Bacterial Sulfite-Oxidizing Enzymes
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Comamonas: Relationship to Aquaspirillum Aquaticum, E
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1991, p. 427-444 Vol. 41, No. 3 0020-7713/91/030427- 18$02 .OO/O Copyright 0 1991, International Union of Microbiological Societies Polyphasic Taxonomic Study of the Emended Genus Comamonas: Relationship to Aquaspirillum aquaticum, E. Falsen Group 10, and Other Clinical Isolates A. WILLEMS,l B. POT,l E. FALSEN,2 P. VANDAMME,' M. GILLIS,l* K. KERSTERS,l AND J. DE LEY' Laboratorium voor Microbiologie en Microbiele Genetica, Rijksuniversiteit, B-9000 Ghent, Belgium, and Culture Collection, Department of Clinical Bacteriology, University of Goteborg, S-413 46 Goteborg, Sweden2 We used DNA-rRNA hybridization, DNA base composition, polyacrylamide gel electrophoresis of whole-cell proteins, DNA-DNA hybridization, numerical analysis of phenotypic features, and immunotyping to study the taxonomy of the genus Comamonas. The relationships of this genus to Aquaspirillum aquaticum and a group of clinical isolates (E. Falsen group 10 [EF lo]) were studied. Our DNA and rRNA hybridization results indicate that the genus Comamonas consists of at least the following five genotypic groups: (i) Comamonas acidovoruns, (ii) Comamonas fesfosferoni,(iii) Comamonas ferrigena, (iv) A. aquaticum and a number of EF 10 strains, and (v) other EF 10 strains, several unnamed clinical isolates, and some misnamed strains of Pseudomonas alcaligenes and Pseudomonas pseudoalcaligenes subsp. pseudoalcaligenes. The existence of these five groups was confirmed by the results of immunotyping and protein gel electrophoresis. A numerical analysis of morpho- logical, auxanographic, and biochemical data for the same organisms revealed the existence of three large phena. Two of these phena (C. acidovorans and C. tesfosferoni)correspond to two of the genotypic groups. -
Sulfite Dehydrogenases in Organotrophic Bacteria : Enzymes
Sulfite dehydrogenases in organotrophic bacteria: enzymes, genes and regulation. Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Fachbereich Biologie vorgelegt von Sabine Lehmann Tag der mündlichen Prüfung: 10. April 2013 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Andrew W. B. Johnston So eine Arbeit wird eigentlich nie fertig, man muss sie für fertig erklären, wenn man nach Zeit und Umständen das möglichste getan hat. (Johann Wolfgang von Goethe, Italienische Reise, 1787) DANKSAGUNG An dieser Stelle möchte ich mich herzlich bei folgenden Personen bedanken: . Prof. Dr. Alasdair M. Cook (Universität Konstanz, Deutschland), der mir dieses Thema und seine Laboratorien zur Verfügung stellte, . Prof. Dr. Bernhard Schink (Universität Konstanz, Deutschland), für seine spontane und engagierte Übernahme der Betreuung, . Prof. Dr. Andrew W. B. Johnston (University of East Anglia, UK), für seine herzliche und bereitwillige Aufnahme in seiner Arbeitsgruppe, seiner engagierten Unter- stützung, sowie für die Übernahme des Koreferates, . Prof. Dr. Frithjof C. Küpper (University of Aberdeen, UK), für seine große Hilfsbereitschaft bei der vorliegenden Arbeit und geplanter Manuskripte, als auch für die mentale Unterstützung während der letzten Jahre! Desweiteren möchte ich herzlichst Dr. David Schleheck für die Übernahme des Koreferates der mündlichen Prüfung sowie Prof. Dr. Alexander Bürkle, für die Übernahme des Prüfungsvorsitzes sowie für seine vielen hilfreichen Ratschläge danken! Ein herzliches Dankeschön geht an alle beteiligten Arbeitsgruppen der Universität Konstanz, der UEA und des SAMS, ganz besonders möchte ich dabei folgenden Personen danken: . Dr. David Schleheck und Karin Denger, für die kritische Durchsicht dieser Arbeit, der durch und durch sehr engagierten Hilfsbereitschaft bei Problemen, den zahlreichen wissenschaftlichen Diskussionen und für die aufbauenden Worte, . -
QM/MM Study of the Reaction Mechanism of Sulfite Oxidase
www.nature.com/scientificreports OPEN QM/MM study of the reaction mechanism of sulfte oxidase Octav Caldararu1, Milica Feldt 2,4, Daniela Cioloboc1, Marie-Céline van Severen1, Kerstin Starke3, Ricardo A. Mata2, Ebbe Nordlander3 & Ulf Ryde 1 Received: 29 November 2017 Sulfte oxidase is a mononuclear molybdenum enzyme that oxidises sulfte to sulfate in many Accepted: 28 February 2018 organisms, including man. Three diferent reaction mechanisms have been suggested, based on Published: xx xx xxxx experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfte substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The frst step is rate limiting, with a barrier of 39–49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refnement calculations indicate that it is in the normal reduced tetrahydro form in this protein. Molybdenum (Mo) is the only second-row transition metal that is used in biological systems1. It is employed in nitrogenases, as well as in a large group of molybdenum oxo-transfer enzymes. -
Sulfur-Dependent Microbial Lifestyles: Deceptively Flexible Roles for Biochemically Versatile Enzymes Crane 141
Available online at www.sciencedirect.com ScienceDirect Sulfur-dependent microbial lifestyles: deceptively flexible roles for biochemically versatile enzymes Edward J Crane III Abstract of sulfur in a manner similar to the utilization of starch granules by yeast [1]. In a series of elegant experiments A wide group of microbes are able to “make a living” on Earth originally designed to confirm the idea that individual by basing their energetic metabolism on inorganic sulfur species of bacteria existed that exhibited defined charac- compounds. Because of their range of stable redox states, teristics (known as monomorphism) Winogradsky not only sulfur and inorganic sulfur compounds can be utilized as either provided support that the microbial community was made oxidants or reductants in a diverse array of energy-conserving up of a diverse array of defined species, he also demon- reactions. In this review the major enzymes and basic strated the first known case of chemolithotrophy, at the chemistry of sulfur-based respiration and chemolithotrophy are same time establishing the fields of geomicrobiology and outlined. The reversibility and versatility of these enzymes, microbial ecology [3]. The importance of the microbes and however, means that they can often be used in multiple ways, enzymes capable of sulfur-based chemolithoautotrophy and several cases are discussed in which enzymes which are and photoautotrophy (using sulfur compounds as energy considered to be hallmarks of a particular respiratory or and/or electron sources, respectively, in theoxidative direc- lithotrophic process have been found to be used in other, often tion) and sulfur-based respiration (in the reductive direc- opposing, metabolic processes. -
Biotransformation of Pharmaceuticals by Comamonas and Aeromonas Species
Biotransformation of Pharmaceuticals by Comamonas and Aeromonas Species Atika Sajid Shaheed Zulqar Ali Bhutto Institute of Science and Technology Saira Yahya ( [email protected] ) Shaheed Zulqar Ali Bhutto Institute of Science and Technology Research Article Keywords: Antibiotic resistance, Biotransformation, Erythromycin, Sulfamethoxazole-trimethoprim, Comamonas jiangduensis, Aeromonas hydrophila, Aeromonas caviae Posted Date: January 15th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-144884/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/22 Abstract Background: Contamination of natural niches with pharmaceutical residues has emerged out as a serious concern. Disposal of untreated euents from the pharmaceutical, hospital, and domestic settings has been identied as a signicant source of such a massive spread of antibiotics. The unnecessary persistence of pharmaceutical residues including antibiotics has been related to the increased risk of resistance selection among pathogenic and non-pathogenic microorganisms. To date, several methods have been devised to eliminate such pollutants from wastewater, but their implication on larger scales is not feasible due to complexities and high costs of the processes, especially in developing and underdeveloped countries. This study aimed to isolate and characterize bacterial strains from domestic and pharmaceutical euents having biotransformation potential towards most persistent antibiotics. Results: Antibiotic resistance screening and MIC determination experiments indicated highest resistivity of three bacterial isolates against two antibiotics Erythromycin and Sulfamethoxazole-trimethoprim, evincing extensive usage of these antibiotics in our healthcare settings. These isolates were identied as Comamonas jiangduensis, Aeromonas caviae and Aeromonas hydrophila by 16S rDNA sequencing. Growth conditions including incubation temperature, initial pH and inoculum size were optimized for these strains. -
Analysis of Thiosulfate Metabolism in a Marine Acidophilic Sulfur-Oxidizing Bacterium, Acidithiobacillus Thiooxidans Strain SH
Analysis of Thiosulfate Metabolism in a Marine Acidophilic Sulfur-Oxidizing Bacterium, Acidithiobacillus thiooxidans strain SH September, 2015 SULTANA SHARMIN Graduate School of Environmental and Life Science (Doctor's Course) OKAYAMA UNIVERSITY CONTENTS Pages CHAPTER 1 1. GENERAL INTRODUCTION……………………………. 1 1.1. Biomining………………………………………............ 1 1.2. Fundamentals of Biomining……………………………. 2 1.2.1.Industrial Biomining…………………………............ 3 1.2.2.Metal Sulfide oxidation- the two pathways……………… 4 1.3. Applications of Biomining………………………………. 5 CHAPTER 2 2.1. INTRODUCTION……………………………………….. 12 2.2 MATERIALS AND METHODS………………………… 15 2.2.1. Bacterial strains, media, and growth conditions……… 15 2.2.2. Enzyme assay…………………………………………. 15 2.2.3. Purification of TSD from At.thiooxidans strain SH…… 16 2.2.4. Protein analysis………………………………………… 17 2.2.5. Analysis of sulfur compound………………………….. 17 2.3. RESULTS AND DISCUSSION…………………………… 19 2.3.1. Detection of TSD activity in thiosulfate-grown At.thiooxidans strain SH………………………………………..19 2.3.2. Purification of TSD from thiosulfate-grown At.thiooxidans strain SH……………………………………... 21 2.3.3. Biochemical Properties of TSD from strain SH………….26 2.3.4. Stoichiometry of thiosulfate oxidation……………………31 2.3.5. Substrate specificity and electron acceptor……………….33 2.3.6. Inhibitors………………………………………………….35 2.3.7. Identification of the gene encoding TSD………………….35 2.3. SUMMARY...……………………………………………………..38 CHAPTER 3 3.1. INTRODUCTION………………………………………………39 3.2. MATERIALS AND METHODS……………………………….41 3.2.1. DNA preparation………………………………………….41 3.2.2. Genome sequencing and draft assembly………………….41 3.2.3. Gene prediction and annotation………………………...41 3.2.4. At. thiooxidans genome sequences………………………..41 3.2.5. Comparative genome analysis…………………………….42 3.2.4. -
Phenotypic and Genetic Diversity of Pseudomonads
PHENOTYPIC AND GENETIC DIVERSITY OF PSEUDOMONADS ASSOCIATED WITH THE ROOTS OF FIELD-GROWN CANOLA A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon By Danielle Lynn Marie Hirkala © Copyright Danielle Lynn Marie Hirkala, November 2006. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Applied Microbiology and Food Science University of Saskatchewan Saskatoon, Saskatchewan, S7N 5A8 i ABSTRACT Pseudomonads, particularly the fluorescent pseudomonads, are common rhizosphere bacteria accounting for a significant portion of the culturable rhizosphere bacteria. -
O O2 Enzymes Available from Sigma Enzymes Available from Sigma
COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc. -
Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax As Acidovorax Avenae Subsp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 107-119 Vol. 42, No. 1 0020-7713/92/010107-13$02 .OO/O Copyright 0 1992, International Union of Microbiological Societies Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov. , Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci A. WILLEMS,? M. GOOR, S. THIELEMANS, M. GILLIS,” K. KERSTERS, AND J. DE LEY Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit Gent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenue, Pseudomonas rubrilineans, “Pseudomonas setariae, ” Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudo- monas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenue. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenue and Acidovorax konjaci. Within Acidovorax avenue we distinguished the following three subspecies: Acidovorax avenue subsp. -
Structural Basis of Interprotein Electron Transfer in Bacterial Sulfite
RESEARCH ARTICLE Structural basis of interprotein electron transfer in bacterial sulfite oxidation Aaron P McGrath1†, Elise L Laming2‡, G Patricia Casas Garcia3, Marc Kvansakul3, J Mitchell Guss2, Jill Trewhella2, Benoit Calmes4,5, Paul V Bernhardt4,5, Graeme R Hanson4,6§, Ulrike Kappler4,5*, Megan J Maher3* 1Structural Biology Program, Centenary Institute, Sydney, Australia; 2School of Molecular Bioscience, University of Sydney, Sydney, Australia; 3Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia; 4Centre for Metals in Biology, The University of Queensland, Brisbane, Australia; 5School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; 6Centre for Advanced Imaging, University of Queensland, Brisbane, Australia Abstract Interprotein electron transfer underpins the essential processes of life and relies on the formation of specific, yet transient protein-protein interactions. In biological systems, the *For correspondence: detoxification of sulfite is catalyzed by the sulfite-oxidizing enzymes (SOEs), which interact with an [email protected] (UK); electron acceptor for catalytic turnover. Here, we report the structural and functional analyses of [email protected] (MJM) the SOE SorT from Sinorhizobium meliloti and its cognate electron acceptor SorU. Kinetic and Present address: † Skaggs thermodynamic analyses of the SorT/SorU interaction show the complex is dynamic in solution, and K ± School of Pharmacy and that the proteins interact with d = 13.5 0.8 mM. The crystal structures of the oxidized SorT and Pharmaceutical Sciences, SorU, both in isolation and in complex, reveal the interface to be remarkably electrostatic, with an University of California, San unusually large number of direct hydrogen bonding interactions. -
Towards X-Ray Structural Analysis of Thermus Thermophilus Sulphite Reductase: Purification Characterisation and Crystallisation
O’Donnell, M.D. Towards X-ray structural analysis of Thermus thermophilus sulphite reductase: Purification characterisation and crystallisation M. Sc. Thesis Michael D. O’Donnell Supervisor: Prof. Tewfik Soulimane A thesis submitted to the University of Limerick in candidature for the degree of Master of Science. Submitted to the University of Limerick 2017 O’Donnell, M.D. i O’Donnell, M.D. Abstract The process of sulfur remediation is an ancient process credited with the origins of life, through the interconversion of sulfur molecule. The sulfite reductases play an essential role, allowing an organism to reduce sulfite, building a range of sulfur based molecules such as the amino acids and vitamins. The sulfite reductases can be divided into different groups. This depends on the number of subunits and whether the sulfite reductase operates via an assimilatory or a dissimilatory mode. While there have been a number of structures solved and a mechanism for this family proposed, the overall understanding of the function of this class of enzymes is still scarce. Here, the sulfite reductase of Thermus thermophilus was studied, with the protein previously cloned BL21* E. coli cells. Initial work revolved around increasing the yield, through the optimization of the lysis and purification protocol leading to homogenous population of the sample required for structural studies. Research was also performed on the optimisation of the crystallisation conditions for the protein. Crystals obtained have been used for the structure determination by X-ray crystallography. The crystal structure has been solved to 2.38 Å resolution. Over the course of the study the yield was increased to 24 mg/L (a 400% increase). -
Delftia Acidovorans Peritonitis in a Patient Undergoing Peritoneal Dialysis
10.5152/turkjnephrol.2020.4204 Case Report Delftia Acidovorans Peritonitis in a Patient Undergoing Peritoneal Dialysis Ayşe Serra Artan , Meltem Gürsu , Ömer Celal Elçioğlu , Rumeyza Kazancıoğlu 326 Department of Nephrology, Bezmialem Vakıf University School of Medicine, İstanbul, Turkey Abstract Peritonitis is the most common complication of peritoneal dialysis. Peritoneal dialysis associated peritonitis caused by Delftia acidovorans has been reported only once in the literature before. Here, we present the second case of D. acidovo- rans peritonitis in a 60-year old male patient undergoing peritoneal dialysis. The patient was treated with intraperitoneal ceftazidim and oral ciprofloxacin, to which the organism was sensitive. The catheter was removed because of refractory peritonitis. Keywords: Delftia acidovorans, end-stage kidney disease, peritoneal dialysis, peritoneal dialysis-associated peritonitis Corresponding Author: Ayşe Serra Artan [email protected] Received: 16.11.2019 Accepted: 29.04.2020 Cite this article as: Artan AS, Gürsu M, Elçioğlu ÖC, Kazancıoğlu R. Delftia Acidovorans Peritonitis in a Patient Undergoing Peritoneal Dialysis. Turk J Nephrol 2020; 29(4): 326-8. INTRODUCTION mg/dL). Peritonitis was diagnosed. Culture samples Bacterial peritonitis is the most common complication of dialysate were inoculated in aerobic and anerobic encountered in peritoneal dialysis. Delftia acidovorans (D. blood culture bottles and an intraperitoneal empiric acidovorans) is a gram-negative aerobic bacteria found in antibiotic treatment with 1 g of cefazol and 1 g of cef- soil and water (1). It has rarely been implicated in serious tazidim daily was started. Gram-negative bacilli were human infections (2). We report a peritoneal dialysis as- visualized on dialysate Gram stain. On day 2, dialysate sociated peritonitis case caused by D.