DOCSLIB.ORG

Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof. dr. ir. D. Springael, Catholic University of Leuven Prof. dr. S. C. de Vries, Wageningen University This project was conducted under the auspices of the graduate school SENSE (Socio-Economic and Natural Sciences of the Environment) Thesis-MJOosterkamp.indd 2 25-11-2013 6:42:09 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday December 18 2013 at 4:00 p.m. in the Aula of Wageningen University Thesis-MJOosterkamp.indd 3 25-11-2013 6:42:09 Margreet J. Oosterkamp Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor 191 pages. Thesis, Wageningen University, Wageningen, NL (2013) With references, with summaries in English and Dutch ISBN 978-94-6173-777-9 Thesis-MJOosterkamp.indd 4 25-11-2013 6:42:10 Dedicated to my parents ‘Je kunt het altijd proberen (You can always try)’ Thesis-MJOosterkamp.indd 5 25-11-2013 6:42:10 Preface In situ bioremediation by using naturally occurring or introduced microorganisms is a very attractive option for remediation of anoxic polluted soil sites. Often the appropriate conditions for microorganisms need to be created and the introduction of electron acceptors is required. Oxygen can be introduced by aeration, however, this is difficult to achieve and very costly. We focused on the use of the alternative electron acceptors nitrate and chlorate. Nitrate and chlorate are more soluble than oxygen and easy to introduce in soil via the groundwater. Some microorganisms are known to degrade soil pollutants with nitrate and/or chlorate. Nitrate-reduction is used as a method for bioremediation of anaerobic polluted soil sites. Degradation of aromatic hydrocarbons is known to involve anaerobic pathways. Interestingly, an alternative nitrate reduction pathway in which oxygen is produced was found. This light-independent in situ oxygen production offers innovative possibilities for bioremediation of anaerobic soils polluted with aromatic hydrocarbons, for example. Biochemical routes for the degradation of such hydrocarbons require mono- and dioxygenases. These enzymes cannot function under anaerobic conditions. Because of the production of oxygen from an alternative nitrate reduction pathway, oxygenases could function. Similarly, oxygen is produced when chlorate is the electron acceptor. Laboratory experiments and additional tests in the field showed that chlorate-enhanced anaerobic benzene degradation with chlorate is possible. A stable enrichment that degraded benzene with chlorate at comparable high rates as reported for aerobic benzene-degrading cultures and at 10 to 100 times higher rates than reported for anaerobic benzene-degrading cultures was obtained. One of the bacteria from this enrichment, a novel Alicycliphilus strain, has been obtained in pure culture. This bacterium degrades benzene and some other aromatic hydrocarbons with chlorate as electron acceptor, but not with nitrate as electron acceptor. The general aim of this project was to get insight into the physiological and biochemical properties of this bacterium and of other aromatic hydrocarbon degrading bacteria that use nitrate and/or chlorate as electron acceptor. Thesis-MJOosterkamp.indd 6 25-11-2013 6:42:10 Contents Page Chapter 1 General introduction 8 Chapter 2 Genome analysis and physiological comparison of 23 T Alicycliphilus denitrificans strains BC and K601 Chapter 3 Metabolic response of Alicycliphilus denitrificans strain BC 43 toward electron acceptor variation Chapter 4 Chlorate-dependent transposon-mediated modification and 62 deletion of narG in Alicycliphilus denitrificans strain BC Chapter 5 Proteomics of nitrate-dependent acetone degradation by 74 Alicycliphilus denitrificans strain BC Chapter 6 Isolation and characterization of the benzene-degrading 87 Pseudomonas stutzeri strain BN Chapter 7 Genome-based metabolic potentials of the anaerobic, 108 monoaromatic compound-degrading bacteriumGeorgfuchsia toluolica strain G5G6T Chapter 8 Proteome and genome analysis of Pseudomonas 127 chloritidismutans AW-1T that oxidizes n-decane with chlorate or oxygen as electron acceptor Chapter 9 General discussion 142 Thesis summary 153 Samenvatting proefschrift 158 References 163 Publications of the author 180 About the author 182 Acknowledgements 184 Certificate of educational PhD programme 188 Thesis-MJOosterkamp.indd 7 25-11-2013 6:42:10 Chapter 1 General introduction 8 Thesis-MJOosterkamp.indd 8 25-11-2013 6:42:10 Author and affiliations Margreet J. Oosterkamp1(a) 1 Wageningen University, Agrotechnology and food sciences group, Laboratory of microbiology, Dreijenplein 10, 6703HB, Wageningen, The Netherlands (a) Present address: Department of Animal Sciences, Energy Biosciences Institute, Institute of Genomic Biology, University of Illinois at Urbana-Champaign, 1207 W Gregory Drive, Urbana, Illinois 61801, USA. Keywords Perchlorate-reducing bacteria, chlorate-reducing bacteria, nitrate-reducing bacteria, chlorate reductase, nitrate reductase, chlorite dismutase Manuscript status Part of this thesis chapter has been published (Oosterkamp, Mehboob et al. 2011) 9 Thesis-MJOosterkamp.indd 9 25-11-2013 6:42:10 Abstract Bacteria that grow with aromatic and aliphatic hydrocarbons and use perchlorate, chlorate and/or nitrate as electron acceptor can be applied for bioremediation of soils polluted with aromatic and aliphatic hydrocarbons. Perchlorate, chlorate and nitrate are more soluble than oxygen and can reach anaerobic soil sites more readily than oxygen. Besides the beneficial effect of the addition of an electron acceptor, (per)chlorate-reducing bacteria possess chlorite dismutase that forms oxygen. This oxygen can be used to degrade aromatic and aliphatic hydrocarbons using aerobic pathways. Aerobic degradation of these compounds is a faster process than anaerobic degradation. (Per)chlorate- and nitrate-reducing microorganisms are present in various ecosystems and interact with each other. The nitrate reduction pathway has been studied in more detail than the perchlorate and chlorate reduction pathways. The nitrate reductase of the NarGHI-type, that converts nitrate to nitrite, can also convert chlorate to chlorite. Furthermore, the subunits of NarGHI-type nitrate reductase and of chlorate reductase are structurally very similar. To get more insight in the metabolism of aromatic and aliphatic hydrocarbon degrading bacteria that can use nitrate and/or chlorate as electron acceptor, further studies are needed. In this introduction chapter the research described in this thesis is defined. The background information summarized above is provided to increase understanding of the research described in this thesis and of the need to do this research. 10 Thesis-MJOosterkamp.indd 10 25-11-2013 6:42:10 Introduction Compared to cost-intensive chemical and physical methods for the clean-up of soil sites polluted with aromatic and aliphatic hydrocarbons, methods using naturally occurring or introduced microorganisms are an attractive option. Recent advances in genomics and proteomics allow more detailed research on such microorganisms (Zhao and Poh 2008). Optimal conditions for pollutant-degrading microorganisms often need to be created. For aromatic and aliphatic hydrocarbon-polluted anaerobic soils the introduction of oxygen via aeration may be used. However, aeration of anaerobic soils is difficult to achieve and very costly. An effective alternative is the use of chlorate or nitrate as terminal electron acceptors. Unlike
Load more

Recommended publications
  • Thesis, Dissertation
    THE COENZYME M BIOSYNTHETIC PATHWAY IN PROTEOBACTERIUM XANTHOBACTER AUTOTROPHICUS PY2 by Sarah Eve Partovi A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry MONTANA STATE UNIVERSITY Bozeman, Montana January 2018 ©COPYRIGHT by Sarah Eve Partovi 2018 All Rights Reserved ii DEDICATION I dedicate this dissertation to my family, without whom none of this would have been possible. My husband Ky has been a part of the graduate school experience since day one, and I am forever grateful for his support. My wonderful family; Iraj, Homa, Cameron, Shireen, Kevin, Lin, Felix, Toby, Molly, Noise, Dooda, and Baby have all been constant sources of encouragement. iii ACKNOWLEDGEMENTS First, I would like to acknowledge Dr. John Peters for his mentorship, scientific insight, and for helping me gain confidence as a scientist even during the most challenging aspects of this work. I also thank Dr. Jennifer DuBois for her insightful discussions and excellent scientific advice, and my other committee members Dr. Brian Bothner and Dr. Matthew Fields for their intellectual contributions throughout the course of the project. Drs. George Gauss and Florence Mus have contributed greatly to my laboratory technique and growth as a scientist, and have always been wonderful resources during my time in the lab. Members of the Peters Lab past and present have all played an important role during my time, including Dr. Oleg Zadvornyy, Dr. Jacob Artz, and future Drs. Gregory Prussia, Natasha Pence, and Alex Alleman. Undergraduate researchers/REU students including Hunter Martinez, Andrew Gutknecht and Leah Connor have worked under my guidance, and I thank them for their dedication to performing laboratory assistance.
    [Show full text]
  • Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
    University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon.
    [Show full text]
  • The Role of Genetic Variation in Predisposition to Alcohol-Related Chronic Pancreatitis
    The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Marianne Lucy Johnstone April 2015 The Role of Genetic Variation in Predisposition to Alcohol-related Chronic Pancreatitis 2015 Abstract Background Chronic pancreatitis (CP) is a disease of fibrosis of the pancreas for which alcohol is the main causative agent. However, only a small proportion of alcoholics develop chronic pancreatitis. Genetic polymorphism may affect pancreatitis risk. Aim To determine the factors required to classify a chronic pancreatic population and identify genetic variations that may explain why only some alcoholics develop chronic pancreatitis. Methods The most appropriate method of diagnosing CP was assessed using a systematic review. Genetics of different populations of alcohol-related chronic pancreatitics (ACP) were explored using four different techniques: genome-wide association study (GWAS); custom arrays; PCR of variable nucleotide tandem repeats (VNTR) and next generation sequencing (NGS) of selected genes. Results EUS and sMR were identified as giving the overall best sensitivity and specificity for diagnosing CP. GWAS revealed two associations with CP (identified and replicated) at PRSS1-PRSS2_rs10273639 (OR 0.73, 95% CI 0.68-0.79) and X-linked CLDN2_rs12688220 (OR 1.39, 1.28-1.49) and the association was more pronounced in the ACP group (OR 0.56, 0.48-0.64)and OR 2.11, 1.84-2.42). The previously identified VNTR in CEL was shown to have a lower frequency of the normal repeat in ACP than alcoholic liver disease (ALD; OR 0.61, 0.41-0.93).
    [Show full text]
  • 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
    [Show full text]
  • Transcriptional Regulation of the Acetone Carboxylase Operon Via Two-Component Signal Transduction in Helicobacter Pylori
    W&M ScholarWorks Undergraduate Honors Theses Theses, Dissertations, & Master Projects 7-2012 Transcriptional Regulation of the Acetone Carboxylase Operon via Two-Component Signal Transduction in Helicobacter pylori Samuel Emerson Harvey College of William and Mary Follow this and additional works at: https://scholarworks.wm.edu/honorstheses Part of the Biology Commons Recommended Citation Harvey, Samuel Emerson, "Transcriptional Regulation of the Acetone Carboxylase Operon via Two- Component Signal Transduction in Helicobacter pylori" (2012). Undergraduate Honors Theses. Paper 471. https://scholarworks.wm.edu/honorstheses/471 This Honors Thesis is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Undergraduate Honors Theses by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Transcriptional Regulation of the Acetone Carboxylase Operon via Two- Component Signal Transduction in Helicobacter pylori A thesis submitted in partial fulfillment of the requirement for the degree of Bachelor of Science in Biology from The College of William & Mary By Samuel Emerson Harvey Accepted for ____________________________ (Honors) _______________________________________ Dr. Mark Forsyth, Chair _______________________________________ Dr. Oliver Kerscher _______________________________________ Dr. Kurt Williamson _______________________________________ Dr. Randolph Coleman Williamsburg, VA April 30, 2012 Abstract Helicobacter pylori is a gram negative gastric pathogen that infects the mucosal lining of the human stomach and is present is nearly half of the human population. H. pylori is the etiologic agent of peptic ulcer disease, and infection is highly associated with the development of gastric cancer. The H. pylori genome encodes three complete two- component signal transduction systems (TCSTs): ArsRS, CrdRS, and FlgRS.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Enzyme DHRS7
    Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d.
    [Show full text]
  • 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.
    [Show full text]
  • Purification and Characterization of Acetone Carboxylase from Xanthobacter Strain Py2
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 8456–8461, August 1997 Biochemistry Purification and characterization of acetone carboxylase from Xanthobacter strain Py2 MIRIAM K. SLUIS AND SCOTT A. ENSIGN* Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300 Communicated by R. H. Burris, University of Wisconsin, Madison, WI, June 9, 1997 (received for review March 24, 1997) ABSTRACT Acetone metabolism in the aerobic bacte- aerobic, Gram-negative bacterium (14). The metabolism of rium Xanthobacter strain Py2 proceeds by a carboxylation acetone by Xanthobacter Py2 was recently shown to proceed by reaction forming acetoacetate as the first detectable product. aCO2-dependent pathway analogous to that discussed above In this study, acetone carboxylase, the enzyme catalyzing this (3). The carboxylation of acetone to form acetoacetate was reaction, has been purified to homogeneity and characterized. reconstituted in cell extracts with the addition of ATP (3). This Acetone carboxylase was comprised of three polypeptides with study provided the first direct evidence for the involvement of molecular weights of 85,300, 78,300, and 19,600 arranged in an an ATP-dependent carboxylase in bacterial acetone metabo- a2b2g2 quaternary structure. The carboxylation of acetone lism. In this study, acetone carboxylase has been purified to was coupled to the hydrolysis of ATP and formation of 1 mol homogeneity. The molecular properties of acetone carboxylase AMP and 2 mol inorganic phosphate per mol acetoacetate are described, and evidence for a novel mechanism of acetone formed. ADP was also formed during the course of acetone carboxylation coupled to ATP hydrolysis and AMP and inor- consumption, but only accumulated at low, substoichiometric ganic phosphate formation is presented.
    [Show full text]
  • Status Report on Innovative in Situ Treatment Technologies Available to Remediate Perchlorate- Contaminated Groundwater
    (ITRC, 2005) Status Report on Innovative In Situ Remediation Technologies Available to Treat Perchlorate-Contaminated Groundwater August 2006 Prepared By Jennifer Raye Hoponick National Network for Environmental Management Studies Fellow for U.S. Environmental Protection Agency Office of Superfund Remediation & Technology Innovation Technology Innovation & Field Services Division Washington, D.C. www.epa.gov www.clu-in.org Status Report on In Situ Treatment Technologies to Remediate Perchlorate-Contaminated Groundwater NOTICE This document was prepared by a National Network of Environmental Management studies grantee under a fellowship from the U.S. Environmental Protection Agency. This report was not subject to EPA peer review or technical review. The EPA makes no warranties, expressed or implied, including without limitation, warranty for completeness, accuracy, or usefulness of the information, warranties as to the merchantability, or fitness for a particular purpose. Moreover, the listing of any technology, corporation, company, person, or facility in this report does not constitute endorsement, approval, or recommendation by the EPA. The report contains information attained from a wide variety of currently available sources, including project documents, reports, periodicals, Internet websites, and personal communication with both academically and commercially employed sources. No attempts were made to independently confirm the resources used. It has been reproduced to help provide federal agencies, states, consulting engineering firms, private industries, and technology developers with information on the current status of this project. About the National Network for Environmental Management Studies The National Network for Environmental Management Studies (NNEMS) is a comprehensive fellowship program managed by the Environmental Education Division of EPA. The purpose of the NNEMS Program is to provide students with practical research opportunities and experiences.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 9,334,531 B2 Li Et Al
    USOO933.4531B2 (12) United States Patent (10) Patent No.: US 9,334,531 B2 Li et al. (45) Date of Patent: *May 10, 2016 (54) NUCLECACIDAMPLIFICATION (56) References Cited U.S. PATENT DOCUMENTS (71) Applicant: LIFE TECHNOLOGIES 5,223,414 A 6/1993 Zarling et al. CORPORATION, Carlsbad, CA (US) 5,616,478 A 4/1997 Chetverin et al. 5,670,325 A 9/1997 Lapidus et al. (72) Inventors: Chieh-Yuan Li, El Cerrito, CA (US); 5,928,870 A 7/1999 Lapidus et al. David Ruff, San Francisco, CA (US); 5,958,698 A 9, 1999 Chetverinet al. Shiaw-Min Chen, Fremont, CA (US); 6,001,568 A 12/1999 Chetverinet al. 6,033,881 A 3/2000 Himmler et al. Jennifer O'Neil, Wakefield, MA (US); 6,074,853. A 6/2000 Pati et al. Rachel Kasinskas, Amesbury, MA (US); 6,306,590 B1 10/2001 Mehta et al. Jonathan Rothberg, Guilford, CT (US); 6.432,360 B1 8, 2002 Church Bin Li, Palo Alto, CA (US); Kai Qin 6,440,706 B1 8/2002 Vogelstein et al. Lao, Pleasanton, CA (US) 6,511,803 B1 1/2003 Church et al. 6,929,915 B2 8, 2005 Benkovic et al. (73) Assignee: Life Technologies Corporation, 7,270,981 B2 9, 2007 Armes et al. 7,282,337 B1 10/2007 Harris Carlsbad, CA (US) 7,399,590 B2 7/2008 Piepenburg et al. 7.432,055 B2 * 10/2008 Pemov et al. ................ 435/6.11 (*) Notice: Subject to any disclaimer, the term of this 7,435,561 B2 10/2008 Piepenburg et al.
    [Show full text]
  • Complete Thesis
    University of Groningen Omega transaminases: discovery, characterization and engineering Palacio, Cyntia Marcela IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2019 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Palacio, C. M. (2019). Omega transaminases: discovery, characterization and engineering. Rijksuniversiteit Groningen. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. 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. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 01-10-2021 Omega transaminases: discovery, characterization and engineering Cyntia Marcela Palacio 2019 Cover design by Cyntia Palacio and Joris Goudsmits, adapted from a decorative mosaic artwork on the railway underpass on Moesstraat, Groningen.
    [Show full text]