Structures of Shikimate Dehydrogenase Aroe and Its Paralog Ydib a COMMON STRUCTURAL FRAMEWORK for DIFFERENT ACTIVITIES*
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Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani Chunyu Liu
The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library 8-2001 Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani Chunyu Liu Follow this and additional works at: http://digitalcommons.library.umaine.edu/etd Part of the Biochemistry Commons, and the Molecular Biology Commons Recommended Citation Liu, Chunyu, "Quinic Acid-Mediated Induction of Hypovirulence and a Hypovirulence-Associated Double-Stranded RNA in Rhizoctonia Solani" (2001). Electronic Theses and Dissertations. 332. http://digitalcommons.library.umaine.edu/etd/332 This Open-Access Dissertation is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. QUlNlC ACID-MEDIATED INDUCTION OF HYPOVIRULENCE AND A HY POVlRULENCE-ASSOCIATED DOUBLESTRANDED RNA IN RHIZOCTONIA SOLANI BY Chunyu Liu B.S. Wuhan University, 1989 MS. Wuhan University. 1992 A THESIS Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Biochemistry and Molecular Biology) The Graduate School The Universrty of Maine August, 2001 Advisory Committee: Stellos Tavantzis, Professor of Plant Pathology, Advisor Seanna Annis, Assistant Professor of Mycology Robert Cashon, Assistant Professor of Biochemistry, Molecular Biology Robert Gundersen, Associate Professor of Biochemistry, Molecular Biology John Singer, Professor of Microbiology QUlNlC ACID-MEDIATED INDUCTION OF HYPOVIRULENCE AND A HYPOVIRULENCE-ASSOCIATED DOUBLE-STRANDED RNA (DSRNA) IN RHIZOCTONIA SOLANI By Chunyu Liu Thesis Advisor: Dr. Stellos Tavantzis An Abstract of the Thesis Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Biochemistry and Molecular Biology) August, 2001 This study is a part of a project focused on the relationship between dsRNA and hypovirulence in R. -
Microbial Degradation of the Morphine Alkaloids Purification and Characterization of Morphine Dehydrogenase from Pseudomonas Putida M10
Biochem. J. (1991) 274, 875-880 (Printed in Great Britain) 875 Microbial degradation of the morphine alkaloids Purification and characterization of morphine dehydrogenase from Pseudomonas putida M10 Neil C. BRUCE,* Clare J. WILMOT, Keith N. JORDAN, Lauren D. Gray STEPHENS and Christopher R. LOWE Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, U.K. The NADP+-dependent morphine dehydrogenase that catalyses the oxidation of morphine to morphinone was detected in glucose-grown cells of Pseudomonas putida M 10. A rapid and reliable purification procedure involving two consecutive affinity chromatography steps on immobilized dyes was developed for purifying the enzyme 1216-fold to electrophoretic homogeneity from P. putida M 10. Morphine dehydrogenase was found to be a monomer of Mr 32000 and highly specific with regard to substrates, oxidizing only the C-6 hydroxy group of morphine and codeine. The pH optimum of morphine dehydrogenase was 9.5, and at pH 6.5 in the presence of NADPH the enzyme catalyses the reduction of codeinone to codeine. The Km values for morphine and codeine were 0.46 mm and 0.044 mm respectively. The enzyme was inhibited by thiol-blocking reagents and the metal-complexing reagents 1, 10-phenanthroline and 2,2'-dipyridyl, suggesting that a metal centre may be necessary for activity of the enzyme. INTRODUCTION EXPERIMENTAL The morphine alkaloids have attracted considerable attention Materials owing to their analgaesic properties and, consequently, much Mimetic Orange 3 A6XL and Mimetic Red A6XL were effort in the past has been directed at the production of new obtained from Affinity Chromatography Ltd., Freeport, morphine alkaloids by micro-organisms (lizuka et al., 1960, Ballasalla, Isle of Man, U.K. -
Downloaded As a Text File, Is Completely Dynamic
BMC Bioinformatics BioMed Central Database Open Access ORENZA: a web resource for studying ORphan ENZyme activities Olivier Lespinet and Bernard Labedan* Address: Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris-Sud, Bâtiment 400, 91405 Orsay Cedex, France Email: Olivier Lespinet - [email protected]; Bernard Labedan* - [email protected] * Corresponding author Published: 06 October 2006 Received: 25 July 2006 Accepted: 06 October 2006 BMC Bioinformatics 2006, 7:436 doi:10.1186/1471-2105-7-436 This article is available from: http://www.biomedcentral.com/1471-2105/7/436 © 2006 Lespinet and Labedan; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) are not associated with any amino acid sequence in major public databases. This wide gap separating knowledge of biochemical function and sequence information is found for nearly all classes of enzymes. Thus, there is an urgent need to explore these sequence-less EC numbers, in order to progressively close this gap. Description: We designed ORENZA, a PostgreSQL database of ORphan ENZyme Activities, to collate information about the EC numbers defined by the NC-IUBMB with specific emphasis on orphan enzyme activities. -
STRUCTURAL STUDIES and EVALUATION of INHIBITORS of Mycobacterium
STRUCTURAL STUDIES AND EVALUATION OF INHIBITORS OF Mycobacterium tuberculosis H37Rv SHIKIMATE DEHYDROGENASE (MtSDH) A Thesis by MALLIKARJUN LALGONDAR Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Chair of Committee, James C. Sacchettini Committee Members, David P. Barondeau Mary Bryk Head of Department, Gregory D. Reinhart May 2014 Major Subject: Biochemistry Copyright 2014 Mallikarjun Lalgondar ABSTRACT Shikimate dehydrogenase (SDH) is a reversible enzyme catalyzing the reduction of 3-dehydroshikimate (3DHS) to shikimate (SKM) utilizing NADPH cofactor in the shikimate pathway, a central route for biosynthesis of aromatic amino acids, folates and ubiquinones in microogransims, plants and parasites, which renders the enzymes of this essential pathway as attractive targets for developing antimicrobials, herbicides and antiparasitic agents. In this study, the crystal structure of Mycobacterium tuberculosis SDH (MtSDH) was determined in the apo-form and in complex with a ligand, SKM. The overall structure of MtSDH contains two structural domains with α/β architecture. The N-terminal substrate binding domain and C-terminal cofactor binding domain are interconnected by two helices forming an active site groove where catalysis occurs. In MtSDH, a series of helices connecting β10 and β11 strands replace a long loop found in other known SDH structures and this region may undergo structural changes upon cofactor binding. NADP+ was modeled reliably in the cofactor binding site to gain insight into specific interactions. The analysis reveals that NADP(H) binds in anti conformation and in addition to residues in “basic patch”, Ser125 within the glycine rich loop may interact with the 2'-phosphate of adenine ribose and form a novel cofactor binding microenvironment in SDH family of enzymes. -
Proof of De Novo Synthesis of the Qa Enzymes of Neurospora Crassa During Induction
Proc. Nati. Acad. Sci. USA Vol. 74, No. 10, pp. 4256-4260, October 1977 Biochemistry Proof of de novo synthesis of the qa enzymes of Neurospora crassa during induction [catabolic dehydroquinase (5-dehydroquinate dehydratase)/quinate dehydrogenase/qa gene cluster/eukaryote gene regulation] WILLIAM R. REINERT AND NORMAN H. GILES Program in Genetics, Department of Zoology, University of Georgia, Athens, Georgia 30602 Contributed by Norman H. Giles, July 22, 1977 ABSTRACT In Neurospora crassa three inducible enzymes There is strong genetic evidence that the qa-1 gene encodes a are necessary to catabolize quinic acid to protocatechuic acid. regulatory protein which, in the presence of quinic acid, exerts The three genes encoding these enzymes are tightly linked on chromosome VII near methionine-7 (me-7). This qa cluster in- positive control over the synthesis of the enzymes encoded in cludes a fourth gene, qa-1, which encodes a regulatory protein the three adjacent structural genes (6, 10). The appearance of apparently exerting positive control over transcription of the enzyme activity is very specifically regulated. In the presence other three qa genes. However, an alternative hypothesis is that of a preferred carbon source, e.g., sucrose, the activities of all the qa-I protein simply activates preformed polypeptides de- three enzymes are quite low. Quinate as a sole carbon source rived from the three structural genes. The use of density labeling causes a coordinate induction of all three enzymes (9). This with D20 demonstrated conclusively that the qa enzymes are synthesized de novo only during induction on quinic acid. Na- increase in enzyme activity can be inhibited by the simulta- tive catabolic dehydroquinase (5-dehydroquinate dehydratase; neous addition of cycloheximide to the medium (ref. -
Elucidating the Role of Shikimate Dehydrogenase in Controlling The
Habashi et al. BMC Plant Biology (2019) 19:476 https://doi.org/10.1186/s12870-019-2042-1 RESEARCH ARTICLE Open Access Elucidating the role of shikimate dehydrogenase in controlling the production of anthocyanins and hydrolysable tannins in the outer peels of pomegranate Rida Habashi1,2, Yael Hacham1,2, Rohit Dhakarey1, Ifat Matityahu1, Doron Holland3, Li Tian4 and Rachel Amir1,2* Abstract Background: The outer peels of pomegranate (Punica granatum L.) possess two groups of polyphenols that have health beneficial properties: anthocyanins (ATs, which also affect peel color); and hydrolysable tannins (HTs). Their biosynthesis intersects at 3-dehydroshikimate (3-DHS) in the shikimate pathway by the activity of shikimate dehydrogenase (SDH), which converts 3-DHS to shikimate (providing the precursor for AT biosynthesis) or to gallic acid (the precursor for HTs biosynthesis) using NADPH or NADP+ as a cofactor. The aim of this study is to gain more knowledge about the factors that regulate the levels of HTs and ATs, and the role of SDH. Results: The results have shown that the levels of ATs and HTs are negatively correlated in the outer fruit peels of 33 pomegranate accessions, in the outer peels of two fruits exposed to sunlight, and in those covered by paper bags. When calli obtained from the outer fruit peel were subjected to light/dark treatment and osmotic stresses (imposed by different sucrose concentrations), it was shown that light with high sucrose promotes the synthesis of ATs, while dark at the same sucrose concentration promotes the synthesis of HTs. To verify the role of SDH, six PgSDHs (PgSDH1, PgSDH3–1,2, PgSDH3a-1,2 and PgSDH4) were identified in pomegranate. -
Building Microbial Factories for The
Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products ∗ Mingfeng Caoa,b,1, Meirong Gaoa,b,1, Miguel Suásteguia,b, Yanzhen Meie, Zengyi Shaoa,b,c,d, a Department of Chemical and Biological Engineering, Iowa State University, USA b NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, USA c Interdepartmental Microbiology Program, Iowa State University, USA d The Ames Laboratory, USA e School of Life Sciences, No.1 Wenyuan Road, Nanjing Normal University, Qixia District, Nanjing, 210023, China ARTICLE INFO ABSTRACT Keywords: The aromatic amino acid biosynthesis pathway, together with its downstream branches, represents one of the Aromatic amino acid biosynthesis most commercially valuable biosynthetic pathways, producing a diverse range of complex molecules with many Shikimate pathway useful bioactive properties. Aromatic compounds are crucial components for major commercial segments, from De novo biosynthesis polymers to foods, nutraceuticals, and pharmaceuticals, and the demand for such products has been projected to Microbial production continue to increase at national and global levels. Compared to direct plant extraction and chemical synthesis, Flavonoids microbial production holds promise not only for much shorter cultivation periods and robustly higher yields, but Stilbenoids Benzylisoquinoline alkaloids also for enabling further derivatization to improve compound efficacy by tailoring new enzymatic steps. This review summarizes the biosynthetic pathways for a large repertoire of commercially valuable products that are derived from the aromatic amino acid biosynthesis pathway, and it highlights both generic strategies and spe- cific solutions to overcome certain unique problems to enhance the productivities of microbial hosts. -
Determining Novel Functions of Arabidopsis 14-3-3 Proteins In
Diaz et al. BMC Systems Biology 2011, 5:192 http://www.biomedcentral.com/1752-0509/5/192 RESEARCHARTICLE Open Access Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes Celine Diaz1, Miyako Kusano1, Ronan Sulpice2, Mitsutaka Araki1, Henning Redestig1, Kazuki Saito1, Mark Stitt2 and Ryoung Shin1* Abstract Background: 14-3-3 proteins are considered master regulators of many signal transduction cascades in eukaryotes. In plants, 14-3-3 proteins have major roles as regulators of nitrogen and carbon metabolism, conclusions based on the studies of a few specific 14-3-3 targets. Results: In this study, extensive novel roles of 14-3-3 proteins in plant metabolism were determined through combining the parallel analyses of metabolites and enzyme activities in 14-3-3 overexpression and knockout plants with studies of protein-protein interactions. Decreases in the levels of sugars and nitrogen-containing-compounds and in the activities of known 14-3-3-interacting-enzymes were observed in 14-3-3 overexpression plants. Plants overexpressing 14-3-3 proteins also contained decreased levels of malate and citrate, which are intermediate compounds of the tricarboxylic acid (TCA) cycle. These modifications were related to the reduced activities of isocitrate dehydrogenase and malate dehydrogenase, which are key enzymes of TCA cycle. In addition, we demonstrated that 14-3-3 proteins interacted with one isocitrate dehydrogenase and two malate dehydrogenases. There were also changes in the levels of aromatic compounds and the activities of shikimate dehydrogenase, which participates in the biosynthesis of aromatic compounds. Conclusion: Taken together, our findings indicate that 14-3-3 proteins play roles as crucial tuners of multiple primary metabolic processes including TCA cycle and the shikimate pathway. -
Subcellular Localization of Quinate: Oxidoreductase from Phaseolus Mungo L. Sprouts Xiangbo Kang, H
Subcellular Localization of Quinate: Oxidoreductase from Phaseolus mungo L. Sprouts Xiangbo Kang, H. Ekkehard Neuhaus and Renate Scheibe Pflanzenphysiologie, Fachbereich Biologie/Chemie, Universität Osnabrück, D-49069 Osnabrück, Bundesrepublik Deutschland Z. Naturforsch. 49c, 415-420 (1994); received March 24/April 27, 1994 Phaseolus mungo, Quinate:Oxidoreductase, Quinic Acid, Prechorismate Pathway, Shikimate Pathway Quinate:oxidoreductase (QORase, EC 1.1.1.24) was isolated and purified from etiolated mung bean (Phaseolus mungo L.) sprouts and a monospecific antiserum was raised in rabbit to the homogeneous protein. Highly intact etioplasts were isolated from the same plant material. The stroma of the purified etioplasts was enzymatically characterized. Contami nation by cytosol, mitochondria and vacuole was estimated from activities of marker en zymes. QORase activity was localized in the stroma (about 91% for both NAD+ and NADP+ as a cofactor). Western blotting and immunoprinting of the stroma proteins revealed a single band that migrated identically with the purified QORase. The results suggest that the QOR ase is localized predominantly, if not exclusively, in the etioplast stroma. The physiological role of the enzyme is discussed. Introduction (Refeno et al., 1982), tobacco callus (Beaudoin Quinic acid is widely distributed among higher and Thorpe, 1983, 1984) and conifer needles (Osi and lower plants (Karrer, 1958; Minamikawa and pov and Shein, 1987). Two of them were reported Yoshida, 1972; Boudet, 1973; Yoshida et al, 1975). to be purified to homogeneity (Refeno et al., 1982; Therefore, its physiological function and metab Kang and Scheibe, 1993). However, the character olism are of interest. At the turn of the 1960’s istics of these enzymes appeared to be very diver Weinstein et al. -
Saccharomyces Cerevisiae—An Interesting Producer of Bioactive Plant Polyphenolic Metabolites
International Journal of Molecular Sciences Review Saccharomyces Cerevisiae—An Interesting Producer of Bioactive Plant Polyphenolic Metabolites Grzegorz Chrzanowski Department of Biotechnology, Institute of Biology and Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland; [email protected]; Tel.: +48-17-851-8753 Received: 26 August 2020; Accepted: 29 September 2020; Published: 5 October 2020 Abstract: Secondary phenolic metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. These compounds play an essential role in plant defense mechanisms and an important role in the pharmaceutical, cosmetics, food, and agricultural industries. Despite the vast chemical diversity of natural compounds, their content in plants is very low, and, as a consequence, this eliminates the possibility of the production of these interesting secondary metabolites from plants. Therefore, microorganisms are widely used as cell factories by industrial biotechnology, in the production of different non-native compounds. Among microorganisms commonly used in biotechnological applications, yeast are a prominent host for the diverse secondary metabolite biosynthetic pathways. Saccharomyces cerevisiae is often regarded as a better host organism for the heterologous production of phenolic compounds, particularly if the expression of different plant genes is necessary. Keywords: heterologous production; shikimic acid pathway; phenolic acids; flavonoids; anthocyanins; stilbenes 1. Introduction Secondary metabolites are defined as valuable natural products synthesized by different organisms that are not essential for growth and development. Plants produce over 200,000 of these compounds, which mostly arise from specialized metabolite pathways. Phenolic compounds play essential roles in interspecific competition and plant defense mechanisms against biotic and abiotic stresses [1] and radiation, and might act as regulatory molecules, pigments, or fragrances [2]. -
Building Microbial Factories for the Production of Aromatic Amino Acid
Chemical and Biological Engineering Publications Chemical and Biological Engineering 8-10-2019 Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products Mingfeng Cao Iowa State University Meirong Gao Iowa State University, [email protected] Miguel Suastegui Iowa State University See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/cbe_pubs Part of the Biochemical and Biomolecular Engineering Commons, and the Biology and Biomimetic Materials Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ cbe_pubs/386. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Chemical and Biological Engineering at Iowa State University Digital Repository. It has been accepted for inclusion in Chemical and Biological Engineering Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Building microbial factories for the production of aromatic amino acid pathway derivatives: From commodity chemicals to plant-sourced natural products Abstract The ra omatic amino acid biosynthesis pathway, together with its downstream branches, represents one of the most commercially valuable biosynthetic pathways, producing a diverse range of complex molecules with many useful bioactive properties. Aromatic compounds are crucial components for major commercial segments, from polymers to foods, nutraceuticals, and pharmaceuticals, and the demand for such products has been projected to continue to increase at national and global levels. -
All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA