DOCSLIB.ORG

Functional Genomics of the Bacterial Degradation of the Emerging Water Contaminants: 1,4-Dioxane and N-Nitrosodimethylamine (NDMA)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Functional genomics of the bacterial degradation of the emerging water contaminants: 1,4-dioxane and N-nitrosodimethylamine (NDMA) by Christopher Michael Sales A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Engineering-Civil and Environmental Engineering in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Lisa Alvarez-Cohen, Chair Professor Kara L. Nelson Professor Mary K. Firestone Spring 2012 Functional genomics of the bacterial degradation of the emerging water contaminants: 1,4-dioxane and N-nitrosodimethylamine (NDMA) Copyright 2012 By Christopher Michael Sales Abstract Functional genomics of the bacterial degradation of the emerging water contaminants: 1,4-dioxane and N-nitrosodimethylamine (NDMA) by Christopher Michael Sales Doctor of Philosophy in Engineering - Civil & Environmental Engineering University of California, Berkeley Professor Lisa Alvarez-Cohen, Chair The emerging water contaminants 1,4-dioxane and N-nitrosodimethylamine (NDMA) are toxic and classified as probable human carcinogens. Both compounds are persistent in the environment and are highly mobile in groundwater plumes due to their hydrophilic nature. The major source of 1,4-dioxane is due to its use as a stabilizer in the chlorinated solvent 1,1,1-trichloroethane. The presence of NDMA as a water contaminant is related to the release of rocket fuels and its formation in the disinfection of water and wastewater. Prior studies have demonstrated that bacteria expressing monooxygenases are capable of degrading 1,4-dioxane and NDMA. While growth on 1,4-dioxane as a sole carbon and energy source has been reported in Pseudonocardia dioxanivorans CB1190 and Pseudonocardia benzenivorans B5, it is also co-metabolically degradable by a variety of monooxygenase-expressing strains. In contrast, NDMA has only been observed to biode- grade co-metabolically after growth on some monooxygenase-inducing substrates. The fastest rates of NDMA degradation occur in Rhodococcus sp. RR1 and Mycobacterium vaccae JOB5 after growth on propane. Pathways have been proposed for 1,4-dioxane biodegradation in P. dioxanivorans and for NDMA biodegradation in propane-induced Rhodococcus sp. RR1 based only on identified intermediates. The overall goal of this dissertation is to gain a better understanding of the genes and biological pathways respon- sible for degradation of 1,4-dioxane and NDMA. Due to the lack of molecular sequence information for organisms capable of growth on 1,4-dioxane, the genome of P. dioxanivorans strain CB1190 was sequenced in this study. The genome has a total size of 7,440,794 bp and consists of four replicons: a circular chromosome, a circular plasmid pPSED01, an unclosed circular plasmid pPSED02, and a linear plasmid pPSED03. Analysis of this genome sequence revealed the presence of eight multicomponent monooxygenases: a propane monooxygenase, a phenol mono- oxygenase, a 4-hydroxyphenylacetate monooxygenase, four aromatic (toluene) mono- oxygenases, and a tetrahydrofuran (THF) monooxygenase. A total of 92 genes identified as putative dioxygenases were identified. Protein-encoding genes involved in transport systems, signal transduction systems, secretion systems, and heavy-metal and antibiotic resistance were identified. The presence of pathways for carbon and nitrogen metabolism was examined. A complete Calvin-Benson-Bassham carbon fixation pathway was found and a number of carboxylases that function in other carbon fixation pathways were identi- fied. AlthoughP. dioxanivorans has been reported to fix nitrogen, no nitrogenase genes 1 were found. The genome sequence of P. dioxanivorans was compared to other sequenced genomes of members in the family Pseudonocardiaceae, including Amycolatopsis medi- terranei S699, Amycolatopsis mediterranei U32, Pseudonocardia sp. P1, Pseudonocardia sp. P2, Saccharomonaspora azurea NA-128, Saccharomonospora paurometabolica YIM 9007, Sacharomonospora viridis DSM43017, Saccharopolyspora erythraea NRRL2338, and Saccharopolyspora spinosa NRRL18395. Genome-aided approaches were employed to identify the protein-encoding genes in- volved in the metabolic degradation of 1,4-dioxane in P. dioxanivorans. These ap- proaches included whole genome expression microarray transcriptomics, quantitative reverse transcriptase PCR (qRT-PCR), enzyme assays, and heterologous expression clones. Genes differentially expressed during growth on 1,4-dioxane, glycolate (a pre- viously identified degradation intermediate), and pyruvate (control) were analyzed to determine genes differentially expressed and involved in the metabolism of 1,4-dioxane. Based on the differentially expressed genes, the 1,4-dioxane degradation pathway was revised and annotated with the enzymes known to catalyze specific transformation steps. Up-regulation of genes were confirmed and quantified by qRT-PCR. Transcriptional analyses, isotopic tracer analyses with 1,4-[U-13C]-dioxane, and glyoxylate carboligase enzymatic activity assays confirmed the role of glyoxylate as a central intermediate in the degradation of 1,4-dioxane. Specifically, transcriptional analyses indicated that the THF monooxygenase, encoded by thmADBC, is up-regulated during growth on 1,4-dioxane and THF. Furthermore, Rhodococcus jostii RHA1 clones heterologously expressing the P. dioxanivorans genes thmADBC demonstrated 1,4-dioxane and THF degradation activity. A surprising result with the THF monooxygenase expressing clones was the accumulation of the intermediate β-hydroxyethoxyacetic acid (HEAA). This result, combined with the non-inhibitory effect of acetylene on HEAA degradation by 1,4-dioxane grown P. dioxa- nivorans indicates that a monooxygenase is not involved in the transformation of HEAA as previously hypothesized. Transcriptomic microarray analysis of THF- and succinate- grown cells led to the first proposed THF metabolic degradation pathway forP. dioxaniv- orans. A novel finding of this transcriptomic microarray analysis was the identification of an alcohol dehydrogenase up-regulated during growth on THF that could catalyze the conversion of 2-hydroxytetrahydrofuran to γ-butyrolactone. The genome sequence of Rhodococcus jostii RHA1 was utilized to determine the pro- pane-induced monooxygenase responsible for NDMA degradation. The degradation of NDMA was characterized in R. jostii RHA1 grown on propane and on non-inducing substrates (LB medium, soy broth, and pyruvate). Propane enhanced the removal rate of NDMA by nearly two orders of magnitude compared to constitutive degradation during growth on non-inducing substrate. Transcriptomic microarray and qRT-PCR analyses demonstrated that propane elicits the up-regulation of a propane monooxygenase gene cluster. Genetic knockouts of the prmA gene encoding the large hydroxylase component of the propane monooxygenase were unable to grow on propane and degrade NDMA. These results indicate that the propane monooxygenase is responsible for NDMA degra- dation by R. jostii and explain the enhanced co-metabolic degradation of NDMA in the presence of propane. With the newly gained knowledge of the role of propane monooxy- genase in NDMA degradation, oligonucleotide degenerate primers targeting prmA were designed and were identify and quantify the presence of propane monooxygenase genes 2 in Rhodoccocus sp. RR1 and M. vaccae JOB5. A homolog to prmA was found in Rhodoc- cocus sp. RR1 but not in M. vaccae JOB5. The prmA gene in Rhodococcus sp. RR1 was up-regulated during growth on propane relative to pyruvate. Characterization of the kinet- ics of propane-enhanced NDMA degradation showed that Rhodococcus sp. RR1 and M. vaccae possess similar maximum transformation rates (44 ± 5 and 28 ± 3 mg NDMA(mg -1 -1 protein) h , respectively). However, a comparison of half saturation constants (Ks,n) and NDMA degradation in the presence of propane revealed pronounced differences be- -1 tween the strains. The Ks,n for Rhodococcus sp. RR1 was 36 ± 10 mg NDMA L while the propane concentration needed to inhibit NDMA rates by 50% (Kinh) occurred at 7,700 mg propane L-1 (R2 = 0.9669). In contrast, M. vaccae had a markedly lower affinity for -1 NDMA verses propane with a calculated Ks,n of 2,200 ± 1,000 mg NDMA L and Kinh of 120 mg propane L-1 (R2 = 0.9895). Differences between the propane monooxygenases in Rhodococcus sp. RR1 and the unidentified enzyme(s) inM. vaccae may explain the disparities in NDMA degradation and inhibition kinetics between these strains. 3 To Hilary i ii Table of Contents Abstract………………………………………………………………………………….....1 Dedication………………………………………………………………………………….i Table of Contents…………………………………………………………………………iii List of Figures…………………………………………………………………………...viii List of Table………………………………………………………………………...…..…x Acknowledgements…………………………………………………………………...….xii Chapter 1: Introduction and Objectives...........................................................................1 1.1 Introduction……………………………………………………………………………2 1.2 Research goal and specific objecties.......……………………………………………...3 1.3 Dissertation overview……………………………………………………………........4 Chapter 2: Background and Literature Review..............................................................5 2.1 Introduction…………………………………………………………………...............6 2.2 1,4-dioxane and NDMA as emerging contaminants…………………………..............7 2.2.1 Drinking water regulations and health effects of 1,4-dioxane…………................7 2.2.2 Uses of 1,4-dioxane………………………………………………….....................9 2.2.3 Occurrence
Recommended publications
  • The Pennsylvania State University the Graduate School Department

    The Pennsylvania State University the Graduate School Department

    The Pennsylvania State University The Graduate School Department of Chemistry SUBSTRATE POSITIONING AND CHANNELING OF ESCHERICHIA COLI QUINOLINATE SYNTHASE A Thesis in Chemistry by Lauren A. Sites 2012 Lauren A. Sites Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science December 2012 ii The thesis of Lauren A. Sites was reviewed and approved* by the following: Squire J. Booker Associate Professor of Chemistry Thesis Advisor Carsten Krebs Professor of Chemistry Scott A. Showalter Assistant Professor of Chemistry Kenneth S. Feldman Professor of Chemistry Head of Department *Signatures are on file in the Graduate School iii ABSTRACT The essential cofactor nicotinamide adenine dinucleotide (NAD) is consumed in many metabolic reactions in the cell, necessitating the need to synthesize NAD. In most bacteria, the de novo pathway to form NAD begins with two unique enzymes that have been extensively studied herein. The first enzyme in the pathway, L-aspartate oxidase, performs a two-electron oxidation of L-aspartate to form iminoaspartate. This flavin containing enzyme can undergo multiple catalytic turnovers given the oxidants, fumarate or molecular oxygen, to afford the oxidized form of the enzyme. The second enzyme in the pathway, quinolinate synthase or NadA, condenses iminoaspartate and dihydroxyacetone phosphate to form quinolinic acid, the backbone of the pyridine ring of NAD. Many have postulated that these two enzymes can operate as an enzyme complex, yet no substantial evidence of this complex has been demonstrated. Investigations to examine the possible protein-protein interactions of the two enzymes were carried out, yet no obvious interaction was seen by the techniques employed.
  • The Safety Evaluation of Food Flavouring Substances

    The Safety Evaluation of Food Flavouring Substances

    Toxicology Research View Article Online REVIEW View Journal The safety evaluation of food flavouring substances: the role of metabolic studies Cite this: DOI: 10.1039/c7tx00254h Robert L. Smith,a Samuel M. Cohen, b Shoji Fukushima,c Nigel J. Gooderham,d Stephen S. Hecht,e F. Peter Guengerich, f Ivonne M. C. M. Rietjens,g Maria Bastaki,h Christie L. Harman,h Margaret M. McGowenh and Sean V. Taylor *h The safety assessment of a flavour substance examines several factors, including metabolic and physio- logical disposition data. The present article provides an overview of the metabolism and disposition of flavour substances by identifying general applicable principles of metabolism to illustrate how information on metabolic fate is taken into account in their safety evaluation. The metabolism of the majority of flavour substances involves a series both of enzymatic and non-enzymatic biotransformation that often results in products that are more hydrophilic and more readily excretable than their precursors. Flavours can undergo metabolic reactions, such as oxidation, reduction, or hydrolysis that alter a functional group relative to the parent compound. The altered functional group may serve as a reaction site for a sub- sequent metabolic transformation. Metabolic intermediates undergo conjugation with an endogenous agent such as glucuronic acid, sulphate, glutathione, amino acids, or acetate. Such conjugates are typi- Received 25th September 2017, cally readily excreted through the kidneys and liver. This paper summarizes the types of metabolic reac- Accepted 21st March 2018 tions that have been documented for flavour substances that are added to the human food chain, the DOI: 10.1039/c7tx00254h methodologies available for metabolic studies, and the factors that affect the metabolic fate of a flavour rsc.li/toxicology-research substance.
  • Functional Properties and Molecular Architecture of Leukotriene A4 Hydrolase, a Pivotal Catalyst of Chemotactic Leukotriene Formation

    Functional Properties and Molecular Architecture of Leukotriene A4 Hydrolase, a Pivotal Catalyst of Chemotactic Leukotriene Formation

    Review Article TheScientificWorldJOURNAL (2002) 2, 1734–1749 ISSN 1537-744X; DOI 10.1100/tsw.2002.810 Functional Properties and Molecular Architecture of Leukotriene A4 Hydrolase, a Pivotal Catalyst of Chemotactic Leukotriene Formation Jesper Z. Haeggström1,*, Pär Nordlund2, and Marjolein M.G.M. Thunnissen2 1Department of Medical Biochemistry and Biophysics, Division of Chemistry 2, Karolinska Institutet, S-171 77 Stockholm, Sweden; 2Department of Biochemistry, University of Stockholm, Arrhenius Laboratories A4, S-106 91 Stockholm, Sweden E-mail: [email protected]; [email protected]; [email protected] Received March 25, 2002; Accepted April 26, 2002; Published June 26, 2002 The leukotrienes are a family of lipid mediators involved in inflammation and allergy. Leukotriene B4 is a classical chemoattractant, which triggers adherence and aggregation of leukocytes to the endothelium at only nM concentrations. In addition, leukotriene B4 modulates immune responses, participates in the host defense against infections, and is a key mediator of PAF-induced lethal shock. Because of these powerful biological effects, leukotriene B4 is implicated in a variety of acute and chronic inflammatory diseases, e.g., nephritis, arthritis, dermatitis, and chronic obstructive pulmonary disease. The final step in the biosynthesis of leukotriene B4 is catalyzed by leukotriene A4 hydrolase, a unique bifunctional zinc metalloenzyme with an anion-dependent aminopeptidase activity. Here we describe the most recent developments regarding our understanding
  • Role of Epoxide Hydrolases in Lipid Metabolism

    Role of Epoxide Hydrolases in Lipid Metabolism

    Biochimie 95 (2013) 91e95 Contents lists available at SciVerse ScienceDirect Biochimie journal homepage: www.elsevier.com/locate/biochi Mini-review Role of epoxide hydrolases in lipid metabolism Christophe Morisseau* Department of Entomology and U.C.D. Comprehensive Cancer Center, One Shields Avenue, University of California, Davis, CA 95616, USA article info abstract Article history: Epoxide hydrolases (EH), enzymes present in all living organisms, transform epoxide-containing lipids to Received 29 March 2012 1,2-diols by the addition of a molecule of water. Many of these oxygenated lipid substrates have potent Accepted 8 June 2012 biological activities: host defense, control of development, regulation of blood pressure, inflammation, Available online 18 June 2012 and pain. In general, the bioactivity of these natural epoxides is significantly reduced upon metabolism to diols. Thus, through the regulation of the titer of lipid epoxides, EHs have important and diverse bio- Keywords: logical roles with profound effects on the physiological state of the host organism. This review will Epoxide hydrolase discuss the biological activity of key lipid epoxides in mammals. In addition, the use of EH specific Epoxy-fatty acids Cholesterol epoxide inhibitors will be highlighted as possible therapeutic disease interventions. Ó Juvenile hormone 2012 Elsevier Masson SAS. All rights reserved. 1. Introduction hydrolyzed by a water molecule [8]. Based on this mechanism, transition-state inhibitors of EHs have been designed (Fig. 1B). Epoxides are three atom cyclic ethers formed by the oxidation of These ureas and amides are tight-binding competitive inhibitors olefins. Because of their highly polarized oxygen-carbon bonds and with low nanomolar dissociation constants (KI) [9] [10].
  • Quantum Chemical Studies of Epoxide- Transforming Enzymes

    Quantum Chemical Studies of Epoxide- Transforming Enzymes

    Quantum Chemical Studies of Epoxide- Transforming Enzymes Kathrin H. Hopmann Department of Theoretical Chemistry Royal Institute of Technology Stockholm, Sweden, 2007 ii © Kathrin H. Hopmann, 2007 ISBN 978-91-7178-640-1 ISSN 1654-2312 TRITA-BIO-Report 2007:3 Printed by Universitetsservice US-AB, Stockholm, Sweden. iii Abstract Density functional theory is employed to study the reaction mechanisms of different epoxide-transforming enzymes. Calculations are based on quantum chemical active site models, which are build from X-ray crystal structures. The models are used to study conversion of various epoxides into their corresponding diols or substituted alcohols. Epoxide-transforming enzymes from three different families are studied. The human soluble epoxide hydrolase (sEH) belongs to the α/β-hydrolase fold family. sEH employs a covalent mechanism to hydrolyze various epoxides into vicinal diols. The Rhodococcus erythrobacter limonene epoxide hydrolase (LEH) constitutes a novel epoxide hydrolase, which is considered the founding member of a new family of enzymes. LEH mediates transformation of limone-1,2-epoxide into the corresponding vicinal diol by employing a general acid/general base-mediated mechanism. The Agrobacterium radiobacter AD1 haloalcohol dehalogenase HheC is related to the short-chain dehydrogenase/reductases. HheC is able to convert epoxides using various nucleophiles such as azide, cyanide, and nitrite. Reaction mechanisms of these three enzymes are analyzed in depth and the role of different active site residues is studied through in silico mutations. Steric and electronic factors influencing the regioselectivity of epoxide opening are identified. The computed energetics help to explain preferred reaction pathways and experimentally observed regioselectivities. Our results confirm the usefulness of the employed computational methodology for investigating enzymatic reactions.
  • 1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental

    1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental

    Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN.
  • Mechanistic Implications for the Chorismatase Fkbo Based on the Crystal Structure

    Mechanistic Implications for the Chorismatase Fkbo Based on the Crystal Structure

    Mechanistic Implications for the Chorismatase FkbO Based on the Crystal Structure Puneet Juneja 1,†, Florian Hubrich 2,†, Kay Diederichs 1, Wolfram Welte 1 and Jennifer N. Andexer 2 1 - Department of Biology, University of Konstanz, D-78457 Konstanz, Germany 2 - Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstr 25, D-79104 Freiburg, Germany Correspondence to Jennifer N. Andexer: [email protected] http://dx.doi.org/10.1016/j.jmb.2013.09.006 Edited by M. Guss Abstract Chorismate-converting enzymes are involved in many biosynthetic pathways leading to natural products and can often be used as tools for the synthesis of chemical building blocks. Chorismatases such as FkbO from Streptomyces species catalyse the hydrolysis of chorismate yielding (dihydro)benzoic acid derivatives. In contrast to many other chorismate-converting enzymes, the structure and catalytic mechanism of a chorismatase had not been previously elucidated. Here we present the crystal structure of the chorismatase FkbO in complex with a competitive inhibitor at 1.08 Å resolution. FkbO is a monomer in solution and exhibits pseudo-3-fold symmetry; the structure of the individual domains indicates a possible connection to the trimeric RidA/YjgF family and related enzymes. The co-crystallised inhibitor led to the identification of FkbO's active site in the cleft between the central and the C-terminal domains. A mechanism for FkbO is proposed based on both interactions between the inhibitor and the surrounding amino acids and an FkbO structure with chorismate modelled in the active site. We suggest that the methylene group of the chorismate enol ether takes up a proton from an active-site glutamic acid residue, thereby initiating chorismate hydrolysis.
  • Download (2MB)

    Download (2MB)

    Enzyme and Microbial Technology 139 (2020) 109592 Contents lists available at ScienceDirect Enzyme and Microbial Technology journal homepage: www.elsevier.com/locate/enzmictec Identification and catalytic properties of new epoxide hydrolases fromthe T genomic data of soil bacteria Gorjan Stojanovskia, Dragana Dobrijevica, Helen C. Hailesb, John M. Warda,* a Department of Biochemical Engineering, University College London, Bernard Katz, London WC1E 6BT, UK b Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK ARTICLE INFO ABSTRACT Keywords: Epoxide hydrolases (EHs) catalyse the conversion of epoxides into vicinal diols. These enzymes have extensive Epoxide hydrolase value in biocatalysis as they can generate enantiopure epoxides and diols which are important and versatile Limonene epoxide hydrolase synthetic intermediates for the fine chemical and pharmaceutical industries. Despite these benefits, theyhave Genome mining seen limited use in the bioindustry and novel EHs continue to be reported in the literature. Biotransformation We identified twenty-nine putative EHs within the genomes of soil bacteria. Eight of these EHs wereexplored in terms of their activity. Two limonene epoxide hydrolases (LEHs) and one ⍺/β EH were active on a model compound styrene oxide and its ring-substituted derivatives, with low to good percentage conversions of 18–86%. Further exploration of the substrate scope with enantiopure (R)-styrene oxide and (S)-styrene oxide, showed different epoxide ring opening regioselectivities. Two enzymes, expressed from plasmids pQR1984and pQR1990 de-symmetrised the meso-epoxide cyclohexene oxide, forming the (R,R)-diol with high enantioselec- tivity. Two LEHs, from plasmids pQR1980 and pQR1982 catalysed the hydrolysis of (+) and (−) limonene oxide, with diastereomeric preference for the (1S,2S,4R)- and (1R,2R,4S)-diol products, respectively.
  • Phza/B Catalyzes the Formation of the Tricycle in Phenazine Biosynthesis Ekta G

    Phza/B Catalyzes the Formation of the Tricycle in Phenazine Biosynthesis Ekta G

    Subscriber access provided by DigiTop | USDA's Digital Desktop Library Article PhzA/B Catalyzes the Formation of the Tricycle in Phenazine Biosynthesis Ekta G. Ahuja, Petra Janning, Matthias Mentel, Almut Graebsch, Rolf Breinbauer, Wolf Hiller, Burkhard Costisella, Linda S. Thomashow, Dmitri V. Mavrodi, and Wulf Blankenfeldt J. Am. Chem. Soc., 2008, 130 (50), 17053-17061 • DOI: 10.1021/ja806325k • Publication Date (Web): 17 November 2008 Downloaded from http://pubs.acs.org on January 15, 2009 More About This Article Additional resources and features associated with this article are available within the HTML version: • Supporting Information • Access to high resolution figures • Links to articles and content related to this article • Copyright permission to reproduce figures and/or text from this article Journal of the American Chemical Society is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published on Web 11/17/2008 PhzA/B Catalyzes the Formation of the Tricycle in Phenazine Biosynthesis Ekta G. Ahuja,† Petra Janning,† Matthias Mentel,‡,§ Almut Graebsch,‡ Rolf Breinbauer,†,‡,§,| Wolf Hiller,‡ Burkhard Costisella,‡ Linda S. Thomashow,⊥,# Dmitri V. Mavrodi,⊥ and Wulf Blankenfeldt*,† Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany, Technical UniVersity of Dortmund, Faculty of Chemistry, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany, UniVersity of Leipzig, Institute of Organic Chemistry, Johannisallee 29, 04103 Leipzig, Germany, Graz UniVersity of
  • Biosynthesis of New Alpha-Bisabolol Derivatives Through a Synthetic Biology Approach Arthur Sarrade-Loucheur

    Biosynthesis of New Alpha-Bisabolol Derivatives Through a Synthetic Biology Approach Arthur Sarrade-Loucheur

    Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach Arthur Sarrade-Loucheur To cite this version: Arthur Sarrade-Loucheur. Biosynthesis of new alpha-bisabolol derivatives through a synthetic biology approach. Biochemistry, Molecular Biology. INSA de Toulouse, 2020. English. NNT : 2020ISAT0003. tel-02976811 HAL Id: tel-02976811 https://tel.archives-ouvertes.fr/tel-02976811 Submitted on 23 Oct 2020 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. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par l'Institut National des Sciences Appliquées de Toulouse Présentée et soutenue par Arthur SARRADE-LOUCHEUR Le 30 juin 2020 Biosynthèse de nouveaux dérivés de l'α-bisabolol par une approche de biologie synthèse Ecole doctorale : SEVAB - Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingenieries Spécialité : Ingénieries microbienne et enzymatique Unité de recherche : TBI - Toulouse Biotechnology Institute, Bio & Chemical Engineering Thèse dirigée par Gilles TRUAN et Magali REMAUD-SIMEON Jury
  • Relating Metatranscriptomic Profiles to the Micropollutant

    Relating Metatranscriptomic Profiles to the Micropollutant

    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
  • Letters to Nature

    Letters to Nature

    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).