, tea breaks and motivation, especially during the writing period. Thank you to everyone who has been generous with their time and equipment, namely Prof. -
Selenium Reduction by Shigella Fergusonii Strain Tb42616 and Pantoea Vagans Strain Ewb32213-2 in Bioreactor Systems
University of Kentucky UKnowledge Theses and Dissertations--Civil Engineering Civil Engineering 2019 BIOLOGICAL SELENIUM CONTROL: SELENIUM REDUCTION BY SHIGELLA FERGUSONII STRAIN TB42616 AND PANTOEA VAGANS STRAIN EWB32213-2 IN BIOREACTOR SYSTEMS Yuxia Ji University of Kentucky, [email protected] Author ORCID Identifier: https://orcid.org/0000-0002-4866-4856 Digital Object Identifier: https://doi.org/10.13023/etd.2019.393 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Ji, Yuxia, "BIOLOGICAL SELENIUM CONTROL: SELENIUM REDUCTION BY SHIGELLA FERGUSONII STRAIN TB42616 AND PANTOEA VAGANS STRAIN EWB32213-2 IN BIOREACTOR SYSTEMS" (2019). Theses and Dissertations--Civil Engineering. 91. https://uknowledge.uky.edu/ce_etds/91 This Doctoral Dissertation is brought to you for free and open access by the Civil Engineering at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Civil Engineering by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes
Sulfite dehydrogenases in organotrophic bacteria: enzymes, genes and regulation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sabine Lehmann Tag der mündlichen Prüfung: 10. April 2013 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Andrew W. B. Johnston So eine Arbeit wird eigentlich nie fertig, man muss sie für fertig erklären, wenn man nach Zeit und Umständen das möglichste getan hat. (Johann Wolfgang von Goethe, Italienische Reise, 1787) DANKSAGUNG An dieser Stelle möchte ich mich herzlich bei folgenden Personen bedanken: . Prof. Dr. Alasdair M. Cook (Universität Konstanz, Deutschland), der mir dieses Thema und seine Laboratorien zur Verfügung stellte, . Prof. Dr. Bernhard Schink (Universität Konstanz, Deutschland), für seine spontane und engagierte Übernahme der Betreuung, . Prof. Dr. Andrew W. B. Johnston (University of East Anglia, UK), für seine herzliche und bereitwillige Aufnahme in seiner Arbeitsgruppe, seiner engagierten Unter- stützung, sowie für die Übernahme des Koreferates, . Prof. Dr. Frithjof C. Küpper (University of Aberdeen, UK), für seine große Hilfsbereitschaft bei der vorliegenden Arbeit und geplanter Manuskripte, als auch für die mentale Unterstützung während der letzten Jahre! Desweiteren möchte ich herzlichst Dr. David Schleheck für die Übernahme des Koreferates der mündlichen Prüfung sowie Prof. Dr. Alexander Bürkle, für die Übernahme des Prüfungsvorsitzes sowie für seine vielen hilfreichen Ratschläge danken! Ein herzliches Dankeschön geht an alle beteiligten Arbeitsgruppen der Universität Konstanz, der UEA und des SAMS, ganz besonders möchte ich dabei folgenden Personen danken: . Dr. David Schleheck und Karin Denger, für die kritische Durchsicht dieser Arbeit, der durch und durch sehr engagierten Hilfsbereitschaft bei Problemen, den zahlreichen wissenschaftlichen Diskussionen und für die aufbauenden Worte, . -
Inactivation Mechanisms of Alternative Food Processes on Escherichia Coli O157:H7
INACTIVATION MECHANISMS OF ALTERNATIVE FOOD PROCESSES ON ESCHERICHIA COLI O157:H7 DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Aaron S. Malone, M.S. ***** The Ohio State University 2009 Dissertation Committee: Approved by Professor Ahmed E. Yousef, Adviser Professor Polly D. Courtney ___________________________________ Professor Tina M. Henkin Adviser Food Science and Nutrition Professor Robert Munson ABSTRACT Application of high pressure (HP) in food processing results in a high quality and safe product with minimal impact on its nutritional and organoleptic attributes. This novel technology is currently being utilized within the food industry and much research is being conducted to optimize the technology while confirming its efficacy. Escherichia coli O157:H7 is a well studied foodborne pathogen capable of causing diarrhea, hemorrhagic colitis, and hemolytic uremic syndrome. The importance of eliminating E. coli O157:H7 from food systems, especially considering its high degree of virulence and resistance to environmental stresses, substantiates the need to understand the physiological resistance of this foodborne pathogen to emerging food preservation methods. The purpose of this study is to elucidate the physiological mechanisms of processing resistance of E. coli O157:H7. Therefore, resistance of E. coli to HP and other alternative food processing technologies, such as pulsed electric field, gamma radiation, ultraviolet radiation, antibiotics, and combination treatments involving food- grade additives, were studied. Inactivation mechanisms were investigated using molecular biology techniques including DNA microarrays and knockout mutants, and quantitative viability assessment methods. The results of this research highlighted the importance of one of the most speculated concepts in microbial inactivation mechanisms, the disruption of intracellular ii redox homeostasis. -
Microbial (Per)Chlorate Reduction in Hot Subsurface Environments
Microbial (Per)chlorate Reduction in Hot Subsurface Environments Martin G. Liebensteiner Thesis committee Promotor Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University Co-promotor Dr Bart P. Lomans Principal Scientist Shell Global Solutions International B.V., Rijswijk Other members Prof. Dr Willem J.H. van Berkel, Wageningen University Prof. Dr Mike S.M. Jetten, Radboud University Nijmegen Prof. Dr Ian Head, Newcastle University, UK Dr Timo J. Heimovaara, Delft University of Technology This research was conducted under the auspices of the Graduate School for Socio-Economic and Natural Sciences of the Environment (SENSE) Microbial (Per)chlorate Reduction in Hot Subsurface Environments Martin G. Liebensteiner Thesis submitted in fulfi lment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnifi cus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 17 October 2014 at 4 p.m. in the Aula. Martin G. Liebensteiner Microbial (Per)chlorate Reduction in Hot Subsurface Environments 172 pages. PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN 978-94-6257-125-9 TABLE OF CONTENTS Chapter 1 General introduction and thesis outline 7 Chapter 2 Microbial redox processes in deep subsurface environments 23 and the potential application of (per)chlorate in oil reservoirs Chapter 3 (Per)chlorate reduction by the hyperthermophilic -
Investigation of the Redox Centres of Periplasmic Selenate Reductase
Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy Elizabeth J Dridge, Carys A Watts, Brian J Jepson, Kirsty Line, Joanne M Santini, David J Richardson, Clive S Butler To cite this version: Elizabeth J Dridge, Carys A Watts, Brian J Jepson, Kirsty Line, Joanne M Santini, et al.. Investigation of the redox centres of periplasmic selenate reductase from Thauera selenatis by EPR spectroscopy. Biochemical Journal, Portland Press, 2007, 408 (1), pp.19-28. 10.1042/BJ20070669. hal-00478807 HAL Id: hal-00478807 https://hal.archives-ouvertes.fr/hal-00478807 Submitted on 30 Apr 2010 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. Biochemical Journal Immediate Publication. Published on 10 Aug 2007 as manuscript BJ20070669 1 Investigation of the redox centres of selenate reductase from Thauera selenatis by electron paramagnetic resonance spectroscopy Elizabeth J. DRIDGE1,2†, Carys A. WATTS2†, Brian J.N. JEPSON3, Kirsty LINE1, Joanne M. SANTINI4, David J. RICHARDSON3 and Clive S. BUTLER1* 1School of -
Enzymes and Electron Transport in Microbial Chlorate Respiration
Faculty of Technology and Science Chemistry Jan Bohlin Enzymes and electron transport in microbial chlorate respiration DISSERTATION Karlstad University Studies 2008:36 Jan Bohlin Enzymes and electron transport in microbial chlorate respiration Karlstad University Studies 2008:36 Jan Bohlin. Enzymes and electron transport in microbial chlorate respiration DISSERTATION Karlstad University Studies 2008:36 ISSN 1403-8099 ISBN 978-91-7063-196-2 © The Author Distribution: Faculty of Technology and Science Chemistry 651 88 Karlstad 054-700 10 00 www.kau.se Printed at: Universitetstryckeriet, Karlstad 2008 Abstract Microbial chlorate respiration plays an important role in the turnover of oxochlorates in nature and in industrial waste management. This thesis deals with the characterization of the molecular components of chlorate respiration in Ideonella dechloratans. Chlorate respiration utilizes two soluble periplasmic enzymes, chlorate reductase and chlorite dismutase, to convert chlorate to chloride and oxygen. The genes encoding the enzymes participating in the chlorate degradation have been sequenced, and are found in close proximity, forming a gene cluster for chlorate metabolism. This work also includes the successful recombinant expression of three genes from Ideonella dechloratans. Two of the gene products, chlorite dismutase and the C subunit of chlorate reductase, participate in the chlorate respiration. The third gene, which is found close to the gene cluster for chlorate metabolism, encodes a soluble c-type cytochrome. The localization of the gene suggests the corresponding protein as a candidate for a role as electron donor to chlorate reductase. Also, the role of soluble periplasmic c cytochromes of Ideonella dechloratans in chlorate respiration was studied. At least one of the soluble c cytochromes was found capable of serving as electron donor for chlorate reduction. -
Supplementary Material Title Comparative Proteomic Analysis Of
Supplementary Material Title Comparative proteomic analysis of wild-type Physcomitrella patens and an OPDA-deficient Physcomitrella patens mutant with disrupted PpAOS1 and PpAOS2 genes after wounding Authors Weifeng Luoa, Setsuko Komatsub, Tatsuya Abea, Hideyuki Matsuuraa, and Kosaku Takahashia,c* Affiliations aResearch Faculty of Agriculture, Hokkaido University, Sapporo 606-8589, Japan bDepartment of Environmental and Food Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, 3-6-1 Gakuen, Fukui 910-8505, Japan cDepartment of Nutritional Science, Faculty of Applied BioScience, Tokyo University of Agriculture, Tokyo 165-8502, Japan. *To whom correspondence should be addressed: Tel.: +81-3-5477-2679; E-mail: [email protected]. Supplementary Fig. S1. Fig. S1. Disruption of PpAOS1 and PpAOS2 genes in P. p a te ns . A, Genomic structures of PpAOS1 and PpAOS2 in the wild-type and targeted PpAOS1 and PpAOS2 knock-out mutants (A5, A19, and A22). The npt II and aph IV expression cassettes were inserted in A5, A19, and A22 strains. B, Genomic PCR data of wild-type, and A5, A19 and A22 strains. P. patens genomic DNA was isolated from protonemata by the CTAB method (Nishiyama et al., Ref. 32). PCR was performed in 50 µL of a reaction mixture containing 1 µL of genomic DNA solution, 1.5 µL of each primer (5 µM), 25 µL of KOD One PCR Master Mix (Toyobo, Japan), and 21 µL of Milli-Q water. PCR was conducted with the following conditions: 30 cycles of 98°C for 10 s, 58°C for 5 s, and 68°C for 15 s. -
The Microbiota-Produced N-Formyl Peptide Fmlf Promotes Obesity-Induced Glucose
Page 1 of 230 Diabetes Title: The microbiota-produced N-formyl peptide fMLF promotes obesity-induced glucose intolerance Joshua Wollam1, Matthew Riopel1, Yong-Jiang Xu1,2, Andrew M. F. Johnson1, Jachelle M. Ofrecio1, Wei Ying1, Dalila El Ouarrat1, Luisa S. Chan3, Andrew W. Han3, Nadir A. Mahmood3, Caitlin N. Ryan3, Yun Sok Lee1, Jeramie D. Watrous1,2, Mahendra D. Chordia4, Dongfeng Pan4, Mohit Jain1,2, Jerrold M. Olefsky1 * Affiliations: 1 Division of Endocrinology & Metabolism, Department of Medicine, University of California, San Diego, La Jolla, California, USA. 2 Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. 3 Second Genome, Inc., South San Francisco, California, USA. 4 Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA. * Correspondence to: 858-534-2230, [email protected] Word Count: 4749 Figures: 6 Supplemental Figures: 11 Supplemental Tables: 5 1 Diabetes Publish Ahead of Print, published online April 22, 2019 Diabetes Page 2 of 230 ABSTRACT The composition of the gastrointestinal (GI) microbiota and associated metabolites changes dramatically with diet and the development of obesity. Although many correlations have been described, specific mechanistic links between these changes and glucose homeostasis remain to be defined. Here we show that blood and intestinal levels of the microbiota-produced N-formyl peptide, formyl-methionyl-leucyl-phenylalanine (fMLF), are elevated in high fat diet (HFD)- induced obese mice. Genetic or pharmacological inhibition of the N-formyl peptide receptor Fpr1 leads to increased insulin levels and improved glucose tolerance, dependent upon glucagon- like peptide-1 (GLP-1). Obese Fpr1-knockout (Fpr1-KO) mice also display an altered microbiome, exemplifying the dynamic relationship between host metabolism and microbiota. -
The DMSO Reductase Family of Microbial Molybdenum Enzymes Alastair G
SHOWCASE ON RESEARCH The DMSO Reductase Family of Microbial Molybdenum Enzymes Alastair G. McEwan and Ulrike Kappler Centre for Metals in Biology, School of Molecular and Microbial Sciences, University of Queensland, QLD 4072 Molybdenum is the only element in the second row of led to a division of the oxotransferases into the sulfite transition metals which has a defined role in biology. It dehydrogenase and the dimethylsulfoxide (DMSO) exhibits redox states of (VI), (V) and (IV) within a reductase families (Fig. 1) (4). The Mo hydroxylases biologically-relevant range of redox potentials and is and oxotransferases can act either as dehydrogenases capable of catalysing both oxygen atom transfer and or reductases in catalysis. This reaction can be proton/electron transfer. Apart from nitrogenase, all summarised by the general scheme: + - enzymes containing molybdenum have an active site X + H2O D X=O + 2H + 2e composed of a molybdenum ion coordinated by one or During this process the Mo ion cycles between the two ene-dithiolate (dithiolene) groups that arise from (IV) and (VI) oxidation states with electrons being an unusual organic moiety known as the pterin transferred to or from an electron transfer partner or molybdenum cofactor or pyranopterin (1,2). The substrate. Experiments with xanthine dehydrogenase mononuclear molybdenum enzymes exhibit remarkable using 18O-labelled water have confirmed that the diversity of function and this is in part due to variations oxygen is incorporated into the product during at the Mo active site that are additional to the common substrate oxidation and this distinguishes the core structure. Prior to the appearance of X-ray crystal mononuclear molybdoenzymes from monoxygenases structures of molybdenum enzymes, EPR spectroscopy, where molecular oxygen rather than water acts as an X-ray absorption fine structure spectroscopy (EXAFS) oxygen atom donor (5). -
Pseudomonas Stutzeri Biology Of
Biology of Pseudomonas stutzeri Jorge Lalucat, Antoni Bennasar, Rafael Bosch, Elena García-Valdés and Norberto J. Palleroni Microbiol. Mol. Biol. Rev. 2006, 70(2):510. DOI: 10.1128/MMBR.00047-05. Downloaded from Updated information and services can be found at: http://mmbr.asm.org/content/70/2/510 These include: http://mmbr.asm.org/ REFERENCES This article cites 395 articles, 145 of which can be accessed free at: http://mmbr.asm.org/content/70/2/510#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» on January 28, 2014 by Red de Bibliotecas del CSIC Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 2006, p. 510–547 Vol. 70, No. 2 1092-2172/06/$08.00ϩ0 doi:10.1128/MMBR.00047-05 Copyright © 2006, American Society for Microbiology. All Rights Reserved. Biology of Pseudomonas stutzeri Jorge Lalucat,1,2* Antoni Bennasar,1 Rafael Bosch,1 Elena Garcı´a-Valde´s,1,2 and Norberto J. Palleroni3 Departament de Biologia, Microbiologia, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain1; Institut Mediterrani d’Estudis Avanc¸ats (CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain2; and Department of Biochemistry and Microbiology, Rutgers University, Cook Campus, 3 New Brunswick, New Jersey 08901-8520 Downloaded from INTRODUCTION .......................................................................................................................................................511 -
A Bacterial Process for Selenium Nanosphere Assembly
A bacterial process for selenium nanosphere assembly Charles M. Debieuxa, Elizabeth J. Dridgea,1, Claudia M. Muellera,1, Peter Splatta, Konrad Paszkiewicza, Iona Knighta, Hannah Florancea, John Lovea, Richard W. Titballa, Richard J. Lewisb, David J. Richardsonc, and Clive S. Butlera,2 aBiosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom; bInstitute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom; and cSchool of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom Edited by Dianne K. Newman, California Institute of Technology/Howard Hughes Medical Institute, Pasadena, CA, and accepted by the Editorial Board July 1, 2011 (received for review April 13, 2011) Thauera selenatis 2− − þ 2− During selenate respiration by , the reduction of SeO4 þ 2e þ 2H ⇆ SeO3 þ H2O [1] selenate results in the formation of intracellular selenium (Se) deposits that are ultimately secreted as Se nanospheres of approxi- and mately 150 nm in diameter. We report that the Se nanospheres 2− − þ 0 SeO þ 4e þ 6H ⇆ Se þ 3H2O: [2] are associated with a protein of approximately 95 kDa. Subsequent 3 experiments to investigate the expression and secretion profile of Thauera selenatis (a β-proteobacterium) is by far the best-studied this protein have demonstrated that it is up-regulated and secreted selenate respiring bacterium (5–8). The selenate reductase in response to increasing selenite concentrations. The protein was (SerABC) isolated from T. selenatis (6) is a soluble periplasmic purified from Se nanospheres, and peptide fragments from a tryp- enzyme.