(12) Patent Application Publication (10) Pub. No.: US 2009/0053736A1 Mattingly Et Al
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Sorgodb: Superoxide Reductase Gene Ontology Curated Database
Lucchetti-Miganeh et al. BMC Microbiology 2011, 11:105 http://www.biomedcentral.com/1471-2180/11/105 DATABASE Open Access SORGOdb: Superoxide Reductase Gene Ontology curated DataBase Céline Lucchetti-Miganeh1*, David Goudenège1, David Thybert1,2, Gilles Salbert1 and Frédérique Barloy-Hubler1 Abstract Background: Superoxide reductases (SOR) catalyse the reduction of superoxide anions to hydrogen peroxide and are involved in the oxidative stress defences of anaerobic and facultative anaerobic organisms. Genes encoding SOR were discovered recently and suffer from annotation problems. These genes, named sor, are short and the transfer of annotations from previously characterized neelaredoxin, desulfoferrodoxin, superoxide reductase and rubredoxin oxidase has been heterogeneous. Consequently, many sor remain anonymous or mis-annotated. Description: SORGOdb is an exhaustive database of SOR that proposes a new classification based on domain architecture. SORGOdb supplies a simple user-friendly web-based database for retrieving and exploring relevant information about the proposed SOR families. The database can be queried using an organism name, a locus tag or phylogenetic criteria, and also offers sequence similarity searches using BlastP. Genes encoding SOR have been re-annotated in all available genome sequences (prokaryotic and eukaryotic (complete and in draft) genomes, updated in May 2010). Conclusions: SORGOdb contains 325 non-redundant and curated SOR, from 274 organisms. It proposes a new classification of SOR into seven different classes and allows biologists to explore and analyze sor in order to establish correlations between the class of SOR and organism phenotypes. SORGOdb is freely available at http://sorgo.genouest.org/index.php. Background (called reactive oxygen species or ROS), particularly Two and a half billion years ago, the intense photosyn- hydroxyl radicals (•OH), hydrogen peroxide (H2O2)and thetic activity of cyanobacteria caused the largest envir- superoxide anion radicals (O2-). -
ABSTRACT JI, MIKYOUNG LEE. Superoxide Reductase from The
ABSTRACT JI, MIKYOUNG LEE. Superoxide Reductase from the Hyperthermophilic Archaeon Pyrococcus furiosus: its Function, Regulation, and Biotechnological Applications. (Under the direction of Amy M. Grunden.) The anaerobic hyperthermophilic archaeon, Pyrococcus furious, possesses a system for the detoxification of reactive oxygen species, which is different from the classical defense mechanisms present in aerobes. P. furiosus employs a novel enzyme system centered on the enzyme superoxide reductase (SOR), which reduces superoxide molecules to hydrogen peroxide without producing oxygen. Surprisingly, P. furiosus SOR, unlike many P. furiosus enzymes, was shown to function at low temperature (<25o C). A model for superoxide reduction by SOR was proposed where the electrons used by SOR to reduce superoxide are supplied by a small iron containing protein, rubredoxin (Rd), and Rd is reduced by the oxidoreductase, NAD(P)H-rubredoxin oxidoreductase (NROR). The first objective of this study was to evaluate the validity of the proposed superoxide reduction pathway by using the recombinant SOR, Rd and NROR enzymes in an in vitro assay as well as to demonstrate in vivo function via complementation studies in superoxide detoxification deficient Escherichia coli strains. The second objective was to investigate the transcriptional expression levels of genes that are involved in the SOR- centered superoxide reduction pathway in order to determine how these genes are expressed and regulated in response to various oxidative stresses. The third objective was to evaluate the efficacy of the biotechnological application of this superoxide detoxification system by expressing SOR in plant cells, which enhanced their survival at high temperature and from drought indicating that it functions successfully in vivo. -
Role of Superoxide Reductase FA796 in Oxidative Stress Resistance in Filifactor Alocis Arunima Mishra✉, Ezinne Aja & Hansel M Fletcher
www.nature.com/scientificreports OPEN Role of Superoxide Reductase FA796 in Oxidative Stress Resistance in Filifactor alocis Arunima Mishra✉, Ezinne Aja & Hansel M Fletcher Filifactor alocis, a Gram-positive anaerobic bacterium, is now a proposed diagnostic indicator of periodontal disease. Because the stress response of this bacterium to the oxidative environment of the periodontal pocket may impact its pathogenicity, an understanding of its oxidative stress resistance strategy is vital. Interrogation of the F. alocis genome identifed the HMPREF0389_00796 gene that encodes for a putative superoxide reductase (SOR) enzyme. SORs are non-heme, iron-containing enzymes that can catalyze the reduction of superoxide radicals to hydrogen peroxide and are important in the protection against oxidative stress. In this study, we have functionally characterized the putative SOR (FA796) from F. alocis ATCC 35896. The recombinant FA796 protein, which is predicted to be a homotetramer of the 1Fe-SOR class, can reduce superoxide radicals. F. alocis FLL141 (∆FA796::ermF) was signifcantly more sensitive to oxygen/air exposure compared to the parent strain. Sensitivity correlated with the level of intracellular superoxide radicals. Additionally, the FA796-defective mutant had increased sensitivity to hydrogen peroxide-induced stress, was inhibited in its ability to form bioflm and had reduced survival in epithelial cells. Collectively, these results suggest that the F. alocis SOR protein is a key enzymatic scavenger of superoxide radicals and protects the bacterium from oxidative stress conditions. All living cells in an oxygen-rich environment encounter oxidative stress due to the generation of reactive oxygen 1,2 species (ROS), including superoxide radicals, hydroxyl radicals and hydrogen peroxide (H2O2) . -
Synergistic Chemo/Biocatalytic Synthesis of Alkaloidal Tetrahydroquinolines
This is a repository copy of Synergistic Chemo/Biocatalytic Synthesis of Alkaloidal Tetrahydroquinolines. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/133028/ Version: Accepted Version Article: Cosgrove, SC, Hussain, S, Turner, NJ et al. (1 more author) (2018) Synergistic Chemo/Biocatalytic Synthesis of Alkaloidal Tetrahydroquinolines. ACS Catalysis, 8 (6). pp. 5570-5573. ISSN 2155-5435 https://doi.org/10.1021/acscatal.8b01220 (c) 2018, American Chemical Society. This is an author produced version of a paper published in ACS Catalysis. Uploaded in accordance with the publisher's self-archiving policy. Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Synergistic chemo/biocatalytic synthesis of alkaloidal tetrahydroquinolines Sebastian C. Cosgrove,1,2 Shahed Hussain,1 Nicholas J. Turner*1 and Stephen P. Marsden*2 1School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manches- ter M1 7DN, United Kingdom 2Institute of Process Research and Development and School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom ABSTRACT: The power of complementary chemo- and biocatalytic transformations is demonstrated in the asymmetric syn- thesis of 2-substituted tetrahydroquinolines. -
Redox Proteomics in Selected Neurodegenerative Disorders: from Its Infancy to Future Applications Allan Butterfield University of Kentucky
Eastern Kentucky University Encompass Chemistry Faculty and Staff choS larship Chemistry 2012 Redox Proteomics in Selected Neurodegenerative Disorders: From Its Infancy to Future Applications Allan Butterfield University of Kentucky Marzia Perluigi Sapienza University of Rome Tanea Reed Eastern Kentucky University Tasneem Muharib University of Kentucky Christopher P. Hughes University of Kentucky See next page for additional authors Follow this and additional works at: http://encompass.eku.edu/che_fsresearch Part of the Chemistry Commons Recommended Citation Butterfield, D. A., Perluigi, M., Reed, T., Muharib, T., Hughes, C. P., Robinson, R. A., & Sultana, R. (2012). Redox Proteomics in Selected Neurodegenerative Disorders: From Its Infancy to Future Applications. Antioxidants & Redox Signaling, 17(11), 1610-1655. doi:10.1089/ars.2011.4109 This Article is brought to you for free and open access by the Chemistry at Encompass. It has been accepted for inclusion in Chemistry Faculty and Staff Scholarship by an authorized administrator of Encompass. For more information, please contact [email protected]. Authors Allan Butterfield, Marzia Perluigi, Tanea Reed, Tasneem Muharib, Christopher P. Hughes, Rena A.S. Robinson, and Rukhsana Sultana This article is available at Encompass: http://encompass.eku.edu/che_fsresearch/3 See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/51828850 Redox Proteomics in Selected Neurodegenerative Disorders: From Its Infancy to Future Applications Article -
Development of Swiss Biotechnology Beyond the Biopharmaceutical Sector in Memoriam Prof
BUILDING BRIDGES BETWEEN BIOTECHNOLOGY AND CHEMISTRY – IN MEMORIAM ORESTE GHISALBA CHIMIA 2020, 74, No. 5 345 doi:10.2533/chimia.2020.345 Chimia 74 (2020) 345–359 © H.P. Meyer and O. Werbitzky Development of Swiss Biotechnology Beyond the Biopharmaceutical Sector In memoriam Prof. Dr. Oreste Ghisalba (1946–2018) Hans-Peter Meyera* and Oleg Werbitzkyb Abstract: Although diverse, the potential business opportunities for biotechnology outside the biopharmaceutical market are very large. White biotechnology can offer sustainable operations and products, while investments tend to be lower than those in red biotechnology. But a number of bottlenecks and roadblocks in Switzerland must be removed to realise the full potential of white biotechnology. This was also the point of view of Oreste Ghisalba, who wanted to be part of a new initiative to facilitate the creation of additional business, new pro- cesses and new products. This initiative requires the identification and the use of synergies and a much better cooperation between academia and industry through targeted networking. Unfortunately, we must carry on with this task without Oreste, whom we will miss for his deep knowledge and friendship. Keywords: Bio-based · Fine chemicals · Industrial biotechnology · Swiss economy · White biotechnology Hans-Peter Meyer holds a PhD in micro- venture partners and Managing Director of NC Health Sciences biology from the University of Fribourg since 2015. (Switzerland). He spent three years post- graduate and postdoc studies at the STFI 1. A Short History of the Swiss Biotechnology Industry in Stockholm (Sweden), the University The Swiss pharmaceutical and chemical industries have been of Pennsylvania and Lehigh University in responsible for almost half of the country’s exports for many years the USA. -
Precursor of Ether Phospholipids Is Synthesized by a Flavoenzyme
Precursor of ether phospholipids is synthesized by a flavoenzyme through covalent catalysis Simone Nencia, Valentina Pianoa, Sara Rosatib, Alessandro Alivertic, Vittorio Pandinic, Marco W. Fraaijed, Albert J. R. Heckb, Dale E. Edmondsone, and Andrea Mattevia,1 aDepartment of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; bBiomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; cDepartment of Biosciences, University of Milan, 20133 Milan, Italy; dMolecular Enzymology Group, University of Groningen, 9747 AG Groningen, The Netherlands; and eDepartment of Biochemistry, Emory University, Atlanta, GA 30322 Edited by Emil F. Pai, Ontario Cancer Institute/Princess Margaret Hospital, Toronto, ON, Canada, and accepted by the Editorial Board October 5, 2012 (received for review August 31, 2012) The precursor of the essential ether phospholipids is synthesized ADPS enzymes, whereas type 1 arises from mutations in PEX7, by a peroxisomal enzyme that uses a flavin cofactor to catalyze the protein mediating the peroxisomal import of ADPS (9–12). a reaction that does not alter the redox state of the substrates. Here we report a structural and mechanistic investigation of The enzyme crystal structure reveals a V-shaped active site with mammalian ADPS in WT and mutated forms. The biochemical a narrow constriction in front of the prosthetic group. Mutations hallmark of the enzyme is that it uses a redox cofactor, flavin causing inborn ether phospholipid deficiency, a very severe adenine dinucleotide (FAD), to catalyze a reaction that does not genetic disease, target residues that are part of the catalytic alter the redox state of the substrates (10, 13). -
Distribution in Different Organisms of Amino Acid Oxidases with FAD Or a Quinone As Cofactor and Their Role As Antimicrobial Proteins in Marine Bacteria
Supplementary Materials: Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria Jonatan C. Campillo‐Brocal, Patricia Lucas‐Elío and Antonio Sanchez‐Amat * Table S1. Amino acid oxidases (AAOs) from microbial sources. Marine microorganisms are shown in bold. * cofactor and/or activity attributed for high similarity with LodA. ND, not determined. NA, not accessible. LAAOs, L‐amino acid oxidases. DAAOs, D‐amino acid oxidases. LASPOs, L‐aspartate oxidases. CTQ, cysteine tryptophilquinone. Microorganism Oligomeric Structure/Mass Accession Activity (Main Substrate) Cofactor Various Reference (Enzyme Name) Molecular Number AAOs with Quinone Cofactor (LodA‐Like Proteins) Marinomonas Homotetramer (80.9 × 4 kDa). Antimicrobial. Biofilms mediterranea MMB‐1 L‐Lysine ε‐oxidase (L‐Lys) CTQ Crystal structure solved, PDB AAY33849 [1,2] dispersion. Extracellular (LodA) ID: 2YMW Marinomonas Other substrates: Gly ethyl mediterranea MMB‐1 Glycine oxidase (Gly) CTQ 76.2 kDa ADZ90918 [3,4] ester (GoxA) Pseudoalteromonas Antimicrobial. Biofilms L‐Lysine ε‐oxidase (L‐Lys) * CTQ 110 kDa Q7X0I8 [5,6] tunicata D2 (AlpP) dispersion Chromobacterium Antimicrobial. Biofilms ND ND ND AAQ60932 [6] violaceum dispersion Antimicrobial. Biofilms Caulobacter crescentus ND ND ND NP_419374 [6] dispersion Pseudoalteromonas flavipulchra JG1 * L‐Lysine ε‐oxidase (* L‐Lys) * CTQ 77 kDa Antimicrobial. pI = 4.6 AFB71049 [7] (PfaP) Broad spectrum oxidase Antimicrobial. pI = 9.4. It Pseudoalteromonas (L‐Lys > L‐Met > L‐Glu > L‐Leu > L‐ ND 60 kDa contains a 9‐residues peptide NA [8] flavipulchra C2 Gln > L‐Tyr > L‐Phe) similar to AlpP S1 Table S1. Cont. Broad spectrum oxidase Pseudoalteromonas (L‐Met > L‐Gln > L‐Leu > L‐Phe > L‐ ND Oligomer (110 kDa) Antimicrobial NA [9] luteoviolacea Glu > L‐Trp) Antimicrobial. -
2010 Physical Biosciences Research Meeting
2010 Physical Biosciences Research Meeting Sheraton Inner Harbor Hotel Baltimore, MD October 17-20, 2010 Office of Basic Energy Sciences Chemical Sciences, Geosciences & Biosciences Division 2010 Physical Biosciences Research Meeting Program and Abstracts Sheraton Inner Harbor Hotel Baltimore, MD October 17-20, 2010 Chemical Sciences, Geosciences, and Biosciences Division Office of Basic Energy Sciences Office of Science U.S. Department of Energy i Cover art is taken from the public domain and can be found at: http://commons.wikimedia.org/wiki/File:Blue_crab_on_market_in_Piraeus_-_Callinectes_sapidus_Rathbun_20020819- 317.jpg This document was produced under contract number DE-AC05-060R23100 between the U.S. Department of Energy and Oak Ridge Associated Universities. The research grants and contracts described in this document are, unless specifically labeled otherwise, supported by the U.S. DOE Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division. ii Foreword This volume provides a record of the 2nd biennial meeting of the Principal Investigators (PIs) funded by the Physical Biosciences program, and is sponsored by the Chemical Sciences, Geosciences, and Biosciences Division of the Office of Basic Energy Sciences (BES) in the U.S. Department of Energy (DOE). Within DOE-BES there are two programs that fund basic research in energy-relevant biological sciences, Physical Biosciences and Photosynthetic Systems. These two Biosciences programs, along with a strong program in Solar Photochemistry, comprise the current Photo- and Bio- Chemistry Team. This meeting specifically brings together under one roof all of the PIs funded by the Physical Biosciences program, along with Program Managers and staff not only from DOE-BES, but also other offices within DOE, the national labs, and even other federal funding agencies. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Retinoid Metabolism in the Rat Small Intestine
Downloaded from https://www.cambridge.org/core British Journal of Nutrition (2005), 93, 59–63 DOI: 10.1079/BJN20041306 q The Authors 2005 Retinoid metabolism in the rat small intestine . IP address: Simmy Thomas, Ramamoorthy Prabhu and Kunissery A. Balasubramanian* 170.106.40.139 The Wellcome Trust Research Laboratory, Department of Gastrointestinal Sciences, Christian Medical College, Vellore-632004, India (Received 1 April 2004 – Revised 27 July 2004 – Accepted 21 September 2004) , on 27 Sep 2021 at 00:14:50 Vitamin A (retinol) is essential for epithelial cell growth, differentiation and proliferation. The absorption of retinol occurs in the small intestine, and the metabolism of this vitamin is not well studied in this organ. The intestinal epithelium has a high rate of cell proliferation and differentiation, and the present study looked at the level of retinoids and metabolizing enzymes involved in their interconversion along the villus–crypt axis under normal conditions. Intes- tine was removed from control rats, and enterocytes at various stages of maturation and differentiation were quantified by the metal chelation method. Using HPLC, various retinoid concentrations in the cell homogenate and the metabolizing enzymes in the cytosol were quantified. The proliferating crypt cells , subject to the Cambridge Core terms of use, available at were found to have a higher level of retinoic acid as well as of the enzymes involved in its formation, such as retinaldehyde oxidase and retinol dehydro- genase, compared with the villus cells, suggesting a possible role for this compound in intestinal epithelial cell proliferation and differentiation. The high level of retinol and high retinaldehyde reductase activity in the villus cells suggest the important role played by this enzyme in the conversion of dietary b- carotene to retinol via retinaldehyde. -
Amino Acid Catabolism by Ribbed Mussel (Modiolus Demissus) Gill Tissue: Studies on Isolated Mitochondria and the L-Amino Acid Oxidase James M
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1983 Amino acid catabolism by ribbed mussel (Modiolus demissus) gill tissue: studies on isolated mitochondria and the L-amino acid oxidase James M. Burcham Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Agriculture Commons, Aquaculture and Fisheries Commons, and the Zoology Commons Recommended Citation Burcham, James M., "Amino acid catabolism by ribbed mussel (Modiolus demissus) gill tissue: studies on isolated mitochondria and the L-amino acid oxidase " (1983). Retrospective Theses and Dissertations. 8456. https://lib.dr.iastate.edu/rtd/8456 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This reproduction was made from a copy of a document sent to us for microfilming. While the most advanced technology has been used to photograph and reproduce this document, the quality of the reproduction is heavily dependent upon the quality of the material submitted. The following explanation of techniques is provided to help clarify markings or notations which may appear on this reproduction. 1.The sign or "target" for pages apparently lacking from the document photographed is "Missing Page(s)". If it was possible to obtain the missing page(s) or section, they are spliced into the film along with adjacent pages.