Azoreductase: a Key Player of Xenobiotic Metabolism Santosh A
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Autotrophy in Groundwater Ecosystems
Dissertation der Fakultät für Biologie der Ludwig-Maximilians-Universität München Autotrophy in Groundwater Ecosystems Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades vorgelegt von Claudia Sabine Kellermann aus München München im November 2008 1. Gutachter: Prof. Dr. Anton Hartmann, LMU München 2. Gutachter: Prof. Dr. Dirk Schüler, LMU München Tag der Abgabe: 06.11.2008 Tag des Promotionskolloquiums: 15.07.2009 Publications originating from this Thesis Chapter 2 Kellermann, C & Griebler, C (2008) Thiobacillus thiophilus D24TNT sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments. International Journal of Systematic and Evolutionary Microbiology (IJSEM), 59: 583-588 Chapter 3 Kellermann, C, Selesi, D, Hartmann, A, Lee, N, Hügler, M, Esperschütz, J, & Griebler, C (2008) Chemolithoautotrophy in an organically polluted aquifer – Potential for CO2 fixation and in situ bacterial autotrophic activity. (in preparation) Contributions Chapter 3 Enzyme assays were performed in cooperation with Dr. Michael Hügler at the IFM- GEOMAR, Kiel, Germany. Chapter 4 FISH-MAR analysis was performed in cooperation with Prof. Dr. Natuschka Lee at the Technical University Munich, Germany. Enzyme assays were performed in cooperation with Dr. Michael Hügler at the IFM-GEOMAR, Kiel, Germany. PLFA analysis was performed by Dr. Jürgen Esperschütz at the Institute of Soil Ecology, Helmholtz Center Munich, Germany. I hereby confirm the above statements Claudia Kellermann Prof. Dr. Anton Hartmann Autotrophy in Groundwater Ecosystems Claudia Kellermann Abstract: The major role in global net CO2 fixation plays photosynthesis of green plants, algae and cyanobacteria, but other microorganisms are also important concerning autotrophy; i.e. autotrophic microorganisms can be found in most bacterial groups (Eubacteria) and there are even numerous representatives within the Archaea. -
Bioenergetics
Bioenergetics Patcharee Boonsiri For Education Only Cell is the smallest unit of life. Metabolic processes that occur in cells help keeping the organism alive. In this ebook, there are 4 chapters. Chapter 1 Bioenergetics : Living organisms use energy for their functions and they have the metabolic pathway to produce energy. Chapter 2 Thermodynamics : The laws of Thermodynamics are about conservation of energy and the order/disorder in living organisms. Chapter 3 Gibbs’ free energy : This help predicting direction of the chemical reactions in cells. Chapter 4 High energy compound ATP : ATP is the energy currency for the living organisms. Part 1 Bioenergetics What are the 4 essential things the cells need? 1.molecular building blocks 2.chemical catalysts 3.genetic information 4.energy The activities of living things require energy. The energy help the cells to perform functions such as growth, maintaining balance of the body or called homeostasis, repair, reproduction, movement, and defense. This means that all living organisms must obtain and use energy for their life. What is energy? Energy is ability to do work. Each cell can convert fuel to energy in the form that our bodies can use. Unit of Energy: Calorie, Joule (SI unit) 1 cal = 4.184 J There are 2 forms of energy 1.Potential energy - is stored energy ( for example, chemical, concentration gradient, electrical potential energy) 2.Kinetic energy - energy that is actively engaged in doing work (for example, radient, thermal, mechanical energy) http://2.bp.blogspot.com/-r7ceqpkN4Y4/VipBXGTSwKI/AAAAAAAAABU /nqex7dmiJ08/s1600/Slide%2Bpicture.png What is work? Work is the use of energy to drive all processes other than heat flow. -
Isolation and Molecular Characterization of Novel
University of Groningen Isolation and molecular characterization of novel glucarpidases Rashidi, Fatma B; AlQhatani, Alanod D; Bashraheel, Sara S; Shaabani, Shabnam; Groves, Matthew R; Dömling, Alexander; Goda, Sayed K Published in: PLoS ONE DOI: 10.1371/journal.pone.0196254 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: 2018 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Rashidi, F. B., AlQhatani, A. D., Bashraheel, S. S., Shaabani, S., Groves, M. R., Dömling, A., & Goda, S. K. (2018). Isolation and molecular characterization of novel glucarpidases: Enzymes to improve the antibody directed enzyme pro-drug therapy for cancer treatment. PLoS ONE, 13(4), [e0196254]. https://doi.org/10.1371/journal.pone.0196254 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. -
Delftia Sp. LCW, a Strain Isolated from a Constructed Wetland Shows Novel Properties for Dimethylphenol Isomers Degradation Mónica A
Downloaded from orbit.dtu.dk on: Sep 28, 2021 Delftia sp LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation Vásquez-Piñeros, Mónica A.; Martinez-Lavanchy, Paula M.; Jehmlich, Nico; Pieper, Dietmar H.; Rincon, Carlos A.; Harms, Hauke; Junca, Howard; Heipieper, Hermann J. Published in: BMC Microbiology Link to article, DOI: 10.1186/s12866-018-1255-z Publication date: 2018 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Vásquez-Piñeros, M. A., Martinez-Lavanchy, P. M., Jehmlich, N., Pieper, D. H., Rincon, C. A., Harms, H., Junca, H., & Heipieper, H. J. (2018). Delftia sp LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation. BMC Microbiology, 18, [108]. https://doi.org/10.1186/s12866- 018-1255-z General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal 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. -
Hydrogenophaga Electricum Sp. Nov., Isolated from Anodic Biofilms of an Acetate-Fed Microbial Fuel Cell
J. Gen. Appl. Microbiol., 59, 261‒266 (2013) Full Paper Hydrogenophaga electricum sp. nov., isolated from anodic biofilms of an acetate-fed microbial fuel cell Zen-ichiro Kimura and Satoshi Okabe* Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060‒8628, Japan (Received October 25, 2012; Accepted April 2, 2013) A Gram-negative, non-spore-forming, rod-shaped bacterial strain, AR20T, was isolated from an- odic biofilms of an acetate-fed microbial fuel cell in Japan and subjected to a polyphasic taxo- nomic study. Strain AR20T grew optimally at pH 7.0‒8.0 and 25°C. It contained Q-8 as the pre- dominant ubiquinone and C16:0, summed feature 3 (C16:1ω7c and/or iso-C15:02OH), and C18:1ω7c as the major fatty acids. The DNA G+C content was 67.1 mol%. A neighbor-joining phylogenetic tree revealed that strain AR20T clustered with three type strains of the genus Hydrogenophaga (H. flava, H. bisanensis and H. pseudoflava). Strain AR20T exhibited 16S rRNA gene sequence similarity values of 95.8‒97.7% to the type strains of the genus Hydrogenophaga. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain AR20T is considered a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga electricum sp. nov. is pro- posed. The type strain is AR20T (= KCTC 32195T = NBRC 109341T). Key Words—Hydrogenophaga electricum; hydrogenotrophic exoelectrogen; microbial fuel cell Introduction the MFC was analyzed. Results showed that bacteria belonging to the genera Geobacter and Hydrogenoph- Microbial fuel cells (MFCs) are devices that are able aga were abundantly present in the anodic biofilm to directly convert the chemical energy of organic community (Kimura and Okabe, 2013). -
Cellular Respiration: Harvesting Chemical Energy
Lecture 13 9/30/05 Lecture Outline Cellular Respiration: 1. Regulation of Enzymes: competitive, allosteric, phosphorylation Harvesting Chemical Energy 2. Equilibrium 3. Digestion vs Metabolism: catabolism and anabolism Chapter 9 4. What is a metabolic pathway? 5. Feedback regulation of pathways 6. Catabolic pathways - stepping down the oxidation series of carbon 7. Harvesting energy from redox reactions I. General - substrate level phosphorylation ATP + Principles – reducing equivalent carriers NADH + H , FADH2 8. Example of a catabolic pathway: Fatty Acid Oxidation 1 2 Figure 9.1 Reactions that proceed in a closed system Living systems = Open System – Eventually reach equilibrium – Must have constant flow of materials in – Constant Energy Input Can do Cannot Do Useful ∆G < 0 ∆G = 0 work work Equilibrium to a living system is called…. ∆G < 0 (b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium. (a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium. Figure 8.7 Figure 8.7 A 3 4 Metabolism – totality of all chemical Metabolism: a series of favorable reactions reactions of an organism Inputs ∆G < 0 digestion ∆G < 0 Hydrolysis of polymers to monomers ∆G < 0 No energy Harvested ! occurs “outside” the cell catabolism –energy capture reactions oxidize substrates, produce energy carriers Figure 8.7 Waste anabolism –energy -
Studies on Triphenylmethane, Azo Dye and Latex Rubber Biodegradation by Actinomycetes
Studies on triphenylmethane, azo dye and latex rubber biodegradation by actinomycetes by Melissa Dalcina Chengalroyen Schoool of Molecular and Cellular Biology Faculty of Science University of Witwatersrand South Africa 2011 I. Declaration I declare that this research is my own unaided work unless otherwise specified. It is being submitted to the University of the Witwatersrand, Johannesburg for the degree of Doctor of Philosophy. It has not previously been submitted for any other degree or examination in this or any other university. Melissa Dalcina Chengalroyen 1st day of June 2011 i II. Acknowledgements I am grateful to my family who have made numerous sacrifices. I would like to thank Prof. E.R. Dabbs for his supervision. I am indebted to my lab colleagues for all their assistance. I would also like to acknowledge the National Research Foundation for financial support. The following were kindly provided for this research: pNV18 and pNV19 by J. Ishikawa, LATZ by the rubber research institute of Malaysia and Streptomycete strains by the John Innes Institute. This study comprises seven components and for clarity has been presented in separate chapters. This is the overall format of the thesis: Chapter I: Identification and characterization of a gene responsible for amido black decolorization isolated from A. orientalis Chapter II: Identification and characterization of genetic elements from Amycolatopsis species contributing to triphenylmethane decolorization Chapter III: Characterization of rubber degrading isolates and the cloning of DNA conferring an apparent latex degrading ability Chapter IV: Preliminary characterization of A. orientlis phytase activity Chapter V: Screening for antimicrobial compounds from soil isolates METHOD DEVELOPMENT Chapter VI: Construction of broad host range positive selection vectors Chapter VII: Adaptation of conventional Rhodococcus spp. -
Delftia Rhizosphaerae Sp. Nov. Isolated from the Rhizosphere of Cistus Ladanifer
TAXONOMIC DESCRIPTION Carro et al., Int J Syst Evol Microbiol 2017;67:1957–1960 DOI 10.1099/ijsem.0.001892 Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer Lorena Carro,1† Rebeca Mulas,2 Raquel Pastor-Bueis,2 Daniel Blanco,3 Arsenio Terrón,4 Fernando Gonzalez-Andr es, 2 Alvaro Peix5,6 and Encarna Velazquez 1,6,* Abstract A bacterial strain, designated RA6T, was isolated from the rhizosphere of Cistus ladanifer. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Delftia within a cluster encompassing the type strains of Delftia lacustris, Delftia tsuruhatensis, Delftia acidovorans and Delftia litopenaei, which presented greater than 97 % sequence similarity with respect to strain RA6T. DNA–DNA hybridization studies showed average relatedness ranging from of 11 to 18 % between these species of the genus Delftia and strain RA6T. Catalase and oxidase were positive. Casein was hydrolysed but gelatin and starch were not. Ubiquinone 8 was the major respiratory quinone detected in strain RA6T together with low amounts of ubiquinones 7 and 9. The major fatty acids were those from summed feature 3 (C16 : 1!7c/C16 : 1 !6c) and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA6T should be considered as a representative of a novel species of genus Delftia, for which the name Delftia rhizosphaerae sp. nov. is proposed. The type strain is RA6T (=LMG 29737T= CECT 9171T). The genus Delftia comprises Gram-stain-negative, non- The strain was grown on nutrient agar (NA; Sigma) for 48 h sporulating, strictly aerobic rods, motile by polar or bipolar at 22 C to check for motility by phase-contrast microscopy flagella. -
Characterization of Azo Dye Reduction in Enterococcus Faecalis
CHARACTERIZATION OF AZO DYE REDUCTION IN ENTEROCOCCUS FAECALIS By SUMIT PUNJ Bachelor of Science University of Mumbai, Mumbai, India 1998 Master of Science University of Mumbai Mumbai, India 2000 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY July, 2008 CHARACTERIZATION OF AZO DYE REDUCTION IN ENTEROCOCCUS FAECALIS Dissertation Approved: Dr. Gilbert H. John Dissertation Adviser Dr. Robert L. Burnap Dr. Rolf A. Prade Dr. Babu Z. Fathepure Dr. Carol L. Bender Dr. A. Gordon Emslie Dean of the Graduate College ii ACKNOWLEDGMENTS I would like to express my gratitude to my adviser, Dr. Gilbert H. John who has been very patient and understanding throughout my years in the program. He has given me the opportunity to develop and execute my ideas and has always been very encouraging. I sincerely thank each one of my committee members; Dr. Robert Burnap, Dr. Rolf Prade, Dr. Babu Fathepure and Dr. Carol Bender who have all been instrumental in guiding me in my research and have always given me excellent suggestions to improve the quality of my work. My gratitude extends towards Susan Macwana and Cristee Wright who have been great laboratory colleagues and friends. It has been a pleasure to work with them and they have always been very supportive of me. I would like to thank all the present and past undergraduates who have contributed to the collegial environment in the laboratory. I am also very grateful to the faculty, staff and graduate students of the Microbiology and Molecular Genetics department at OSU who have been extremely helpful, supportive and encouraging. -
Diaphorobacter Nitroreducens Gen. Nov., Sp. Nov., a Poly (3
J. Gen. Appl. Microbiol., 48, 299–308 (2002) Full Paper Diaphorobacter nitroreducens gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge Shams Tabrez Khan and Akira Hiraishi* Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi 441–8580, Japan (Received August 12, 2002; Accepted October 23, 2002) Three denitrifying strains of bacteria capable of degrading poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were isolated from activated sludge and characterized. All of the isolates had almost identical phenotypic characteristics. They were motile gram-negative rods with single polar flagella and grew well with simple organic com- pounds, as well as with PHB and PHBV, as carbon and energy sources under both aerobic and anaerobic denitrifying conditions. However, none of the sugars tested supported their growth. The cellular fatty acid profiles showed the presence of C16:1w7cis and C16:0 as the major com- ponents and of 3-OH-C10:0 as the sole component of hydroxy fatty acids. Ubiquinone-8 was de- tected as the major respiratory quinone. A 16S rDNA sequence-based phylogenetic analysis showed that all the isolates belonged to the family Comamonadaceae, a major group of b-Pro- teobacteria, but formed no monophyletic cluster with any previously known species of this fam- (DSM 13225؍) ily. The closest relative to our strains was an unidentified bacterium strain LW1 (99.9% similarity), reported previously as a 1-chloro-4-nitrobenzene degrading bacterium. DNA- DNA hybridization levels among the new isolates were more than 60%, whereas those between our isolates and strain DSM 13225 were less than 50%. -
Delftia Sp. LCW, a Strain Isolated from a Constructed Wetland Shows Novel Properties for Dimethylphenol Isomers Degradation Mónica A
Vásquez-Piñeros et al. BMC Microbiology (2018) 18:108 https://doi.org/10.1186/s12866-018-1255-z RESEARCHARTICLE Open Access Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation Mónica A. Vásquez-Piñeros1, Paula M. Martínez-Lavanchy1,2, Nico Jehmlich3, Dietmar H. Pieper4, Carlos A. Rincón1, Hauke Harms5, Howard Junca6 and Hermann J. Heipieper1* Abstract Background: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems. Results: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. -
The Function of Energy-Dependent Redox Reactions in Cell Metabolism
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Volume 117, Supplement FEBS LETTERS 25 August 1980 THE FUNCTION OF ENERGY-DEPENDENT REDOX REACTIONS IN CELL METABOLISM Michael N. BERRY Department of Clinical Biochemistry, Flinders University School of Medicine, Flinders Medical Centre, Bedford Park, SA JO42, Australia 1. Introduction and no shuttle is required for reducing-equivalent transfer between mitochondrial matrix and inner A major interest of H. A. Krebs has been the membrane. The redox state of this putative pool mechanisms that regulate the steady-state concentra- could be determined by measurement of the sub- tions of metabolic intermediates within the various strates either for the 3-hydroxybutyrate dehydro- ceil compartments. Almost 15 years ago, studies by genase or the glutamate dehydrogenase reactions, and Williamson et al. [l] confirmed earlier findings [2,3] proved to be some lOO-times more reduced than the which suggested that the components of the lactate cytoplasmic compartment [7]. dehydrogenase system in liver are maintained in a This work was subsequently expanded to include constant state apparently close to thermodynamic the NADP-linked couples of the cytoplasm and mito- equilibrium. The ratio, [lactate]/ [pyruvate] was thus chondria, and the relationship of the redox state for considered to reflect the ‘redox state’, the ratio of cytoplasmic NAD(H) to the phosphorylation state of free [NAD]/ [NADH], within the cytoplasmic com- the cytoplasmic and mitochondrial compartments partment of the hepatic cell [ 1,4]. Estimates of cyto- [8]. From these studies developed the concept that a plasmic [NAD] /NADH] ratios of about 400-2000 network of near-equilibria exists within the living cell, under various experimental circumstances were calcu- ultimately regulated by the phosphorylation state of lated from the values found for [lactate]/ [pyruvate] the respiratory chain, poising the redox states of [5-71.