DOCSLIB.ORG

Investigations on a Chloroform Reductive Dehalogenase

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Investigations on a Chloroform Reductive Dehalogenase INVESTIGATIONS ON A CHLOROFORM REDUCTIVE DEHALOGENASE Bat-Erdene Jugder A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science July 2017 THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: JUGDER First name: BAT-ERDENE Other name/s: Abbreviation for degree as given in the University calendar: PhD School: School of Biotechnology and Biomolecular Sciences Faculty: Science Title: Investigations on a chloroform reductive dehalogenase Abstract 350 words maximum: (PLEASE TYPE) Halogenated organic compounds (organohalides) are globally prevalent, recalcitrant toxic and carcinogenic environmental pollutants contaminating soil and groundwater. Organohalide respiring bacteria provide a potential solution to remediate contaminated sites, as they are capable of utilising organohalides as electron acceptors for the generation of cellular energy. At the heart of these processes are reductive dehalogenases (RDase; EC 1.97.1.8), which are membrane bound enzymes that catalyse reductive dehalogenation reactions resulting in the generation of lesser-halogenated compounds that may be less toxic and more biodegradable. Chloroform (CF), primarily used in the production of refrigerants, is very prevalent and recalcitrant organohalide contamination and its improper disposal also caused groundwater pollution at industrial sites in Sydney, Australia. Its hazardous effect on environment and carcinogenic and organo-toxic effects on human health prompts bioremediation research towards its detoxification. Recently, Dehalobacter (Dhb) sp. strain UNSWDHB, which is capable of respiring CF and converting it to dichloromethane has been identified. The UNSWDHB strain was revealed to produce CF-RDase, as termed TmrA, which has been the focus of the research carried out in this thesis. Firstly, the response of Dhb sp. UNSWDHB to the addition of CF was evaluated from a transcriptomic and proteomic perspective. The elevated expressions of TmrABC proteins, key bioenergetics related membrane-associated and cytoplasmic proteins, enzymes associated with functional Wood-Ljungdahl pathway and complete corrinoid de novo synthesis were revealed, providing a broader view on the bioenergetics and general physiology of the Dehalobacter cells actively respiring with CF. Furthermore, TmrA was produced and purified from the membrane fraction of the UNSWDHB cells to apparent homogeneity, using detergent-based membrane solubilisation and anion exchange chromatographic purification. This allowed further biochemical characterisation of the purified enzyme. Lastly, an extensive study to heterologously express TmrA was conducted under several expression conditions to address a reportedly challenging issue with soluble, functional expression and purification of a respiratory RDase. The xylose-inducible expression in a corrinoid-producing Bacillus megaterium as an expression host and two liquid chromatographic steps resulted in a generation of a soluble and functional recombinant TmrA. Declaration relating to disposition of project thesis/dissertation I hereby grant to the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or in part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all property rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstracts International (this is applicable to doctoral theses only). …………………………………………………………… ……………………………………..……………… ……….……………………...…….… Signature Witness Signature Date The University recognises that there may be exceptional circumstances requiring restrictions on copying or conditions on use. Requests for restriction for a period of up to 2 years must be made in writing. Requests for a longer period of restriction may be considered in exceptional circumstances and require the approval of the Dean of Graduate Research. FOR OFFICE USE ONLY Date of completion of requirements for Award: COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied//wwill apply for a parti al restriction of the digital copy of my thesis or dissertation.' Signed ………………………………………………………………………………………............. Date ………………………10 July 2017…………………………………………………............. AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format.’ Signed ……………………………………………………………………………………….............. Date ………………………10 July 2017…………………………………………………............. iv ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed …………………………………………….............. Date …………10 July 2017…………………….............. iii Abstract Halogenated organic compounds (organohalides) are globally prevalent, recalcitrant toxic and carcinogenic environmental pollutants contaminating soil and groundwater. Organohalide respiring bacteria provide a potential solution to remediate contaminated sites, as they are capable of utilising organohalides as electron acceptors for the generation of cellular energy. At the heart of these processes are reductive dehalogenases (RDase; EC 1.97.1.8), which are membrane bound enzymes that catalyse reductive dehalogenation reactions resulting in the generation of lesser-halogenated compounds that may be less toxic and more biodegradable. Chloroform (CF), primarily used in the production of refrigerants, is very prevalent and recalcitrant organohalide contamination and its improper disposal also caused groundwater pollution at industrial sites in Sydney, Australia. Its hazardous effect on environment and carcinogenic and organo-toxic effects on human health prompts bioremediation research towards its detoxification. Recently, Dehalobacter (Dhb) sp. strain UNSWDHB, which is capable of respiring CF and converting it to dichloromethane has been identified. The UNSWDHB strain was revealed to produce CF-RDase, as termed TmrA, which has been the focus of the research carried out in this thesis. Firstly, the response of Dhb sp. UNSWDHB to the addition of CF was evaluated from a transcriptomic and proteomic perspective. The elevated expressions of TmrABC proteins, key bioenergetics related membrane-associated and cytoplasmic proteins, enzymes associated with functional Wood-Ljungdahl pathway and complete corrinoid de novo synthesis were revealed, providing a broader view on the bioenergetics and general physiology of the Dehalobacter cells actively respiring with CF. Furthermore, TmrA was produced and purified from the membrane fraction of the UNSWDHB cells to apparent homogeneity, using detergent-based membrane solubilisation and anion exchange chromatographic purification. This allowed further biochemical characterisation of the purified enzyme. Lastly, an extensive study to heterologously express TmrA was conducted under several expression conditions to address a reportedly challenging issue with soluble, functional expression and purification of a respiratory RDase. The xylose-inducible expression in a corrinoid-producing Bacillus i megaterium as an expression host and two liquid chromatographic steps resulted in a generation of a soluble and functional recombinant TmrA. ii Acknowledgement There are many individuals whom I would like to express my gratitude and appreciation for their help in my pursuit of a PhD at UNSW Sydney. The first and foremost thanks must go out to my family: my parents, wife, son and daughter. I would not be writing this acknowledgement if I were not fortunate enough to have my wife and best friend Alta in my life, whose love and encouragement are always beyond imagination and expectation.
Load more

Recommended publications
  • Araştırma Isolation and Characterization of Bacillus
    Akademik Ziraat Dergisi 7(1):21-28 (2018) Araştırma ISSN: 2147-6403 DOI: http://dx.doi.org/10.29278/azd.440586 (Research) Isolation and characterization of Bacillus megaterium isolates from dead pentatomids and their insecticidal activity to Palomena prasina nymphs Hasan Murat AKSOY1, Celal TUNCER1, Islam SARUHAN1, Ismail ERPER1, Murat OZTURK1, Izzet AKCA1 1Ondokuz Mayis University, Faculty of Agriculture, Department of Plant Protection, SAMSUN , Kabul tarihi 06 Nisan 2018 Sorumlu yazar: , e-posta:[email protected] Alınış tarihi: 19 Aralık 2017 İslam SARUHAN Abstract Ölü pentatomidlerden Bacillus megaterium Bacillus megaterium isolates, were demonstrated to izolatlarının izolasyonu, karekterizasyonu ve be efficient biocontrol agents against the green Palomena prasina nimflerine insektisital etkisi shield bug (Palomena prasina Pentatomidae). Firstly hazelnut orchards were Öz surveyed and four B. megateriumL., isolatesHeteroptera: were Bacillus megaterium obtained from P. prasina. The morphological, Palomena prasina physiological and biochemical characteristics of B. Bu çalışma, izolatlarının fındık megaterium isolates were determined according to kokarcasına ( L., Heteroptera: the standardized methodology. Additionally 16S Pentatomidae) karşıP. etkinprasina biyokontrol Bacillusajanları to megateriumolduğu gösterilmiştir. Öncelikle fındıkB. bahçelerindemegaterium survey yapılarak, 'dan dört rRNA gene sequence analyse was performed gene confirmed that isolates Sa-1, Sa-5, SAk-2 and izolatı elde edilmiştir. determine the isolates. Analysis of the 16S rRNA SAkc-19 are B. megaterium izolatlarının morfolojik, fizyolojik ve biyokimyasal homology to the type strains of B. megaterium. özellikleri standart tanı yöntemlerine göre Effectiveness of these isolates, withwas tested100% againstsequence P. sonucu;belirlenmiştir. Sa-1, Sa Ayrıca-5, SAk izolatların-2 ve SAkc tanısı- için 16S rRNAB. prasina nymphs in laboratory, at 25±1°C and 70±5 megateriumgen dizi analizi yapılmıştır.
    [Show full text]
  • Engineering Bacillus Megaterium for Production of Functional Intracellular Materials Katrin Grage1, Paul Mcdermott2 and Bernd H
    Grage et al. Microb Cell Fact (2017) 16:211 DOI 10.1186/s12934-017-0823-5 Microbial Cell Factories RESEARCH Open Access Engineering Bacillus megaterium for production of functional intracellular materials Katrin Grage1, Paul McDermott2 and Bernd H. A. Rehm3* Abstract Background: Over the last 10–15 years, a technology has been developed to engineer bacterial poly(3-hydroxybu- tyrate) (PHB) inclusions as functionalized beads, for applications such as vaccines, diagnostics and enzyme immobili- zation. This has been achieved by translational fusion of foreign proteins to the PHB synthase (PhaC). The respective fusion protein mediates self-assembly of PHB inclusions displaying the desired protein function. So far, beads have mainly been produced in recombinant Escherichia coli, which is problematic for some applications as the lipopolysac- charides (LPS) co-purifed with such inclusions are toxic to humans and animals. Results: In this study, we have bioengineered the formation of functional PHB inclusions in the Gram-positive bac- terium Bacillus megaterium, an LPS-free and established industrial production host. As B. megaterium is a natural PHB producer, the PHB-negative strain PHA05 was used to avoid any background PHB production. Plasmid-mediated T7 promoter-driven expression of the genes encoding β-ketothiolase (phaA), acetoacetyl-CoA-reductase (phaB) and PHB synthase (phaC) enabled PHB production in B. megaterium PHA05. To produce functionalized PHB inclusions, the N- and C-terminus of PhaC was fused to four and two IgG binding Z-domains from Staphylococcus aureus, respectively. The ZZ-domain PhaC fusion protein was strongly overproduced at the surface of the PHB inclusions and the cor- responding isolated ZZ-domain displaying PHB beads were found to purify IgG with a binding capacity of 40–50 mg IgG/g beads.
    [Show full text]
  • Biochemistry and Physiology of Halorespiration by Desulfitobacterium Dehalogenans
    Biochemistry and Physiology of Halorespiration by Desulfitobacterium dehalogenans ..?.^TJ?*LE_ LANDBOUWCATALOGU S 0000 0807 1728 Promotor: Dr.W.M . deVo s hoogleraar in de microbiologie Co-promotoren: Dr.ir .A.J.M .Stam s universitair hoofddocent bij deleerstoelgroe p Microbiologie Dr.ir . G. Schraa universitair docent bij deleerstoelgroe p Microbiologie Stellingen 1. Halorespiratie is een weinig efficiente wijze van ademhalen. Dit proefschrift 2. Halorespiratie moet worden opgevat als verbreding en niet als specialisatie van het genus Desulfitobacterium. Dit proefschrift 3. Reductieve dehalogenases zijn geen nieuwe enzymen. 4. 16S-rRNA probes zijn minder geschikt voor het aantonen van specifieke metabole activiteiten in een complex ecosysteem. Loffler etal. (2000) AEM66 : 1369;Gottscha l &Kroonema n (2000)Bode m3 : 102 5. Het "twin-arginine" transportsysteem wordt niet goed genoeg begrepen om op basis van het voorkomen van het "twin-arginine" motief enzymen te lokaliseren. Berks etal. (2000)Mol .Microbiol .35 : 260 6. Asbesthoudende bodem is niet verontreinigd. 7. Biologische groente is een pleonasme. Stellingen behorende bij het proefschrift 'Biochemistry and physiology of halorespiration by Desulfitobacterium dehalogenans' van Bram A. van de Pas Wageningen, 6 december 2000 MJOQ^O \lZ°]0 ^ Biochemistry and Physiology of Halorespiration by Desulfitobacterium dehalogenans BramA. van de Pas Proefschrift ter verkrijging van de graad van doctor op gezag van derecto r magnificus van Wageningen Universiteit, dr. ir. L. Speelman, in het openbaar
    [Show full text]
  • Selection, Identification and Optimization of the Growth Water Probiotic Consortium of Mangrove Ecosystems As Bioremediation and Biocontrol in Shrimp Ponds
    Selection, Identification and Optimization of The Growth, Setyati et al. JPHPI 2014, Volume 17 Nomor 3 Selection, Identification and Optimization of the Growth Water Probiotic Consortium of Mangrove Ecosystems as Bioremediation and Biocontrol in Shrimp Ponds Wilis Ari Setyati*1, Erni Martani², Triyanto², Subagiyo³, Muhammad Zainuddin⁴ 1) Departement of Marine Science, Faculty of Fisheries and Marine Science Diponegoro University, Post-graduate Student, Gadjah Mada University 2)Departement of Biotechnology, Post-graduate, Gadjah Mada University. ³)Marine Science Laboratory, Marine Science Departement, Diponegoro University. ⁴)Natural Product Laboratory, UPT (Integrated Laboratory), Diponegoro University. Faculty of Fisheries and Marine – Tembalang – Semarang Telp 024 7474698 *Coresponding author: [email protected] Accepted April 15th, 2014/Approved Agustus 10th, 2014 Abstract Shrimp aquaculture is an activity that potentially generates organic waste. The accumulation of organic matter is becoming one of the main factors causing the emergence of disease. Problem-solving approach that is most effective is through bioremediation. The aims of this study were to select, identify and cultivate bacteria from mangrove sediments from Cilacap, Rembang and Banyuwangi which potentially as probiotic consortium of bioremediation activity and biocontrol. The results showed that total of 45 isolates (proteolytic), 35 isolates (amylolytic), 35 isolates (lipolytic), and 18 isolates (cellulolytic). There were 59 bacterial isolates had antibacterial activity of vibrio (V. harveyi, V. alginolyticus, V. vulnificus and V. anguilarum). Based on the identification of 16 S-rRNA genes, 4 isolates showed that the C2 isolate was identified as Bacillus subtilis, C11 isolate was identified as Bacillus firmus, C13 and C14 isolates were identified as B. Flexus. This study concluded that cultivation of Bacillus subtilis C2 optimum at 2% molase and yeast extract 0.5% at pH 8 and 30 0C.
    [Show full text]
  • Identification and Classification of Known and Putative Antimicrobial Compounds Produced by a Wide Variety of Bacillales Species Xin Zhao1,2 and Oscar P
    Zhao and Kuipers BMC Genomics (2016) 17:882 DOI 10.1186/s12864-016-3224-y RESEARCH ARTICLE Open Access Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species Xin Zhao1,2 and Oscar P. Kuipers1* Abstract Background: Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. Results: We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. Conclusions: Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified. Keywords: Antimicrobials, Bacillales, Bacillus, Genome-mining, Lanthipeptides, Sactipeptides, Thiopeptides, NRPs, PKs Background (bacteriocins) [4], as well as non-ribosomally synthesized Most of the species of the genus Bacillus and related peptides (NRPs) and polyketides (PKs) [5].
    [Show full text]
  • Study of Novel Endophytic Bacteria for Biocontrol of Black Pepper Root-Knot Nematodes in the Central Highlands of Vietnam
    agronomy Article Study of Novel Endophytic Bacteria for Biocontrol of Black Pepper Root-knot Nematodes in the Central Highlands of Vietnam Thi Phuong Hanh Tran 1, San-Lang Wang 2,3,* , Van Bon Nguyen 4,* , Dinh Minh Tran 5 , Dinh Sy Nguyen 5 and Anh Dzung Nguyen 5,* 1 Department of Science and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; [email protected] 2 Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan 3 Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan 4 Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam 5 Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; [email protected] (D.M.T.); [email protected] (D.S.N.) * Correspondence: [email protected] (S.-L.W.); [email protected] (V.B.N.); [email protected] (A.D.N.); Tel.: +886-2-2621-5656 (S.-L.W.); Fax: +886-2-2620-9924 (S.-L.W.) Received: 29 August 2019; Accepted: 31 October 2019; Published: 5 November 2019 Abstract: Black pepper is an industrial crop with high economic and export value. However, black pepper production in Vietnam has been seriously affected by the root-knot nematodes, Meloidogyne spp. The purpose of this study was to select active endophytic bacteria (EB) for the cost-effective and environmentally friendly management of Meloidogyne sp. Thirty-four EB strains were isolated. Of these, five isolates displayed the highest activity, demonstrating 100% mortality of J2 nematodes. These active EB were identified based on sequencing and phylogenetic analysis of the 16S rRNA gene; notably, all the potential endophytic bacterial strains belong to the genus of Bacillus.
    [Show full text]
  • Anaerobic Transformation of Brominated Aromatic Compounds by Dehalococcoides Mccartyi Strain CBDB1
    Anaerobic transformation of brominated aromatic compounds by Dehalococcoides mccartyi strain CBDB1 vorgelegt von Master of Engineering Chao Yang geb. in Henan. China von der Fakultät III – Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktor der Naturwissenschaften - Dr.-rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. Stephan Pflugmacher Lima Gutachter: Prof. Dr. Peter Neubauer Gutachter: Prof. Dr. Lorenz Adrian Gutachter: PD Dr. Ute Lechner Tag der wissenschaftlichen Aussprache: 28. August 2017 Berlin 2017 Declaration Chao Yang Declaration for the dissertation with the tittle: “Anaerobic transformation of brominated aromatic compounds by Dehalococcoides mccartyi strain CBDB1” This dissertation was carried out at The Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany between October, 2011 and September, 2015 under the supervision of PD Dr. Lorenz Adrian and Prof. Dr. Peter Neubauer. I herewith declare that the results of this dissertation were my own research and I also certify that I wrote all sentences in this dissertation by my own construction. Signature Date Acknowledgement This research work was conducted from October, 2011 to September, 2015 in the research group of PD Dr. Lorenz Adrian at the Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research Leipzig (UFZ). The research project was funded by the Chinese Scholarship Council and supported by Deutsche Forschungsgemeinschaft (DFG) (FOR1530). It was also supported by Tongji University (in China) and Technische Universität Berlin (in Germany). I would like to say sincere thanks to PD Dr. Lorenz Adrian for the opportunity to work and learn in his unitive and creative research group. Also many thanks to him for leading me into the amazing and interesting microbial research fields, for sharing his extensive knowledge, for the productive discussion and precise supervision, and for his firm support both in work and life.
    [Show full text]
  • Bacillus Megaterium Isolated from Non-Saline Soils Under Salt Stressed Conditions
    Journal of Bacteriology & Mycology: Open Access Research Article Open Access Phosphate solubilization of Bacillus megaterium isolated from non-saline soils under salt stressed conditions Abstract Volume 6 Issue 6 - 2018 Phosphate solubilizing Bacillus megaterium was isolated from non rhizospheric soils. Five isolates were identified by 16s rDNA sequencing. According to sequencing Sabae Thant, Nwe Nwe Aung, Ohn Mar Aye, and phylogenetic tree analysis, these five isolates were in high similarity with B. Nan Na Oo, Thywe Mya Mya Htun, Aye Aye megaterium. Abiotic stresses such as temperature, pH and salt tolerance of five Mon, Khin Thae’ Mar, Kyaing Kyaing, Kay strains were examined for the application for abiotic stressed agricultural soils. All Khine Oo, Mya Thywe, Phwe Phwe, Thazin five strains could grow well above 40ºC. For pH, five strains demonstrated their Soe Yu Hnin, Su Myat Thet, Zaw Ko Latt growth on minimal media at pH 9 but the growth rates were decreased. Among abiotic stress factors, to obtain salt tolerance phosphate solubilizing B. megaterium was the Microbiology Laboratory, Biotechnology Research Department, Myanmar main objective of this research work. So, salt tolerance of isolates were screened preliminary, all five strains had the ability to grow on minimal media containing 6% Correspondence: Zaw Ko Latt, Microbiology Laboratory, NaCl concentration but the growth rates were not in high rates. Preliminary screening Biotechnology Research Department, Myanmar, Tel +95 9 results enhanced to continue for quantative determination of phosphate solubilization 973084176, Email under salt stressed conditions. In detection of phosphate solubilization by the method of Olsen P, all five strains could solubilize insoluble phosphate, Tricalcium phosphate, Received: December 05, 2018 | Published: December 28, under NaCl stressed conditions.
    [Show full text]
  • Biosynthesis of Cobalamin (Vitamin B12) in Salmonella Typhimurium
    Biosynthesis of cobalamin (vitamin B^^) in Salmonella typhimurium and Bacillus megaterium de Bary; Characterisation of the anaerobic pathway. By Evelyne Christine Raux A thesis submitted to the University of London for the degree of doctorate (PhD.) in Biochemistry. -k H « i d University College London Department of Molecular Genetics, Institute of Ophthalmology, London. Jan 1999 ProQuest Number: U121800 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U121800 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract The transformation of uroporphyrinogen HI into cobalamin (vitamin B 1 2 ) requires about 25 enzymes and can be performed by either aerobic or anaerobic pathways. The aerobic route is dependent upon molecular oxygen, and cobalt is inserted after the ring contraction process. The anaerobic route occurs in the absence of oxygen and cobalt is inserted into precorrin- 2 , several steps prior to the ring contraction. A study of the biosynthesis in both S. typhimurium and B. megaterium reveals that two genes, cbiD and cbiG, are essential components of the pathway and constitute genetic hallmarks of the anaerobic pathway.
    [Show full text]
  • Molecular Analysis of Halorespiration in Desulfitobacterium Spp
    Molecular analysis of halorespiration in Desulfitobacterium spp. − CATALYSIS AND TRANSCRIPTIONAL REGULATION Promotoren Prof. dr. W. M. de Vos Hoogleraar Microbiologie Wageningen Universiteit Prof. dr. J. van der Oost Hoogleraar Microbiologie en Biochemie Wageningen Universiteit Co-promotor Dr. H. Smidt Universitair docent Laboratorium voor Microbiologie Wageningen Universiteit Leden van de Dr. D. Leys promotiecommissie Manchester Interdisciplinary Biocentre, UK Dr. R. J. M. van Spanning Vrije Universiteit, Amsterdam Prof. dr. I. M. C. M. Rietjens Wageningen Universiteit Prof. dr. S. C. de Vries Wageningen Universiteit Krisztina Gábor Molecular analysis of halorespiration in Desulfitobacterium spp. − catalysis and transcriptional regulation Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. dr. M. J. Kropff, in het openbaar te verdedigen op woensdag 1 november 2006 des namiddags te vier uur in de Aula Gábor, Krisztina − Molecular analysis of halorespiration in Desulfitobacterium spp.: catalysis and transcriptional regulation Ph.D. thesis Wageningen University, Wageningen, The Netherlands (2006) 152 p., with summary in Dutch ISBN 90-8504-529-0 Szüleimnek ABSTRACT Gábor, K. (2006). Molecular analysis of halorespiration in Desulfitobacterium spp.: catalysis and transcriptional regulation. PhD thesis. Laboratory of Microbiology, Wageningen University, The Netherlands. Soil and ground water contamination by halogenated organic compounds mainly used as biocides in agriculture or solvents and cleaning agents in industry has been a long-standing problem. The main barrier in the chemical degradation of organohalides is the presence of the halogen group in the molecule, which also contributes to the toxic nature of these compounds. However, a remarkable group of microorganisms, the halorespiring bacteria, are able to reductively dehalogenate organohalides under anaerobic conditions and use the energy generated via a proton gradient pump for bacterial growth (halorespiration).
    [Show full text]
  • Isolation and Characterization of an Endophytic Bacterium, Bacillus Megaterium BMN1, Associated with Root-Nodules of Medicago Sativa L
    Ann Microbiol (2015) 65:1017–1026 DOI 10.1007/s13213-014-0946-4 ORIGINAL ARTICLE Isolation and characterization of an endophytic bacterium, Bacillus megaterium BMN1, associated with root-nodules of Medicago sativa L. growing in Al-Ahsaa region, Saudi Arabia Ashraf Y. Z. Khalifa & Mohammed A. Almalki Received: 4 April 2014 /Accepted: 15 July 2014 /Published online: 13 August 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract Medicago sativa L. (Alfalfa) is an important forage plants. In conclusion, BMN1 belongs to the group of plant crop legume in Saudi Arabia due to its high nutritive value and growth promoting rhizobacteria and could have significant yield. Soil bacteria exist in root or root-nodules of Medicago agricultural applications. sativa in either symbiotic relationships or in associations. In the current study, the endophytic bacterium Bacillus Keywords Bacillus megaterium . Lens esculentus . megaterium BMN1 was isolated from surface-sterilized root- Phaseolus vulgaris . Pisum sativum nodules of Medicago sativa and characterized phenotypically and genotypically. The results indicated that BMN1 consumed a variety of sugars as sole carbon source, and produced catalase and amylase but not urease. BMN1 exhibited some Introduction plant growth-promoting traits, such as production of indole acetic acid and acetoin, and solublization of inorganic phos- Medicago sativa L. (Alfalfa) is an important perennial legumi- phate. In addition, comparative sequence analysis of the 16S nous plant that is cultivated as livestock fodder because it has a rRNA gene showed that BMN1 exhibited 99 % homology high feeding value and wide adaptability. Furthermore, with Bacillus megaterium. In addition, BMN1 could not Medicago sativa is used in production of biofuel and pest nodulate alfalfa when re-inoculated but the strain enhanced management (Samac et al.
    [Show full text]
  • Reductive Dechlorination in the Energy Metabolism of Anaerobic Bacteria
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by RERO DOC Digital Library FEMS Microbiology Reviews 22 (1999) 383^398 Review Reductive dechlorination in the energy metabolism of anaerobic bacteria Christof Holliger a, Gert Wohlfarth b, Gabriele Diekert b;* a Swiss Federal Institute for Environmental Science and Technology (EAWAG), Limnological Research Center, CH-6047 Kastanienbaum, Switzerland b University of Stuttgart, Institute for Microbiology, Allmandring 31, D-70569 Stuttgart, Germany Received 12 July 1998; received in revised form 22 September 1998; accepted 1 October 1998 Abstract Within the last few decades, several anaerobic bacteria have been isolated which are able to reductively dechlorinate chlorinated aliphatic and aromatic compounds at catabolic rates. For some of these bacteria, it has been shown that the reductive dechlorination is coupled to energy conservation, a process designated as `dehalorespiration'. Somewhat simple respiratory chains seem to be involved that utilize the free energy that could be gained from the exergonic dechlorination reaction quite inefficiently. With one exception, all reductive dehalogenases isolated to date contain a corrinoid and iron^sulfur clusters as cofactors. During the course of the catalytic reaction cycle, the cobalt of the corrinoid is subjected to a change in its redox state. Hence, reductive dechlorination represents a new type of biochemical reaction. z 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved. Keywords: Reductive dehalogenation; Dehalorespiration; Chlorophenol; Tetrachloroethene; Corrinoid; Vitamin B12 Contents 1. Introduction . ....................................................................... 384 2. Anaerobic bacteria capable of reductive dechlorination in their energy metabolism . .................... 385 2.1. Desulfomonile tiedjei ...............................................................
    [Show full text]