DOCSLIB.ORG

An Investigation of Laccase-Like Multicopper

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Investigation of Laccase-Like Multicopper AN INVESTIGATION OF LACCASE-LIKE MULTICOPPER OXIDASES (LMCOs): STRUCTURE AND FUNCTION STUDIES By James Todd Hoopes (under the Direction of Jeffrey F. D. Dean) ABSTRACT This dissertation describes investigations into the structure and function of selected laccase-like multi-copper oxidases (LMCOs). A plant LMCO from Acer pseudoplatanus has been expressed in tobacco BY2 cell ands compared to the native LMCO isolated from Acer pseudoplatanus cell suspension cultures. It was found to be nearly identical to the native enzyme except with respect to the Kms for certain substrates. A LMCO gene cloned from yellow-poplar (Liriodendron tulipifera) and expressed in transgenic tobacco cells showed ferroxidase activity. This marks the first report of ferroxidase activity associated with a plant LMCO, and suggests an alternative physiological function for these enzymes. Molecular modeling of the Fet3 LMCO gave insight into which amino acids could be involved in iron binding in LMCOs. Additionally, a new chromogenic substrate for laccases and peroxidases, 1,8-diaminonapthalene, was found to be more sensitive and less toxic than traditional substrates when used in SDS-PAGE zymograms. INDEX WORDS: Dissertation, Laccase, Multi-Copper Oxidase, MCO, Copper,Iron Metabolism, Ferroxidase, Lignin, Lignification, Liriodendron tulipifera, Acer pseudoplatanus AN INVESTIGATION OF LACCASE-LIKE MULTICOPPER OXIDASES (LMCOs): STRUCTURE AND FUNCTION STUDIES By James Todd Hoopes B.S. University of Georgia 1992 A Dissertation Submitted To The Graduate Faculty of The University of Georgia In Partial Fulfillment of the Requirements for the Degree DOCTOROF PHILOSPHY. ATHENS, GEORGIA 2004 iii © 2004 James Todd Hoopes All Rights Reserved iv AN INVESTIGATION OF LACCASE-LIKE MULTICOPPER OXIDASES (LMCOs): STRUCTURE AND FUNCTION STUDIES by James Todd Hoopes Major Professor: Jeffrey F.D.Dean Committee: Robert A. Scott Ronald C. Orlando Bi-Cheng Wang Zheng-Hua Ye Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia May 2004 iv DEDICATION For my Father who gave me my love of science. For my Mother who fought for my education. v PREFACE Philosophy is nothing more than the persistent desire to think clearly. Would that man applied this practice to all his endeavors. vi TABLE OF CONTENTS page PREFACE......................................................................................................v CHAPTER (1) Introduction...................................................................................1 (2) Staining Electrophoretic Gels for Laccase and Peroxidase Activity Using 1,8-Diaminonaphthalene.........................................29 (3) Altered glycosylation of a LMCO from Acer pseudoplatanus expressed in suspension-cultured tobacco cells.............................49 (4) Ferroxidase Activity in a Laccase-like Multicopper Oxidase from Yellow-poplar (Liriodendron tulipifera L.)...........................................80 (5) Homology Modeling of the Fet3 Multicopper Oxidase Identifies Active Site Residues Likely Involved in Ferroxidase Activity...............104 (6) Conclusion/Discussion................................................................132 REFERENCES...........................................................................................135 1 CHAPTER 1 INTRODUCTION Nomenclature: The enzymatic reaction catalyzed by laccase (EC 1.10.3.2) is amongst the oldest studied biochemical activities and was first mentioned by Yoshida in 1883 (Yoshida, 1883). Around the same time, Bertrand did pioneering research on laccase isolated from Japanese lacquer tree sap (Bertrand, 1894, 1895), and in his descriptions coined the terms “laccase” and “oxidase” (Messerschmidt, 1997). As will be described in more detail below, similar enzymes have been found in a great many organisms and have been the subject of much study. However, for all the study, these enzymes remain quite mysterious with the exact physiological substrates and functions known only for the lacquer tree laccase and a handful of related enzymes (Omura, 1961; Askwith et al., 1994). Part of the problem stems from the broad range of substrates that laccases and related enzymes are capable of utilizing in vitro (Fahraeus and Ljunggren, 1961). This promiscuity created considerable difficulties for the identification and classification of these enzymes. Consequently, on the basis of 2 their oxidative activities, copper content and blue color, laccase, ascorbate oxidase and ceruloplasmin defined the early blue-copper oxidase enzyme family. As the name implies, blue-copper oxidase are characterized by their blue color caused by a strong absorbance band at approximately 600 nm related to the Type-1 copper center (Keilin and Mann, 1939). Traditionally, this group of enzymes was comprised of laccase, ascorbate oxidase, and ceruloplasmin, as well as cytochrome c oxidase and bilirubin oxidase, and more recently the yeast FET3 protein and hephaestin (Askwith et al., 1994; Conrad et al., 1999; Vulpe et al., 1999). Grouping these enzymes together, however, can be somewhat misleading. While ascorbate oxidase and laccase share a tremendous sequence and structural homology with each other, these enzymes share only small regions of similarity with ceruloplasmin and almost none at all with cytochrome c oxidase. As additional enzymatic activities were used to help define enzyme families, laccase, ascorbate oxidase, tyrosinase and catechol oxidase were grouped together as similar enzymes (phenoloxidases) that could be distinguished on the basis of their substrate and inhibitor specificities (Mayer and Harel, 1979). Thus, structurally distinct enzymes – laccases and catechol oxidases – were linked by their ability to remove protons from many of the same phenolic 3 compounds, although laccases were thought to be distinguishable by their ability to oxidize para-substituted substrates. Adding to the confusion, the name catechol oxidase was also used interchangeably with names such as polyphenoloxidase, tyrosinase, catecholase or cresolase, for enzymes derived from a wide variety of plant and microbial sources. For a brief period, even the IUPAC Enzyme Commission grouped these enzymes together under the classification number EC 1.14.18.1 (Mayer and Harel, 1979; Mayer, 1987). However, with increasing availability of phenoloxidases from diverse sources it soon became apparent that substrate and inhibitor studies could not provide clear-cut distinctions between the different classes of enzymes (Kahn and Andrawis, 1986; Walker and Ferrar, 1998). Much of this early ambiguity and imprecision in terminology is being removed by application of recently acquired structural information. Structurally, the enzymes placed in the original EC 1.14.18.1 category obviously comprised two distinct groups. Methane monooxygenase, tyrosinase and catechol oxidase are distinguished by a single binuclear copper center and no blue Type-1 coppers (Mayer et al., 1966; Sanchez-Ferrer et al., 1995). All of the copper ions in these enzymes are in Type-3 centers, which cycle from Cu2+ to Cu1+ and back during oxidation of the electron donor (Sanchez-Ferrer et al., 1995; McGuirl and Dooley, 1999). This is quite distinct from laccase, 4 ascorbate oxidase, and ceruloplasmin, which contain both Type-1 and Type-2 centers in addition to a Type-3 pair. Today, with the increasing availability of genomic sequence information, enzymes are most reliably assigned to families on the basis of their sequence similarity and structural properties, and only secondarily on their specific enzymatic activities. These new methods of classification highlight misleading classifications in the older nomenclature where implied similarities between enzymes based on activity provide no insight into mechanisms of catalysis or physiological function. Consequently, the nomenclature evolved so that group of enzymes originally referred to as the blue copper oxidases, was absorbed into the more general category of multicopper oxidases. Thus, besides classical blue-copper oxidases (laccase, ascorbate oxidase and ceruloplasmin), the multicopper oxidase family contains the yeast FET3 protein, tyrosinase, catechol oxidase, methane monooxygenase, sulochrin oxidase, dihydrogeodin oxidase, phenoxazinone synthase, and bilirubin oxidase (Askwith et al., 1994; Messerschmidt, 1997; McGuirl and Dooley, 1999). The members of this enzyme group are obviously diverse in function and in structure, requiring only two criteria for inclusion -- multiple copper ions in their catalytic centers and the ability to utilize diatomic oxygen as a co-substrate. The evolution of this category of enzymes and the characteristics that distinguish them have been 5 extensively review elsewhere (Mayer and Harel, 1979; Mayer, 1987; Messerschmidt, 1993; Solomon et al., 1996; Messerschmidt, 1997). Recent acquisition of large amounts of genomic sequence data has enabled identification of numerous genes that appear to encode enzymes bearing the structural hallmarks of laccases (Wojtas-Wasilewska and Trojanowski, 1975; Kurtz and Champe, 1981; Banerjee and Vohra, 1991; de Silva et al., 1995; Claus and Filip, 1997; Klomp et al., 1997; Eck et al., 1999; Fernandez et al., 1999; Syed et al., 2002; Wartmann et al., 2002). Sequence comparisons of these putative enzymes show them all to contain the invariant copper-binding domains that were first identified in laccase. Thus, to distinguish this group of structurally related enzymes from unrelated members of the blue-copper and multicopper oxidase
Load more

Recommended publications
  • Bacterial-Type Plant Ferroxidases Tune Local Phosphate Sensing in Root Development
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436157; this version posted March 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Bacterial-type plant ferroxidases tune local phosphate sensing in root development Christin Naumann1, Marcus Heisters1,2, Wolfgang Brandt3, Philipp Janitza4, Carolin Alfs1, Nancy Tang1, Alicia Toto Nienguesso1,5, Joerg Ziegler1, Richard Imre6,7, Karl Mechtler6,7, Yasin Dagdas6, Wolfgang Hoehenwarter8, Gary Sawers9, Marcel Quint4, and Steffen Abel1,10,11 1Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 2VEROVACCiNES GmbH, Halle (Saale), Germany 3Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 4Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle- Wittenberg, Halle (Saale), Germany 5Department of Anatomy and Cell Biology, University Hospital Halle, Halle (Saale), Germany 6Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria 7Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria 9Institute of Biology/Microbiology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany 8Proteome Analytics, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany 10Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany 11Department of Plant Sciences, University of California, Davis, CA, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436157; this version posted March 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Fluctuating bioavailability of inorganic phosphate (Pi), often caused by complex Pi-metal interactions, guide root tip growth and root system architecture for maximizing the foraged soil volume.
    [Show full text]
  • Geometric and Electronic Structure Differences Between the Type 3 Copper Sites of the Multicopper Oxidases and Hemocyanin/Tyrosinase
    Geometric and electronic structure differences between the type 3 copper sites of the multicopper oxidases and hemocyanin/tyrosinase Jungjoo Yoon, Satoshi Fujii1, and Edward I. Solomon2 Department of Chemistry, Stanford University, Stanford, CA 94305-5080 Contributed by Edward I. Solomon, February 25, 2009 (sent for review January 31, 2009) The coupled binuclear ‘‘type 3’’ Cu sites are found in hemocyanin (Hc), tyrosinase (Tyr), and the multicopper oxidases (MCOs), such as laccase (Lc), and play vital roles in O2 respiration. Although all type 3 Cu sites share the same ground state features, those of Hc/Tyr have very different ligand-binding properties relative to those of the MCOs. In particular, the type 3 Cu site in the MCOs (LcT3)isa part of the trinuclear Cu cluster, and if the third (i.e., type 2) Cu is T3 removed, the Lc site does not react with O2. Density functional ؊1 theory calculations indicate that O2 binding in Hc is Ϸ9 kcal mol more favorable than for LcT3. The difference is mostly found in the Ϸ ؊1 total energy difference of the deoxy states ( 7 kcal mol ), where Fig. 1. O2 binding in the type 3 Cu sites of Hc/Tyr and MCOs. the stabilization of deoxy LcT3 derives from its long equilibrium Cu–Cu distance of Ϸ5.5–6.5 Å, relative to Ϸ4.2 Å in deoxy Hc/Tyr. The O2 binding in Hc is driven by the electrostatic destabilization Cu–Cu distance of Ϸ3.6 Å (Fig. 1A) (7, 8, 10). The side-on 2Ϫ ␲ of the deoxy Hc site, in which the two Cu(I) centers are kept close geometry promotes a large overlap between the O2 * and the together by the protein for facile 2-electron reduction of O2.
    [Show full text]
  • Yeast Genome Gazetteer P35-65
    gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal
    [Show full text]
  • Downloaded Using the Database on Presence of This Metal for 24 H
    fmicb-11-01834 August 10, 2020 Time: 12:25 # 1 ORIGINAL RESEARCH published: 10 August 2020 doi: 10.3389/fmicb.2020.01834 Metabolic Adaptation of Paracoccidioides brasiliensis in Response to in vitro Copper Deprivation Guilherme Petito1,2†, Juliana Santana de Curcio1†, Maristela Pereira1, Alexandre Melo Bailão1, Juliano Domiraci Paccez1, Gabriel Brum Tristão1, Camila Oliveira Barbosa de Morais1, Marcelo Valle de Souza3, Agenor de Castro Moreira Santos Junior3, Wagner Fontes3, Carlos André Ornelas Ricart3 and Célia Maria de Almeida Soares1* Edited by: 1 Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil, Carlos Pelleschi Taborda, 2 Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal de Goiás, Goiânia, Brazil, University of São Paulo, Brazil 3 Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, Brazil Reviewed by: Rosana Puccia, Federal University of São Paulo, Brazil Copper is an essential micronutrient for the performance of important biochemical Sandro Rogerio Almeida, processes such as respiration detoxification, and uptake of metals like iron. Studies University of São Paulo, Brazil Elizabeth R. Ballou, have shown that copper deprivation is a strategy used by the host against pathogenic University of Birmingham, fungi such as Cryptoccocus neoformans and Candida albicans during growth and United Kingdom development of infections in the lungs and kidneys. Although there are some *Correspondence: studies, little is known about the impact of copper deprivation in members of the Célia Maria de Almeida Soares [email protected] Paracoccidioides genus. Therefore, using isobaric tag labeling (iTRAQ)-Based proteomic †These authors have contributed approach and LC-MS/MS, we analyzed the impact of in vitro copper deprivation in equally to this work the metabolism of Paracoccidioides brasiliensis.
    [Show full text]
  • Rotating Magnetic Field As Tool for Enhancing Enzymes Properties
    www.nature.com/scientificreports OPEN Rotating magnetic feld as tool for enhancing enzymes properties - laccase case study Received: 23 July 2018 Agata Wasak 1, Radosław Drozd 1, Dorota Jankowiak1 & Rafa Rakoczy2 Accepted: 21 January 2019 The aim of this study was to analyse the efect of rotating magnetic feld (RMF) exposition on the fungal Published: xx xx xxxx laccase catalytic properties. The results obtained in the study revealed that RMF may positively alter the laccase activity. A signifcant increase in activities of 11%, 11%, and 9% were observed at 10 Hz, 40 Hz and 50 Hz, respectively. Exposure of laccase to the rotating magnetic feld resulted in its increased activity at broader pH range and a slight shift in optimum pH from 4.0 to 4.5 at RMF with frequency 20 Hz. The results show that the enzyme activity, stability, and optimum pH can be signifcantly altered depending on the characteristic of the applied RMF. Application of rotating magnetic feld opens a new way for controlling and directions of enzyme-based bioprocessing. Numerous industry branches use enzymatic processes because, compared to chemical catalysts, they are rapid, carry out specifc chemical transformations, save reagents as well as energy1,2. Te nature of designed enzymes to catalyse chemical reactions to be highly selective and efcient in terms of energy saving3. Despite the fact that enzymes are enormously applicable, their use in industrial processes on a large scale is hampered in many cases by their poor operational stability and low resistance to the process conditions. At present, the main research is focused on protein engineering solutions; unfortunately their use is limited due to insufcient knowledge about the enzyme structure and its mechanism of action4,5.
    [Show full text]
  • Fe-S Protein Synthesis in Green Algae Mitochondria
    plants Review Fe-S Protein Synthesis in Green Algae Mitochondria Diego F. Gomez-Casati * , Maria V. Busi *, Julieta Barchiesi, Maria A. Pagani , Noelia S. Marchetti-Acosta and Agustina Terenzi Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Universidad Nacional de Rosario, 2000 Rosario, Argentina; [email protected] (J.B.); [email protected] (M.A.P.); [email protected] (N.S.M.-A.); [email protected] (A.T.) * Correspondence: [email protected] (D.F.G.-C.); [email protected] (M.V.B.); Tel.: +54-341-4391955 (ext. 113) (D.F.G.-C. & M.V.B.) Abstract: Iron and sulfur are two essential elements for all organisms. These elements form the Fe-S clusters that are present as cofactors in numerous proteins and protein complexes related to key processes in cells, such as respiration and photosynthesis, and participate in numerous enzymatic reactions. In photosynthetic organisms, the ISC and SUF Fe-S cluster synthesis pathways are located in organelles, mitochondria, and chloroplasts, respectively. There is also a third biosynthetic machinery in the cytosol (CIA) that is dependent on the mitochondria for its function. The genes and proteins that participate in these assembly pathways have been described mainly in bacteria, yeasts, humans, and recently in higher plants. However, little is known about the proteins that participate in these processes in algae. This review work is mainly focused on releasing the information on the existence of genes and proteins of green algae (chlorophytes) that could participate in the assembly process of Fe-S groups, especially in the mitochondrial ISC and CIA pathways.
    [Show full text]
  • Crystal Structures of Multicopper Oxidase Cueo G304K Mutant
    www.nature.com/scientificreports OPEN Crystal structures of multicopper oxidase CueO G304K mutant: structural basis of the increased Received: 17 November 2017 Accepted: 5 September 2018 laccase activity Published: xx xx xxxx Hanqian Wang1, Xiaoqing Liu2, Jintong Zhao2, Qingxia Yue2, Yuhua Yan1,3, Zengqiang Gao4, Yuhui Dong1,4, Zhiyong Zhang5, Yunliu Fan2, Jian Tian2, Ningfeng Wu2 & Yong Gong1 The multicopper oxidase CueO is involved in copper homeostasis and copper (Cu) tolerance in Escherichia coli. The laccase activity of CueO G304K mutant is higher than wild-type CueO. To explain this increase in activity, we solved the crystal structure of G304K mutant at 1.49 Å. Compared with wild- type CueO, the G304K mutant showed dramatic conformational changes in methionine-rich helix and the relative regulatory loop (R-loop). We further solved the structure of Cu-soaked enzyme, and found that the addition of Cu ions induced further conformational changes in the R-loop and methionine-rich helix as a result of the new Cu-binding sites on the enzyme’s surface. We propose a mechanism for the enhanced laccase activity of the G304K mutant, where movements of the R-loop combined with the changes of the methionine-rich region uncover the T1 Cu site allowing greater access of the substrate. Two of the G304K double mutants showed the enhanced or decreased laccase activity, providing further evidence for the interaction between the R-loop and the methionine-rich region. The cuprous oxidase activity of these mutants was about 20% that of wild-type CueO. These structural features of the G304K mutant provide clues for designing specifc substrate-binding mutants in the biotechnological applications.
    [Show full text]
  • Finding New Enzymes from Bacterial Physiology: a Successful Approach Illustrated by the Detection of Novel Oxidases in Marinomonas Mediterranea
    Mar. Drugs 2010, 8, 519-541; doi:10.3390/md8030519 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Review Finding New Enzymes from Bacterial Physiology: A Successful Approach Illustrated by the Detection of Novel Oxidases in Marinomonas mediterranea Antonio Sanchez-Amat 1,*, Francisco Solano 2 and Patricia Lucas-Elío 1 1 Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Campus de Espinardo, Murcia 30100, Spain; E-Mail: [email protected] 2 Department of Biochemistry and Molecular Biology B and Immunology, School of Medicine, University of Murcia, Murcia 30100, Spain; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +34-868884955; Fax: +34-868883963. Received: 10 February 2010; in revised form: 21 February 2010 / Accepted: 22 February 2010 / Published: 5 March 2010 Abstract: The identification and study of marine microorganisms with unique physiological traits can be a very powerful tool discovering novel enzymes of possible biotechnological interest. This approach can complement the enormous amount of data concerning gene diversity in marine environments offered by metagenomic analysis, and can help to place the activities associated with those sequences in the context of microbial cellular metabolism and physiology. Accordingly, the detection and isolation of microorganisms that may be a good source of enzymes is of great importance. Marinomonas mediterranea, for example, has proven to be one such useful microorganism. This Gram-negative marine bacterium was first selected because of the unusually high amounts of melanins synthesized in media containing the amino acid L-tyrosine. The study of its molecular biology has allowed the cloning of several genes encoding oxidases of biotechnological interest, particularly in white and red biotechnology.
    [Show full text]
  • BMC Structural Biology Biomed Central
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central BMC Structural Biology BioMed Central Research article Open Access Crystal structure of a blue laccase from Lentinus tigrinus: evidences for intermediates in the molecular oxygen reductive splitting by multicopper oxidases Marta Ferraroni1, Nina M Myasoedova2, Vadim Schmatchenko2, Alexey A Leontievsky2, Ludmila A Golovleva2, Andrea Scozzafava1 and Fabrizio Briganti*1 Address: 1Department of Chemistry University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy and 2G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms Russian Accademy of Science, Pushchino, Moscow Region, 1422920, Russia Email: Marta Ferraroni - [email protected]; Nina M Myasoedova - [email protected]; Vadim Schmatchenko - [email protected]; Alexey A Leontievsky - [email protected]; Ludmila A Golovleva - [email protected]; Andrea Scozzafava - [email protected]; Fabrizio Briganti* - [email protected] * Corresponding author Published: 26 September 2007 Received: 28 March 2007 Accepted: 26 September 2007 BMC Structural Biology 2007, 7:60 doi:10.1186/1472-6807-7-60 This article is available from: http://www.biomedcentral.com/1472-6807/7/60 © 2007 Ferraroni et al; 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: Laccases belong to multicopper oxidases, a widespread class of enzymes implicated in many oxidative functions in pathogenesis, immunogenesis and morphogenesis of organisms and in the metabolic turnover of complex organic substances.
    [Show full text]
  • Growth Control of the Eukaryote Cell: a Systems Biology
    BioMed Central Open Access Research article Growth control of the eukaryote cell: a systems biology study in yeast Juan I Castrillo1¤, Leo A Zeef1¤, David C Hoyle2¤, Nianshu Zhang1, Andrew Hayes1, David CJ Gardner1, Michael J Cornell1,3, June Petty1, Luke Hakes1, Leanne Wardleworth1, Bharat Rash1, Marie Brown4, Warwick B Dunn6, David Broadhurst4,6, Kerry O’Donoghue5, Svenja S Hester5, Tom PJ Dunkley5, Sarah R Hart4, Neil Swainston6, Peter Li6, Simon J Gaskell4,6, Norman W Paton3,6, Kathryn S Lilley5, Douglas B Kell4,6 and Stephen G Oliver1,6 Addresses: 1Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK. 2Northwest Institute for Bio-Health Informatics (NIBHI), School of Medicine, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK. 3School of Computer Science, Kilburn Building, University of Manchester, Oxford Road, Manchester M13 9PL, UK. 4School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK. 5Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, UK. 6Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester M1 7DN, UK. ¤These authors contributed equally to this work. Correspondence: Stephen G Oliver. E-mail: [email protected] Published: 30 April 2007 Received: 21 July 2006 Revised: 20 November 2006 Journal of Biology 2007, 6:4 Accepted: 7 February 2007 The electronic version of this article is the complete one and can be found online at http://jbiol.com/content/6/2/4 © 2007 Castrillo et al.; licensee BioMed Central Ltd.
    [Show full text]
  • The Copper-Iron Connection in Biology: Structure of the Metallo-Oxidase Fet3p
    The copper-iron connection in biology: Structure of the metallo-oxidase Fet3p Alexander B. Taylor*, Christopher S. Stoj†, Lynn Ziegler†, Daniel J. Kosman†, and P. John Hart*‡ *Department of Biochemistry and the X-Ray Crystallography Core Laboratory, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900; and †Department of Biochemistry, School of Medicine and Biological Sciences, State University of New York, 140 Farber Hall, 3435 Main Street, Buffalo, NY 14214 Edited by Douglas C. Rees, California Institute of Technology, Pasadena, CA, and approved September 8, 2005 (received for review July 21, 2005) Fet3p is a multicopper-containing glycoprotein localized to the the liver and extrahepatic tissues. A role for Cp (and its paralog, yeast plasma membrane that catalyzes the oxidation of Fe(II) to hephaestin) in iron metabolism is now generally accepted (11), Fe(III). This ferrous iron oxidation is coupled to the reduction of O2 and the pathology observed in aceruloplasminemic patients is to H2O and is termed the ferroxidase reaction. Fet3p-produced stark evidence for this role (12). Fe(III) is transferred to the permease Ftr1p for import into the The molecular basis of the Fe(II) specificity exhibited by Cp cytosol. The posttranslational insertion of four copper ions into but not by the other MCO proteins (e.g., several laccases and Fet3p is essential for its activity, thus linking copper and iron ascorbate oxidase) has not been fully elucidated, and how this homeostasis. The mammalian ferroxidases ceruloplasmin and hep- ferroxidase activity is linked to iron homeostasis in mammals haestin are homologs of Fet3p.
    [Show full text]
  • Genome-Wide Investigation of Cellular Functions for Trna Nucleus
    Genome-wide Investigation of Cellular Functions for tRNA Nucleus- Cytoplasm Trafficking in the Yeast Saccharomyces cerevisiae DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-Yi Chu Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2012 Dissertation Committee: Anita K. Hopper, Advisor Stephen Osmani Kurt Fredrick Jane Jackman Copyright by Hui-Yi Chu 2012 Abstract In eukaryotic cells tRNAs are transcribed in the nucleus and exported to the cytoplasm for their essential role in protein synthesis. This export event was thought to be unidirectional. Surprisingly, several lines of evidence showed that mature cytoplasmic tRNAs shuttle between nucleus and cytoplasm and their distribution is nutrient-dependent. This newly discovered tRNA retrograde process is conserved from yeast to vertebrates. Although how exactly the tRNA nuclear-cytoplasmic trafficking is regulated is still under investigation, previous studies identified several transporters involved in tRNA subcellular dynamics. At least three members of the β-importin family function in tRNA nuclear-cytoplasmic intracellular movement: (1) Los1 functions in both the tRNA primary export and re-export processes; (2) Mtr10, directly or indirectly, is responsible for the constitutive retrograde import of cytoplasmic tRNA to the nucleus; (3) Msn5 functions solely in the re-export process. In this thesis I focus on the physiological role(s) of the tRNA nuclear retrograde pathway. One possibility is that nuclear accumulation of cytoplasmic tRNA serves to modulate translation of particular transcripts. To test this hypothesis, I compared expression profiles from non-translating mRNAs and polyribosome-bound translating mRNAs collected from msn5Δ and mtr10Δ mutants and wild-type cells, in fed or acute amino acid starvation conditions.
    [Show full text]