DOCSLIB.ORG

Stress and Signalling in Arabidopsis in Response to the Pollutant 2,4,6-Trinitrotoluene (TNT)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Stress and Signalling in Arabidopsis in Response to the Pollutant 2,4,6-Trinitrotoluene (TNT) Stress and signalling in Arabidopsis in response to the pollutant 2,4,6-trinitrotoluene (TNT) Emily Jane Johnston Doctor of Philosophy University of York Biology September 2015 Abstract The explosive 2,4,6-trinitrotoluene (TNT) is a persistent and toxic pollutant. High levels of TNT and the water-mobile co-pollutant Royal Demolition Explosive (RDX) have accumulated at manufacturing waste sites and military training ranges. Due to the scale of these sites, phytoremediation could be the most cost-effective and environmentally-friendly means of cleaning up the pollution. Plant lines which are both tolerant to, and able to degrade explosives pollution, are therefore being developed. Prior to this PhD research, it was identified that Arabidopsis thaliana L. (Arabidopsis) plants deficient in MONODEHYDROASCORBATE REDUCTASE 6 (MDHAR6; At1g63940) have hugely enhanced TNT tolerance. In Chapter 3, the means behind this enhanced TNT tolerance is investigated. Enzymatic analysis identified that purified MDHAR6 reduces TNT by one electron, to a TNT nitro radical which autoxidises, generating superoxide. Reactive superoxide can oxidise and damage protein, DNA and lipids. This reaction could also be inhibitory to plant development, due to the futile use of NADH. In Chapter 4, the organelle-targeting of MDHAR6 is investigated; MDHAR6 is unusual in that dual targeting to mitochondria or plastids appears to be dependent on the transcription start site used. A further understanding of MDHAR6 location would provide useful insight as to the endogenous role of this enzyme. Preliminary experiments indicate that MDHAR6 is more highly expressed in roots than leaves, and that a previously undescribed third transcription start site is dominant, encoding plastid-targeted MDHAR6. The induction of detoxification genes following TNT treatment is explored in Chapter 5; the profile of detoxification genes induced following TNT treatment is similar to that following phytoprostane treatment, which requires class II TGACG-binding (TGA) factors. It is identified that induction of detoxification genes following TNT treatment also requires class II TGA factors, but the induction is not mediated by phytoprostanes. i Table of contents Abstract ........................................................................................................................................... i Table of contents ........................................................................................................................... ii List of figures ............................................................................................................................... viii List of tables .................................................................................................................................. xi Acknowledgements ...................................................................................................................... xii Author’s declaration ................................................................................................................... xiii 1 Introduction .......................................................................................................................... 1 1.1 The explosive 2,4,6-trinitrotoluene (TNT) ..................................................................... 1 1.1.1 Chemical properties .............................................................................................. 1 1.1.2 History ................................................................................................................... 2 1.1.3 Detrimental effects ............................................................................................... 3 1.2 Explosives pollution ...................................................................................................... 4 1.2.1 Co-pollutants with TNT ......................................................................................... 4 1.2.2 Lifetime health advisory limits .............................................................................. 6 1.2.3 Sites of contamination .......................................................................................... 7 1.3 Remediation of TNT from polluted sites ..................................................................... 10 1.3.1 Ex situ granular activated carbon treatment of groundwater and wastewater . 10 1.3.2 In situ bioremediation in groundwater ............................................................... 10 1.3.3 Ex situ incineration of soil ................................................................................... 11 1.3.4 Ex situ composting of soil .................................................................................... 11 1.3.5 In situ landfarming of soil .................................................................................... 11 1.3.6 In situ phytoremediation from soil and groundwater ........................................ 11 1.4 Detoxification in plants ............................................................................................... 13 1.4.1 The process of detoxification in plants ............................................................... 13 1.4.2 Arabidopsis detoxification genes induced by TNT treatment ............................ 14 1.4.3 Detoxification of TNT in Arabidopsis .................................................................. 16 1.5 Regulation of detoxification genes in plants............................................................... 20 ii 1.5.1 Xenobiotic-response signalling in animal biology ............................................... 20 1.5.2 Defence signalling in plants ................................................................................ 21 1.5.3 Focus on TGA factors .......................................................................................... 31 1.5.4 Studies specifically on plant detoxification gene regulation .............................. 37 1.6 Thesis objectives ......................................................................................................... 40 2 Materials and methods ....................................................................................................... 41 2.1 Materials and Methods ............................................................................................... 41 2.1.1 Plant material ...................................................................................................... 41 2.1.2 Plant growth conditions ...................................................................................... 41 2.1.3 Source of TNT ...................................................................................................... 43 2.1.4 Growth of plants on TNT-treated soil ................................................................. 43 2.1.5 Recovery of TNT from soil ................................................................................... 43 2.1.6 High Performance Liquid Chromatography (HPLC) ............................................. 44 2.1.7 Root length analysis ............................................................................................ 44 2.1.8 Ascorbate measurement ..................................................................................... 44 2.1.9 Glutathione measurement .................................................................................. 45 2.1.10 Plant protein extraction and analysis of extract activity .................................... 45 2.1.11 Production of MDHAR6 in Escherichia coli ......................................................... 46 2.1.12 Purification of Strep-tagged MDHAR6 ................................................................ 47 2.1.13 SDS-PAGE electrophoresis .................................................................................. 47 2.1.14 Western blot against HIS-tag .............................................................................. 47 2.1.15 Protein identification following Strep-MDHAR6 purification ............................. 48 2.1.16 Michaelis-Menten plots for MDHAR6 activity towards MDA, TNT and CDNB ... 48 2.1.17 Electron Paramagnetic Resonance spectrometry ............................................... 48 2.1.18 Staining with 3,3’diaminobenzene...................................................................... 49 2.1.19 Genomic DNA (gDNA) extraction ........................................................................ 49 2.1.20 Polymerase chain reaction (PCR) ........................................................................ 49 2.1.21 DNA sequencing .................................................................................................. 49 2.1.22 RNA extraction and cDNA preparation ............................................................... 49 iii 2.1.23 Quantitative PCR ................................................................................................. 49 2.1.24 Treatment of root and leaf tissue with antimycin A, TNT or methyl viologen for MDHAR6 transcription start site study ............................................................................... 50 2.1.25 Antibody raised against MDHAR6 ....................................................................... 50 2.1.26 Western blot using antibody raised against MDHAR6 ........................................ 50 2.1.27 Cloning of promoter:GUS contructs .................................................................... 51 2.1.28 Stable transformation of Arabidopsis
Load more

Recommended publications
  • Comparing the Reaction Mechanism of Dark-Operative Protochlorophyllide
    With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase Pedro J. Silva REQUIMTE, Faculdade de Cienciasˆ da Saude,´ Universidade Fernando Pessoa, Rua Carlos da Maia, Porto, Portugal ABSTRACT The addition of two electrons and two protons to the C17DC18 bond in protochloro- phyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a .Cys/3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17DC18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311CG(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the .Cys/3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be Submitted 24 March 2014 the rate-limiting stage of the process. Poisson–Boltzmann computations on the Accepted 9 August 2014 full enzyme–substrate complex, followed by Monte Carlo simulations of redox Published 2 September 2014 and protonation titrations revealed a hitherto unsuspected pH-dependence of the Corresponding author reaction potential of the Fe–S cluster.
    [Show full text]
  • Surprising Roles for Bilins in a Green Alga Jean-David Rochaix1 Departments of Molecular Biology and Plant Biology, University of Geneva,1211 Geneva, Switzerland
    COMMENTARY COMMENTARY Surprising roles for bilins in a green alga Jean-David Rochaix1 Departments of Molecular Biology and Plant Biology, University of Geneva,1211 Geneva, Switzerland It is well established that the origin of plastids which serves as chromophore of phyto- can be traced to an endosymbiotic event in chromes (Fig. 1). An intriguing feature of which a free-living photosynthetic prokaryote all sequenced chlorophyte genomes is that, invaded a eukaryotic cell more than 1 billion although they lack phytochromes, their years ago. Most genes from the intruder genomes encode two HMOXs, HMOX1 were gradually transferred to the host nu- andHMOX2,andPCYA.InPNAS,Duanmu cleus whereas a small number of these genes et al. (6) investigate the role of these genes in were maintained in the plastid and gave the green alga Chlamydomonas reinhardtii rise to the plastid genome with its associated and made unexpected findings. protein synthesizing system. The products of Duanmu et al. first show that HMOX1, many of the genes transferred to the nucleus HMOX2, and PCYA are catalytically active were then retargeted to the plastid to keep it and produce bilins in vitro (6). They also functional. Altogether, approximately 3,000 demonstrate in a very elegant way that these nuclear genes in plants and algae encode proteins are functional in vivo by expressing plastid proteins, whereas chloroplast ge- a cyanobacteriochrome in the chloroplast Fig. 1. Tetrapyrrole biosynthetic pathways. The heme nomes contain between 100 and 120 genes of C. reinhardtii, where, remarkably, the and chlorophyll biosynthetic pathways diverge at pro- (1). A major challenge for eukaryotic pho- photoreceptor is assembled with bound toporphyrin IX (ProtoIX).
    [Show full text]
  • Chromophores in Photomorphogenesis W
    Encyclopedia of Plant Physiolo New Series Volume 16 A Editors A.Pirson, Göttingen M.H.Zimmermann, Harvard Photo- morphogenesis Edited by W. Shropshire, Jr. and H. Möhr Contributors K. Apel M. Black A.E. Canham J.A. De Greef M.J. Dring H. Egnéus B. Frankland H. Frédéricq L. Fukshansky M. Furuya V. Gaba A.W. Galston J. Gressel W. Haupt S.B. Hendricks M.G. Holmes M. Jabben H. Kasemir C. J.Lamb M.A. Lawton K. Lüning A.L. Mancinelli H. Möhr D.C.Morgan L.H.Pratt P.H.Quail R.H.Racusen W. Rau W. Rüdiger E. Schäfer H. Scheer J.A. Schiff P. Schopfer S. D. Schwartzbach W. Shropshire, Jr. H. Smith W.O. Smith R. Taylorson W.J. VanDerWoude D. Vince-Prue H.I. Virgin E. Wellmann With 173 Figures Springer-Verlag Berlin Heidelberg New York Tokyo 1983 Univers;:^.'::- Bibüw i-,L* München W. SHROPSHIRE, JR. Smithsonian Institution Radiation Biology Laboratory 12441 Parklawn Drive Rockville, MD 20852/USA H. MOHR Biologisches Institut II der Universität Lehrstuhl für Botanik Schänzlestr. 1 D-7800 Freiburg/FRG ISBN 3-540-12143-9 (in 2 Bänden) Springer-Verlag Berlin Heidelberg New York Tokyo ISBN 0-387-12143-9 (in 2 Volumes) Springer-Verlag New York Heidelberg Berlin Tokyo Library of Congress Cataloging in Publication Data. Main entry under title: Pholomorphogcncsis. (Encyclo• pedia of plant physiology; new ser., v. 16) Includes indexes. 1. Plants Photomorphogenesis Addresses, essays, lectures. I. Shropshire, Walter. II. Mohr, Hans, 1930. III. Apel, K. IV. Scries. QK711.2.E5 vol. 16 581.1s [581.L9153] 83-10615 [QK757] ISBN 0-387-12143-9 (U.S.).
    [Show full text]
  • Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme
    Structural and Functional Studies of the Light-Dependent Protochlorophyllide Oxidoreductase Enzyme David Robert Armstrong Department of Molecular Biology and Biotechnology A thesis submitted for the degree of Doctor of Philosophy September 2014 Abstract The light-dependent enzyme protochlorophyllide oxidoreductase (POR) is a key enzyme in the chlorophyll biosynthesis pathway, catalysing the reduction of the C17 - C18 bond in protochlorophyllide (Pchlide) to form chlorophyllide (Chlide). This reaction involves the light- induced transfer of a hydride from the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor, followed by proton transfer from a catalytic tyrosine residue. Much work has been done to elucidate the catalytic mechanism of POR, however little is known about the protein structure. POR isoforms in plants are also notable as components of the prolamellar bodies (PLBs), large paracrystalline structures that are precursors to the thylakoid membranes in mature chloroplasts. Bioinformatics studies have identified a number of proteins, related to POR, which contain similar structural features, leading to the production of a structural model for POR. A unique loop region of POR was shown by EPR to be mobile, with point mutations within this region causing a reduction in enzymatic activity. Production of a 2H, 13C, 15N-labelled sample of POR for NMR studies has enabled significant advancement in the understanding of the protein structure. This includes the calculation of backbone torsion angles for the majority of the protein, in addition to the identification of multiple dynamic regions of the protein. The protocol for purification of Pchlide, the substrate for POR, has been significantly improved, providing high quality pigment for study of the POR ternary complex.
    [Show full text]
  • A Multifaceted Analysis Reveals Two Distinct Phases of Chloroplast
    RESEARCH ARTICLE A multifaceted analysis reveals two distinct phases of chloroplast biogenesis during de-etiolation in Arabidopsis Rosa Pipitone1, Simona Eicke2, Barbara Pfister2, Gaetan Glauser3, Denis Falconet4, Clarisse Uwizeye4, Thibaut Pralon1, Samuel C Zeeman2, Felix Kessler1*, Emilie Demarsy1,5* 1Plant Physiology Laboratory, University of Neuchaˆtel, Neuchaˆtel, Switzerland; 2Institute of Molecular Plant Biology, Department of Biology, ETH Zurich, Zurich, Switzerland; 3Neuchaˆtel Platform of Analytical Chemistry, University of Neuchaˆtel, Neuchaˆtel, Switzerland; 4Universite´ Grenoble Alpes, CNRS, CEA, INRAE, IRIG- DBSCI-LPCV, Grenoble, France; 5Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland Abstract Light triggers chloroplast differentiation whereby the etioplast transforms into a photosynthesizing chloroplast and the thylakoid rapidly emerges. However, the sequence of events during chloroplast differentiation remains poorly understood. Using Serial Block Face Scanning Electron Microscopy (SBF-SEM), we generated a series of chloroplast 3D reconstructions during differentiation, revealing chloroplast number and volume and the extent of envelope and thylakoid membrane surfaces. Furthermore, we used quantitative lipid and whole proteome data to complement the (ultra)structural data, providing a time-resolved, multi-dimensional description of chloroplast differentiation. This showed two distinct phases of chloroplast biogenesis: an initial photosynthesis-enabling ‘Structure Establishment Phase’ followed by a ‘Chloroplast Proliferation Phase’ during cell expansion. Moreover, these data detail thylakoid membrane expansion during *For correspondence: de-etiolation at the seedling level and the relative contribution and differential regulation of [email protected] (FK); proteins and lipids at each developmental stage. Altogether, we establish a roadmap for [email protected] (ED) chloroplast differentiation, a critical process for plant photoautotrophic growth and survival.
    [Show full text]
  • Biosynthesis of Cobalamin (Vitamin B12) in Salmonella Typhimurium
    Biosynthesis of cobalamin (vitamin B^^) in Salmonella typhimurium and Bacillus megaterium de Bary; Characterisation of the anaerobic pathway. By Evelyne Christine Raux A thesis submitted to the University of London for the degree of doctorate (PhD.) in Biochemistry. -k H « i d University College London Department of Molecular Genetics, Institute of Ophthalmology, London. Jan 1999 ProQuest Number: U121800 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U121800 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Abstract The transformation of uroporphyrinogen HI into cobalamin (vitamin B 1 2 ) requires about 25 enzymes and can be performed by either aerobic or anaerobic pathways. The aerobic route is dependent upon molecular oxygen, and cobalt is inserted after the ring contraction process. The anaerobic route occurs in the absence of oxygen and cobalt is inserted into precorrin- 2 , several steps prior to the ring contraction. A study of the biosynthesis in both S. typhimurium and B. megaterium reveals that two genes, cbiD and cbiG, are essential components of the pathway and constitute genetic hallmarks of the anaerobic pathway.
    [Show full text]
  • And Formation
    J Med Genet: first published as 10.1136/jmg.17.1.1 on 1 February 1980. Downloaded from Review article Journal of Medical Genetics, 1980, 17, 1-14 Haems and chlorophylls: comparison of function and formation G A F HENDRY AND 0 T G JONES From the Department ofBiochemistry, The Medical School, University ofBristol, Bristol BS8 ITD In 1844 Verdeill reported that acid treatment of at the same time by McMunn3 of cytochromes, chlorophyll or haem yielded apparently similar red another group of haem proteins. compounds; he even postulated that chlorophylls It was the demonstration by Nencki and co- would contain iron. Hoppe-Seyler2 confirmed the workers 45 that the degradation of both chlorophylls apparent similarity of acid derivatives of haems and and haems yielded monopyrroles that led them, in chlorophylls from their light absorption charac- true neo-Darwinian fashion, to postulate a common teristics, a point rather overshadowing the discovery origin for animals and plants. 0 0-'I CH2 II copyright. CH CH3 COOH CIH2 CH2 C-O CH2 http://jmg.bmj.com/ NH2 ( CH3' 'CH3 ® 5- Aminolaevulinic acid a CH2 2 1 12 2 CH2 )H COOH CD FIG 1 Structures ofprotohaem and Protoporphyrin IX chlorophyll a and two of their precursors, acid and 5-aminolaevulinic on September 30, 2021 by guest. Protected protoporphyrin IX (with substituent numbering positions). CH2 CH CH.--,j CH2 CH2 COOCH3 Protohoem (haem- b) CooC20H39 Chlorophyll a 1 J Med Genet: first published as 10.1136/jmg.17.1.1 on 1 February 1980. Downloaded from 2 G A F Hendry and 0 T G Jones Following the work ofWillstatter6 and Fischer and particularly those of avian egg shells, have no Stern,7 the structure of most natural and many central complexed metal.
    [Show full text]
  • Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria Under Aerobic and Anaerobic Environments
    Life 2015, 5, 1172-1203; doi:10.3390/life5021172 OPEN ACCESS life ISSN 2075-1729 www.mdpi.com/journal/life Review Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments Yuichi Fujita *, Ryoma Tsujimoto and Rina Aoki Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan; E-Mails: [email protected] (R.T.); [email protected] (R.A.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +81-52-789-4105; Fax: +81-52-789-4107. Academic Editors: Robert Haselkorn and John C. Meeks Received: 10 November 2014 / Accepted: 24 March 2015 / Published: 30 March 2015 Abstract: Chlorophyll a (Chl) is a light-absorbing tetrapyrrole pigment that is essential for photosynthesis. The molecule is produced from glutamate via a complex biosynthetic pathway comprised of at least 15 enzymatic steps. The first half of the Chl pathway is shared with heme biosynthesis, and the latter half, called the Mg-branch, is specific to Mg-containing Chl a. Bilin pigments, such as phycocyanobilin, are additionally produced from heme, so these light-harvesting pigments also share many common biosynthetic steps with Chl biosynthesis. Some of these common steps in the biosynthetic pathways of heme, Chl and bilins require molecular oxygen for catalysis, such as oxygen-dependent coproporphyrinogen III oxidase. Cyanobacteria thrive in diverse environments in terms of oxygen levels. To cope with Chl deficiency caused by low-oxygen conditions, cyanobacteria have developed elaborate mechanisms to maintain Chl production, even under microoxic environments. The use of enzymes specialized for low-oxygen conditions, such as oxygen-independent coproporphyrinogen III oxidase, constitutes part of a mechanism adapted to low-oxygen conditions.
    [Show full text]
  • Introduction (Pdf)
    Dictionary of Natural Products on CD-ROM This introduction screen gives access to (a) a general introduction to the scope and content of DNP on CD-ROM, followed by (b) an extensive review of the different types of natural product and the way in which they are organised and categorised in DNP. You may access the section of your choice by clicking on the appropriate line below, or you may scroll through the text forwards or backwards from any point. Introduction to the DNP database page 3 Data presentation and organisation 3 Derivatives and variants 3 Chemical names and synonyms 4 CAS Registry Numbers 6 Diagrams 7 Stereochemical conventions 7 Molecular formula and molecular weight 8 Source 9 Importance/use 9 Type of Compound 9 Physical Data 9 Hazard and toxicity information 10 Bibliographic References 11 Journal abbreviations 12 Entry under review 12 Description of Natural Product Structures 13 Aliphatic natural products 15 Semiochemicals 15 Lipids 22 Polyketides 29 Carbohydrates 35 Oxygen heterocycles 44 Simple aromatic natural products 45 Benzofuranoids 48 Benzopyranoids 49 1 Flavonoids page 51 Tannins 60 Lignans 64 Polycyclic aromatic natural products 68 Terpenoids 72 Monoterpenoids 73 Sesquiterpenoids 77 Diterpenoids 101 Sesterterpenoids 118 Triterpenoids 121 Tetraterpenoids 131 Miscellaneous terpenoids 133 Meroterpenoids 133 Steroids 135 The sterols 140 Aminoacids and peptides 148 Aminoacids 148 Peptides 150 β-Lactams 151 Glycopeptides 153 Alkaloids 154 Alkaloids derived from ornithine 154 Alkaloids derived from lysine 156 Alkaloids
    [Show full text]
  • The Enzyme Database: New Enzymes 06/27/2006 05:11 PM
    The Enzyme Database: New Enzymes 06/27/2006 05:11 PM Home Search Enzymes by Class New/Amended Enzymes Statistics Forms Advanced Search Information Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) Proposed Changes to the Enzyme List The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC- IUBMB by Keith Tipton, Sinéad Boyce, Gerry Moss and Hal Dixon, with occasional help from other Committee members, and were put on the web by Gerry Moss. Comments and suggestions on these draft entries should be sent to Professor K.F. Tipton and Dr S. Boyce (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland) by 20 May 2006, after which, the entries will be made official and will be incorporated into the main enzyme list. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list. Many thanks to those of you who have submitted details of new enzymes or updates to existing enzymes. An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry. Contents *EC 1.1.1.262 4-hydroxythreonine-4-phosphate dehydrogenase EC 1.1.1.289 sorbose reductase EC 1.1.1.290 4-phosphoerythronate dehydogenase EC 1.1.99.19 transferred *EC 1.2.1.10 acetaldehyde dehydrogenase (acetylating) EC 1.2.1.71 succinylglutamate-semialdehyde dehydrogenase EC 1.2.1.72 erythrose-4-phosphate dehydrogenase EC 1.2.99.1 transferred *EC 1.3.99.19 quinoline-4-carboxylate 2-oxidoreductase
    [Show full text]
  • A Prokaryotic Origin for Light-Dependent Chlorophyll
    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 3749-3753, April 1995 Plant Biology A prokaryotic origin for light-dependent chlorophyll biosynthesis of plants (protochlorophyllide reductase/bacteriochlorophyll/Synechocystis/ Rhodobacter capsulatus) JON Y. SUZUKI* AND CARL E. BAUERt Department of Biology, Indiana University, Bloomington, IN 47405 Communicated by Diter von Wettstein, Carlsberg Laboratory, Copenhagen Valby, Denmark, January 3, 1995 (received for review November 21, 1994) ABSTRACT Flowering plants require light for chloro- light-independent protochlorophyllide reductase that cata- phyll synthesis. Early studies indicated that the dependence on lyzes the reduction of protochlorophyllide (and hence pro- light for greening stemmed in part from the light-dependent motes photopigment biosynthesis) in the dark. Recent studies reduction of the chlorophyll intermediate protochlorophyllide with the bacteriochlorophyll-producing, purple, nonsulfur, to the product chlorophyllide. Light-dependent reduction of photosynthetic bacterium Rhodobacter capsulatus have re- protochlorophyllide by flowering plants is contrasted by the sulted in the identification of three genes, bchN, bchB, and ability of nonflowering plants, algae, and photosynthetic bchL, that code for putative subunits of the light-independent bacteria to reduce protochlorophyllide and, hence, synthesize protochlorophyllide reductase (5-7). The studies with R. cap- (bacterio)chlorophyll in the dark. In this report, we function- sulatus have also led, in part, to the identification of one or ally complemented a light-independent protochlorophyllide more corresponding light-independent protochlorophyllide re- reductase mutant of the eubacterium Rhodobacter capsulatus ductase genes (chiN, chlB, chiL) in cyanobacteria (8-10) and with an expression library composed of genomic DNA from in the chloroplast genomes of numerous dark-greening pho- the cyanobacterium Synechocystis sp.
    [Show full text]
  • Eukaryotic Genomes from a Global Metagenomic Dataset Illuminate Trophic Modes and Biogeography of Ocean Plankton
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.25.453713; this version posted July 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton Harriet Alexander1,*, Sarah K. Hu2, Arianna I. Krinos1,3, Maria Pachiadaki1, Benjamin J. Tully4, Christopher J. Neely5, and Taylor Reiter6 1Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, 02543 2Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, 02543 3MIT-WHOI Joint Program in Oceanography, Cambridge and Woods Hole, MA, 02540 4Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089 5Department of Computational and Quantitative Biology, University of Southern California, Los Angeles, CA 90089 6Population Health and Reproduction, University of California, Davis, Davis, CA, 95616 *Correspondence; [email protected] Abstract Molecular and genomic approaches that target mixed microbial communities (e.g., metagenomics or metatranscriptomics) provide insight into the ecological roles, evolutionary histories, and phys- iological capabilities of the microorganisms and the processes in the environment. Computational tools that harness large-scale sequence surveys have become a valuable resource for characterizing 5 the genetic make-up of the bacterial and archaeal component of the marine microbiome. Yet, fewer studies have focused on the unicellular eukaryotic fraction of the community. Here, we developed the EukHeist automated computational pipeline, to retrieve eukaryotic and prokaryotic metagenome assembled genomes (MAGs).
    [Show full text]