DOCSLIB.ORG

Abstract a Comprehensive Phylogenetic Study of The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Abstract a Comprehensive Phylogenetic Study of The ABSTRACT A COMPREHENSIVE PHYLOGENETIC STUDY OF THE CORE GENOME OF THIRTEEN BACILLUS AND RELATED SPECIES USING KNOWN AND NOVEL TECHNIQUES Jennifer Diane Hintzsche, Ph.D. Department of Biological Sciences Northern Illinois University, 2014 Mitrick A. Johns, Director A comprehensive study into the phylogeny of the Bacillus core genome was accomplished using two primary studies. The first study involved two previously studied methods, MUMmer and BSR, and one novel approach, RINC, to compare core genome phylogeny. BSR analysis revealed genomic rearrangements among the genomes of interest. MUMmer was used to confirm these genomic rearrangements and provide evidence that 76.2% of the inverted regions were statistically significant. Circular chromosome comparisons connecting homologous core genes revealed an ancestral inversion pivoted on the terminus in several species. The inversions were resolved, allowing for the identification of the location of the core genome before the inversion event. These analyses led to development of a novel approach to core genome phylogeny, RINC. Based on the tree produced, as well as agreement of groups of nodes with previous studies, the RINC approach was successful at comparing the core genome of Bacillus. RINC offers a simplistic yet powerful tool for core genome phylogeny. In the second study, core genomes of Bacillus and Eudicot were determined individually from whole genome sequences of members of each genus, along with closely related species using BSRs. The Eudicot core genome was used as a control for evidence that results observed in the Bacillus core genomes were not due to horizontal gene transfer. Each core genome was analyzed with MrBayes and BUCKy to test the robustness of both approaches using sequences from different domains of life. Three multiple sequence alignments, ClustalW2, MUSCLE, and T-COFFEE, were used as inputs for MrBayes. Over 75% of all genes studied had a resolved gene tree topology after one of ten million generations of MrBayes, regardless of MSA. BUCKy calculated concordance trees for both core genomes. BUCKy tree topology was not affected by the MSAs. In both core genomes, high concordance factors were found on interior nodes, defining the relationship between groups of species. Outer nodes between outgroups had lower concordance factors, leading to the conclusion that genomes of more species would need to be included in order to resolve the phylogeny from more distant relatives. NORTHERN ILLINOIS UNIVERSITY DEKALB, ILLINOIS DECEMBER 2014 A COMPREHENSIVE PHYLOGENETIC STUDY OF THE CORE GENOME OF THIRTEEN BACILLUS AND RELATED SPECIES USING KNOWN AND NOVEL TECHNIQUES BY JENNIFER DIANE HINTZSCHE ©2014 Jennifer Diane Hintzsche A DISSERTATION SUBMITTED TO THE GRADUATE SCHOOL IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES Doctoral Director: Mitrick A. Johns ACKNOWLEDGEMENTS I am most grateful to the many people who have contributed their time, expertise, ideas, and resources to help complete this project. First of all, thank you to Dr. Mitrick Johns for years of training, education, and support. Without y skill set and capabilities needed for the next step in my career. Thank you for taking a chance on me in the beginning. Thank you for knowing when to let my independence shine and also when I needed your guidance. Perhaps most of all, thank you for your continued inspiration and motivation to become the best scientist I can be. Dr. Gordon Pusch, thank you for your countless hours offering critical insight and expertise. Thank you also for providing me with training and access to the computational resources at Argonne National Laboratory, which was integral in my being able to complete this project. Thank you Dr. Melvin Duvall, for your phylogenetic expertise, advice, and mentoring. Thank you Dr. Thomas Sims, for advising me since the start of my graduate career, and your continued expertise and advice. Thank you Dr. Wesley Swingley, for your expertise and advice about this project and my career options. DEDICATION To my Mom, Dad, Jessica, Lera, and Ryan TABLE OF CONTENTS Page LIST OF TABLES .............................................................................................................. x LIST OF FIGURES ............................................................................................................. xi LIST OF APPENDICES ..................................................................................................... xiv Chapter 1. INTRODUCTION ............................................................................................... 1 Phylogeny of the Bacillus Genus .................................................................. 2 Significance of Species Studied .................................................................... 10 Outline of Study ............................................................................................ 18 2. BSR & CORE GENOME .................................................................................... 26 Introduction ................................................................................................... 26 Methods ......................................................................................................... 27 Bacillus Genomes ................................................................................. 27 Bidirectional Best Hits ......................................................................... 27 BLAST Score Ratio .............................................................................. 28 Plotting BSR ......................................................................................... 28 Results and Discussion .................................................................................. 29 Core Genome ........................................................................................ 29 BSR Plots .............................................................................................. 30 vii Chapter Page 3. MUMmer ............................................................................................................. 41 Introduction ................................................................................................... 41 Methods ......................................................................................................... 44 Number of MUMs ................................................................................ 44 Length of MUMs .................................................................................. 45 Results and Discussion .................................................................................. 46 Range of MUMmer Results .................................................................. 46 Total MUMs Found .............................................................................. 52 MUMs on the Forward Diagonal ......................................................... 56 MUMs on the Reverse Diagonal .......................................................... 61 Statistical Significance with Respect to the Number of MUMs ........... 65 Significance of the number of MUMs on the Forward Diagonal ........................................................................................ 66 Significance of the number of MUMs on the Reverse Diagonal ........................................................................................ 69 Statistical Significance with Respect to the Length of MUMs ............ 73 Significance of MUM Length on the Forward Diagonal .............. 73 Significance of MUM Length on the Reverse Diagonal............... 75 Conclusions ................................................................................................... 77 4. CIRCULAR CHROMOSOMAL COMPARISON ............................................. 79 Introduction ................................................................................................... 79 Methods ......................................................................................................... 80 viii Chapter Page Circular Chromosomal Comparisons ...................................................... 80 Resolved Inversion Comparisons ............................................................ 81 Results and Discussion .................................................................................. 82 Circular Chromosomal Comparisons ...................................................... 82 Number of Inverted Genes ...................................................................... 87 Resolved Inversions Comparison ............................................................ 94 Conclusions ................................................................................................... 97 5. RINC .................................................................................................................... 99 Introduction ................................................................................................... 99 Methods ......................................................................................................... 100 Results and Discussion .................................................................................. 103 RINC Distance ......................................................................................... 103 RINC Phylogeny ..................................................................................... 110 Conclusions ........................................................................................................
Load more

Recommended publications
  • Summaries of FY 2001 Activities Energy Biosciences
    Summaries of FY 2001 Activities Energy Biosciences August 2002 ABSTRACTS OF PROJECTS SUPPORTED IN FY 2001 (NOTE: Dollar amounts are for a twelve-month period using FY 2001 funds unless otherwise stated) 1. U.S. Department of Agriculture Urbana, IL 61801 Biochemical and molecular analysis of a new control pathway in assimilate partitioning Daniel R. Bush, USDA-ARS and Department of Plant Biology, University of Illinois at Urbana- Champaign $72,666 (21 months) Plant leaves capture light energy from the sun and transform that energy into a useful form in the process called photosynthesis. The primary product of photosynthesis is sucrose. Generally, 50 to 80% of the sucrose synthesized is transported from the leaf to supply organic nutrients to many of the edible parts of the plant such as fruits, grains, and tubers. This resource allocation process is called assimilate partitioning and alterations in this system are known to significantly affect crop productivity. We recently discovered that sucrose plays a second vital role in assimilate partitioning by acting as a signal molecule that regulates the activity and gene expression of the proton-sucrose symporter that mediates long-distance sucrose transport. Research this year showed that symporter protein and transcripts turn-over with half-lives of about 2 hr and, therefore, sucrose transport activity and phloem loading are directly proportional to symporter transcription. Moreover, we showed that sucrose is a transcriptional regulator of symporter expression. We concluded from those results that sucrose-mediated transcriptional regulation of the sucrose symporter plays a key role in coordinating resource allocation in plants. 2. U.
    [Show full text]
  • Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam
    Bacterial Degradation of Isoprene in the Terrestrial Environment Myriam El Khawand A thesis submitted to the University of East Anglia in fulfillment of the requirements for the degree of Doctor of Philosophy School of Environmental Sciences November 2014 ©This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derive there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Abstract Isoprene is a climate active gas emitted from natural and anthropogenic sources in quantities equivalent to the global methane flux to the atmosphere. 90 % of the emitted isoprene is produced enzymatically in the chloroplast of terrestrial plants from dimethylallyl pyrophosphate via the methylerythritol pathway. The main role of isoprene emission by plants is to reduce the damage caused by heat stress through stabilizing cellular membranes. Isoprene emission from microbes, animals, and humans has also been reported, albeit less understood than isoprene emission from plants. Despite large emissions, isoprene is present at low concentrations in the atmosphere due to its rapid reactions with other atmospheric components, such as hydroxyl radicals. Isoprene can extend the lifetime of potent greenhouse gases, influence the tropospheric concentrations of ozone, and induce the formation of secondary organic aerosols. While substantial knowledge exists about isoprene production and atmospheric chemistry, our knowledge of isoprene sinks is limited. Soils consume isoprene at a high rate and contain numerous isoprene-utilizing bacteria. However, Rhodococcus sp. AD45 is the only terrestrial isoprene-degrading bacterium characterized in any detail.
    [Show full text]
  • Metabolic Engineering of Escherichia Coli for Natural Product Biosynthesis
    Trends in Biotechnology Special Issue: Metabolic Engineering Review Metabolic Engineering of Escherichia coli for Natural Product Biosynthesis Dongsoo Yang,1,4 Seon Young Park,1,4 Yae Seul Park,1 Hyunmin Eun,1 and Sang Yup Lee1,2,3,∗ Natural products are widely employed in our daily lives as food additives, Highlights pharmaceuticals, nutraceuticals, and cosmetic ingredients, among others. E. coli has emerged as a prominent host However, their supply has often been limited because of low-yield extraction for natural product biosynthesis. from natural resources such as plants. To overcome this problem, metabolically Escherichia coli Improved enzymes with higher activity, engineered has emerged as a cell factory for natural product altered substrate specificity, and product biosynthesis because of many advantages including the availability of well- selectivity can be obtained by structure- established tools and strategies for metabolic engineering and high cell density based or computer simulation-based culture, in addition to its high growth rate. We review state-of-the-art metabolic protein engineering. E. coli engineering strategies for enhanced production of natural products in , Balancing the expression levels of genes together with representative examples. Future challenges and prospects of or pathway modules is effective in natural product biosynthesis by engineered E. coli are also discussed. increasing the metabolic flux towards target compounds. E. coli as a Cell Factory for Natural Product Biosynthesis System-wide analysis of metabolic Natural products have been widely used in food and medicine in human history. Many of these networks, omics analysis, adaptive natural products have been developed as pharmaceuticals or employed as structural backbones laboratory evolution, and biosensor- based screening can further increase for the development of new drugs [1], and also as food and cosmetic ingredients.
    [Show full text]
  • Isoprene Synthase and Polynucleotide Encoding Same, and Method for Producing Isoprene Monomer
    (19) TZZ Z_T (11) EP 2 857 509 A1 (12) EUROPEAN PATENT APPLICATION published in accordance with Art. 153(4) EPC (43) Date of publication: (51) Int Cl.: 08.04.2015 Bulletin 2015/15 C12N 15/09 (2006.01) C08F 36/08 (2006.01) C12N 1/21 (2006.01) C12N 9/88 (2006.01) (2006.01) (21) Application number: 13796298.1 C12P 5/02 (22) Date of filing: 12.03.2013 (86) International application number: PCT/JP2013/056866 (87) International publication number: WO 2013/179722 (05.12.2013 Gazette 2013/49) (84) Designated Contracting States: • FUKUSHIMA, Yasuo AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Kodaira-shi GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Tokyo 187-8531 (JP) PL PT RO RS SE SI SK SM TR • YOKOYAMA, Keiichi Designated Extension States: Kawasaki-shi BA ME Kanagawa 210-8681 (JP) • NISHIO, Yosuke (30) Priority: 30.05.2012 JP 2012123724 Kawasaki-shi 30.05.2012 JP 2012123728 Kanagawa 210-8681 (JP) • TAJIMA, Yoshinori (71) Applicants: Kawasaki-shi • Bridgestone Corporation Kanagawa 210-8681 (JP) Tokyo 104-8340 (JP) • MIHARA, Yoko • Ajinomoto Co., Inc. Kawasaki-shi Tokyo 104-8315 (JP) Kanagawa 210-8681 (JP) • NAKATA, Kunio (72) Inventors: Kawasaki-shi • HAYASHI, Yasuyuki Kanagawa 210-8681 (JP) Kodaira-shi Tokyo 187-8531 (JP) (74) Representative: Grünecker Patent- und • HARADA, Minako Rechtsanwälte Kodaira-shi PartG mbB Tokyo 187-8531 (JP) Anwaltssozietät • TAKAOKA, Saaya Leopoldstrasse 4 Kodaira-shi 80802 München (DE) Tokyo 187-8531 (JP) (54) ISOPRENE SYNTHASE AND POLYNUCLEOTIDE ENCODING SAME, AND METHOD FOR PRODUCING ISOPRENE MONOMER (57) The present invention provides means useful for (b) a polynucleotide that comprises a nucleotide se- establishing an excellent isoprene monomer production quence having 90% or more identity to the nucleotide system.
    [Show full text]
  • Genetic Variants in Root Architecture-Related Genes in A
    Prince et al. BMC Genomics (2015) 16:132 DOI 10.1186/s12864-015-1334-6 RESEARCH ARTICLE Open Access Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean Silvas J Prince1†, Li Song1†, Dan Qiu1, Joao V Maldonado dos Santos1,2, Chenglin Chai1, Trupti Joshi2,3, Gunvant Patil1, Babu Valliyodan1, Tri D Vuong1, Mackensie Murphy1, Konstantinos Krampis4, Dominic M Tucker4, Ruslan Biyashev4, Anne E Dorrance5, MA Saghai Maroof4, Dong Xu2,3, J Grover Shannon1 and Henry T Nguyen1,2* Abstract Background: Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja. Results: Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (Dtypecyclinand auxin efflux carrier protein) with insertion/ deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean.
    [Show full text]
  • KNIGHT-DISSERTATION-2014.Pdf
    Copyright by Rebecca Anne Knight 2014 The Dissertation Committee for Rebecca Anne Knight Certifies that this is the approved version of the following dissertation: Coordinated Response and Regulation of Carotenogenesis in Thermosynechococcus elongatus (BP-1): Implications for Commercial Application Committee: Jerry J. Brand, Supervisor Hal S. Alper, Co-Supervisor Enamul Huq Robert K. Jansen David R. Nobles Coordinated Response and Regulation of Carotenogenesis in Thermosynechococcus elongatus (BP-1): Implications for Commercial Application by Rebecca Anne Knight, B.A., B.S.E., M.S.E. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin December 2014 Dedication Dedicated to my parents, who taught me to always work hard, and never stop learning. Acknowledgements I think there is a unique experience that people like myself undergo when working in industry then returning to academia. Very little is taken for granted on campus, so much to learn and take advantage of knowledge-wise. Then there is the flip side; long hours in the lab, the struggle to find your niche and contribution to the scientific community, and a much tighter budget both for research and personal life. I am here to say that without my family and their encouragement and sacrifices I would not have made it. My loving husband, who’s been my biggest supporter, and my wonderful step-daughters, whom I have dragged to campus numerous times and have essentially lived in my shoes for six whole years.
    [Show full text]
  • Molecular Ecology of Marine Isoprene Degradation Antonia Johnston University of East Anglia
    Molecular Ecology of Marine Isoprene Degradation Antonia Johnston University of East Anglia 2014 A thesis submitted to the School of Environmental Sciences in fulfilment of the requirements for the degree of Doctor of Philosophy University of East Anglia, Norwich, UK September 2014 This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Declaration I declare that the content of this thesis entitled “Molecular Ecology of Marine Isoprene Degradation” was undertaken and completed by myself under the supervision of Professor J.C.Murrell, unless otherwise acknowledged and has not been submitted in support of an application for another degree or qualification in this or any other university or institution Antonia Johnston Acknowledgements I would like to thank my primary supervisor, Professor J.C.Murrell, for his help and guidance throughout my PhD. I would also like to thank past and present members of the Murrell lab at the University of Warwick and the University of East Anglia, especially Myriam El Khawand and Dr. Andrew Crombie for their help and collaboration on this project. I thank my secondary supervisor Dr. Jonathon Todd for his advice. I would especially like to thank our collaborators on this project, including Dr. Terry McGenity at the University of Essex, Professor Dan Arp at Oregon State University, Capt. Collett at the 47th Regiment Royal Horse Artillery for assistance with sampling, and Sue Slade at the University of Warwick proteomics facility.
    [Show full text]
  • Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece Sp
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Chemical and Biomolecular Engineering -- All Chemical and Biomolecular Engineering, Faculty Papers Department of 2012 Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803 Rajib Saha Pennsylvania State University, rsaha2@unl.edu Alex T. Verseput The Pennsylvania State University Bertram M. Berla Washington University Thomas J. Mueller Pennsylvania State University Himadri B. Pakrasi Washington University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/chemengall Saha, Rajib; Verseput, Alex T.; Berla, Bertram M.; Mueller, Thomas J.; Pakrasi, Himadri B.; and Maranas, Costas D., "Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803" (2012). Chemical and Biomolecular Engineering -- All Faculty Papers. 48. https://digitalcommons.unl.edu/chemengall/48 This Article is brought to you for free and open access by the Chemical and Biomolecular Engineering, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Chemical and Biomolecular Engineering -- All Faculty Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Rajib Saha, Alex T. Verseput, Bertram M. Berla, Thomas J. Mueller, Himadri B. Pakrasi, and Costas D. Maranas This article is available at DigitalCommons@University
    [Show full text]
  • Methyltransferases from Ruta Graveolens L.: Molecular Biology
    Methyltransferases from Ruta graveolens L.: Molecular Biology and Biochemistry Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Pharmazie der Philipps-Universität Marburg vorgelegt von Laura Nicoleta Burga aus Fagaras, Rumänien Marburg/Lahn 2005 Vom Fachbereich Pharmazie der Philipps-Universität Marburg als Dissertation angenomen am: 13. 07. 2005 Erstgutachter: Prof. Dr. Ulrich Matern Zweitgutachter: Prof. Dr. Maike Petersen Tag der mündlische Prüfung am: 12. 07. 2005 Publication Laura Burga, Frank Wellmann, Richard Lukacin, Simone Witte, Wilfried Schwab, Joachim Schröder and Ulrich Matern (2005) Unusual pseudosubstrate specificity of a novel 3,5-dimethoxyphenol O-methyltransferase cloned from Ruta graveolens L. Arch Biochem Biophys 2005 Aug 1; 440(1):54-64. _____________________________________________________________________ Table of contents ___ Table of contents i Abreviations vi 1. INTRODUCTION 1.1 Ruta graveolens L. 1 1.1.1 General features 1 1.1.2 Content 2 1.2 Acridone alkaloids 3 1.2.1 Biosynthesis of acridone alkaloids 4 1.2.2 Anthranilate synthase 5 1.2.3 Anthranilate N-methyltransferase 6 1.2.4 N-methylanthranilate:CoA-ligase 6 1.2.5 Acridone synthase 7 1.2.6 Rutacridone and furacridone 7 1.3 Methyltransferases 8 1.3.1 Plant methyltransferases 8 1.3.2 Conserved motifs 15 1.3.3 Active site 16 1.3.4 Importance of methyltransferases in humans 19 1.4 Plant volatile compounds 23 1.4.1 Methyltransferases involved in methylation of volatile compounds 24 1.4.2 Volatile compounds in
    [Show full text]
  • Investigation of the Methylerythritol 4-Phosphate Pathway for Microbial
    Volke et al. Microb Cell Fact (2019) 18:192 https://doi.org/10.1186/s12934-019-1235-5 Microbial Cell Factories RESEARCH Open Access Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis Daniel Christoph Volke1,2, Johann Rohwer3, Rainer Fischer1,4 and Stefan Jennewein1* Abstract Background: Terpenoids are of high interest as chemical building blocks and pharmaceuticals. In microbes, terpe- noids can be synthesized via the methylerythritol phosphate (MEP) or mevalonate (MVA) pathways. Although the MEP pathway has a higher theoretical yield, metabolic engineering has met with little success because the regulation of the pathway is poorly understood. Results: We applied metabolic control analysis to the MEP pathway in Escherichia coli expressing a heterologous isoprene synthase gene (ispS). The expression of ispS led to the accumulation of isopentenyl pyrophosphate (IPP)/ dimethylallyl pyrophosphate (DMAPP) and severely impaired bacterial growth, but the coexpression of ispS and iso- pentenyl diphosphate isomerase (idi) restored normal growth and wild-type IPP/DMAPP levels. Targeted proteomics and metabolomics analysis provided a quantitative description of the pathway, which was perturbed by randomizing the ribosome binding site in the gene encoding 1-deoxyxylulose 5-phosphate synthase (Dxs). Dxs has a fux control coefcient of 0.35 (i.e., a 1% increase in Dxs activity resulted in a 0.35% increase in pathway fux) in the isoprene-pro- ducing strain and therefore exerted signifcant control over the fux though the MEP pathway. At higher dxs expres- sion levels, the intracellular concentration of 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate (MEcPP) increased substantially in contrast to the other MEP pathway intermediates, which were linearly dependent on the abundance of Dxs.
    [Show full text]
  • Gene Expression and Characterization of Isoprene Synthase from Populus Alba
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 579 (2005) 2514–2518 FEBS 29501 Gene expression and characterization of isoprene synthase from Populus alba Kanako Sasaki, Kazuaki Ohara, Kazufumi Yazaki* Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan Received 9 February 2005; revised 21 March 2005; accepted 21 March 2005 Available online 7 April 2005 Edited by Ulf-Ingo Flu¨gge ature [7,9]. Despite the purification of isoprene synthase pro- Abstract Isoprene synthase cDNA from Populus alba (PaIspS) was isolated by RT-PCR. This PaIspS mRNA, which was pre- teins from several plants, isolation of its gene has only been dominantly observed in the leaves, was strongly induced by heat reported from hybrid poplar (Populus alba · P. tremula) [10], stress and continuous light irradiation, and was substantially de- and P. tremuloides and Pueraria montana [11], and very little creased in the dark, suggesting that isoprene emission was regu- is known about its physiological role in plants; e.g., even its lated at the transcriptional level. The subcellular localization of subcellular location has not yet been clarified. PaIspS protein with green fluorescent protein fusion was shown To obtain biochemical and molecular biological insights into to be in plastids. PaIspS expressed in Escherichia coli was char- isoprene synthase, we cloned isoprene synthase cDNA from P. acterized enzymatically: it had an optimum pH of approximately alba (PaIspS) and studied gene expression in response to envi- 8.0, and an optimum temperature 40 °C.
    [Show full text]
  • 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
    [Show full text]