Differential Expression and Functional Analysis of Two Short-Chain Alcohol
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Sunlight-Driven Environmental Benign Production of Bioactive Natural Products with Focus on Diterpenoids and the Pathways Involved in Their Formation
Natural Products: source of INNovatIoN CHIMIA 2017, 71, No. 12 851 doi:10.2533/chimia.2017.851 Chimia 71 (2017) 851–858 © Swiss Chemical Society Sunlight-driven Environmental Benign Production of Bioactive Natural Products with Focus on Diterpenoids and the Pathways Involved in their Formation Dan Luo, Birger Lindberg Møller, and Irini Pateraki* Abstract: Diterpenoids are high value compounds characterized by high structural complexity. They constitute the largest class of specialized metabolites produced by plants. Diterpenoids are flexible molecules able to engage in specific binding to drug targets like receptors and transporters. In this review we provide an account on how the complex pathways for diterpenoids may be elucidated. Following plant pathway discovery, the com- pounds may be produced in heterologous hosts like yeasts and E. coli. Environmentally contained production in photosynthetic cells like cyanobacteria, green algae or mosses are envisioned as the ultimate future production system. Keywords: Alcohol dehydrogenases · Cytochrome P450s · Ingenol mebutate · Light-driven production · Terpene synthases 1. Introduction anticancer agent widely used today as a Coleus forskohlii, is used in the treatment therapeutic in combinatorial treatments of glaucoma and heart failure based on 1.1 Plant Diterpenoids and their of ovarian cancer, breast cancer, lung can- its activity as a cyclic AMP booster.[8,9] Application as Pharmaceuticals cer, Kaposi sarcoma, cervical cancer, and Ginkgolides from the leaves of Ginkgo bi- Plants produce a wide variety of natural pancreatic cancer.[6,7] Forskolin, a labdane- loba L. are a series of diterpene lactones products that play important roles in both type diterpene produced from the roots of with anti-platelet-activating antagonist ac- general and specialized metabolism.[1,2] Terpenoids constitute the largest and most diverse class of bio-active natural prod- Fig 1. -
Drug Metabolism Chemical and Enzymatic Aspects Textbook Edition
DRUG METABOLISM Chemical and Enzymatic Aspects TEXTBOOK EDITION Jack P. Uetrecht University of Toronto Ontario, Canada William Trager University of Washington Seattle, Washington, USA Uetrecht_978-1420061031_TP.indd 2 5/11/07 2:28:26 PM OTE/SPH OTE/SPH uetrecht IHUS001-Uetrecht May 10, 2007 3:29 Char Count= Informa Healthcare USA, Inc. 52 Vanderbilt Avenue New York, NY 10017 C 2007 by Informa Healthcare USA, Inc. Informa Healthcare is an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10987654321 International Standard Book Number-10: 1-4200-6103-8 International Standard Book Number-13: 978-1-4200-6103-1 This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequence of their use. No part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechan- ical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC) 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registra- tion for a variety of users. -
Acyclic Monoterpene Primary Alcohol :NADP+ Oxidoreductase of Rauwolfia Serpentina Cells: the Key Enzyme in Biosynthesis of Monoterpene Alcohols
J. Biochem. 109, 341-347 (1991) Acyclic Monoterpene Primary Alcohol :NADP+ Oxidoreductase of Rauwolfia serpentina Cells: The Key Enzyme in Biosynthesis of Monoterpene Alcohols Hiromitsu Ikeda, * Nobuyoshi Esaki, ** Shunji Nakai, * Keij i Hashimoto, Shinichi Uesato,*•' Kenji Soda,** and Tetsuro Fujita*2 *Department of Natural Product Chemistry , Faculty of Pharmaceutical Sciences,Kyoto University,Sakyo-ku, Kyoto, Kyoto 606; **Laboratory of Microbial Biochemistry,Institute for ChemicalResearch, Kyoto University, Uji, Kyoto 611; and *`'Kyoto Pharmaceutical University, Yamashina-ku, Kyoto, Kyoto 607 Received for publication, August 1, 1990 Acyclic monoterpene primary alcohol: NADP+ oxidoreductase, a key enzyme in the biosynthesis of monoterpene alcohols in plants, is unstable and has been only poorly characterized. However we have established conditions which stabilize the enzyme from Rauwolfza serpentina cells, and then purified it to homogeneity. It is a monomer with a molecular weight of about 44,000 and contains zinc ions. Various branched-chain allylic primary alcohols such as nerol, geraniol, and 10-hydroxygeraniol were substrates, but ethanol was inert. The enzyme exclusively requires NADP+ or NADPH as the cofactor. Steady-state kinetic studies showed that the nerol dehydrogenation proceeds by an ordered Bi-Bi mechanism. NADP+ binds the enzyme first and then NADPH is the second product released from it. Gas chromatography-mass spectrometric analysis of the reaction products showed that 10-hydroxygeraniol undergoes a reversible dehydrogenation to produce 10-oxogeraniol or 10-hydroxygeranial, which are oxidized further to give 10-oxogeranial, the direct precursor of iridodial. The enzyme has been found to exclusively transfer the pro-R hydrogen of NADPH to neral. The N-terminal sequence of the first 21 amino acids revealed no significant homology with those of various other proteins including the NAD(P)+-dependent alcohol dehydrogenases registered in a protein data bank. -
High Throughput Search of Drought Tolerant Genes in Agave Sisalana L
High Throughput Search of Drought Tolerant Genes in Agave sisalana L. SANIA RIAZ CENTRE OF EXCELLENCE IN MOLECULAR BIOLOGY UNIVERSITY OF THE PUNJAB LAHORE PAKISTAN (2015) High Throughput Search of Drought Tolerant Genes in Agave sisalana L. A THESIS SUBMITTED TO UNIVERSITY OF THE PUNJAB IN FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN MOLECULAR BIOLOGY By SANIA RIAZ Supervisor: Dr. Tayyab Husnain (Prof & Acting Director) Centre of Excellence in Molecular Biology. University of the Punjab, Lahore CERTIFICATE It is certified that the research work described in this thesis is the original work of the author Ms. Sania Riaz and has been carried out under my direct supervision. I have personally gone through all the data reported in the manuscript and certify their correctness and authenticity. It is further certified that the material included in this thesis have not been used in part or full manuscript already submitted or in the process of submission in partial/complete fulfillment of the award of any other degree from any other institution. It is also certified that the thesis has been prepared under my supervision according to the prescribed format and we endorse its evaluation for the award of Ph.D degree through the official procedures of the university. In accordance with the rules of the centre, data book #852 is declared as unexpendable document that will be kept in the registry of the Centre for a minimum of three years from the date of the Thesis defense examination. Signature of the supervisor________________________________ Name: Dr. Tayyab Husnain Designation: Prof & Acting Director (Allah) Most Gracious! It is He Who has taught the Qur'an. -
Deciphering the Genome Repertoire of Pseudomonas Sp. M1 Toward B-Myrcene Biotransformation
GBE Deciphering the Genome Repertoire of Pseudomonas sp. M1 toward b-Myrcene Biotransformation Pedro Soares-Castro and Pedro M. Santos* CBMA—Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, Braga, Portugal *Corresponding author: E-mail: [email protected]. Accepted: November 21, 2014 Data deposition: The Whole Genome Shotgun project of Pseudomonas sp. M1 has been deposited at DNA Data Bank of Japan/EMBL/GenBank under the accession ANIR00000000. The version described in this paper is ANIR00000000.2. Abstract Pseudomonas sp. M1 is able to mineralize several unusual substrates of natural and xenobiotic origin, contributing to its competence to thrive in different ecological niches. In this work, the genome of M1 strain was resequenced by Illumina MiSeq to refine the quality of a published draft by resolving the majority of repeat-rich regions. In silico genome analysis led to the prediction of metabolic pathways involved in biotransformation of several unusual substrates (e.g., plant-derived volatiles), providing clues on the genomic complement required for such biodegrading/biotransformation functionalities. Pseudomonas sp. M1 exhibits a particular sensory and biotransformation/biocatalysis potential toward b-myrcene, a terpene vastly used in industries worldwide. Therefore, the genomic responsiveness of M1 strain toward b-myrcene was investigated, using an RNA sequencing approach. M1 cells challenged with b-myrcene(compared with cells grown in lactate) undergo an extensive alteration of the transcriptome expression profile, including 1,873 genes evidencing at least 1.5-fold of altered expression (627 upregulated and 1,246 downregulated), toward b-myrcene- imposed molecular adaptation and cellular specialization. -
Alternative Treatments for Cancer Prevention and Cure [Part 1]
Advances in Pharmacology and Clinical Trials ISSN: 2474-9214 Alternative Treatments for Cancer Prevention and Cure [Part 1] Abdul Kader Mohiuddin* Review Article Secretary & Treasurer Dr M. Nasirullah Memorial Trust, Tejgaon, Dhaka, Bangladesh Volume 4 Issue 4 Received Date: September 02, 2019 *Corresponding author: Abdul Kader Mohiuddin, Secretary & Treasurer Dr M Published Date: October 17, 2019 Nasirullah Memorial Trust, Tejgaon, Dhaka, Bangladesh, Tel: +8802-9110553; Email: DOI: 10.23880/apct-16000168 [email protected] Abstract Many lay people along with some so called “key opinion leaders” have a common slogan “There's no answer for cancer”. Again, mistake delays proper treatment and make situation worse, more often. Compliance is crucial to obtain optimal health outcomes, such as cure or improvement in QoL. Patients may delay treatment or fail to seek care because of high out-of- pocket expenditures. Despite phenomenal development, conventional therapy falls short in cancer management. There are two major hurdles in anticancer drug development: dose-limiting toxic side effects that reduce either drug effectiveness or the QoL of patients and complicated drug development processes that are costly and time consuming. Cancer patients are increasingly seeking out alternative medicine and might be reluctant to disclose its use to their oncology treatment physicians. But there is limited available information on patterns of utilization and efficacy of alternative medicine for patients with cancer. As adjuvant therapy, many traditional medicines shown efficacy against brain, head and neck, skin, breast, liver, pancreas, kidney, bladder, prostate, colon and blood cancers. The literature reviews non-pharmacological interventions used against cancer, published trials, systematic reviews and meta-analyses. -
European Patent Office U.S. Patent and Trademark Office
EUROPEAN PATENT OFFICE U.S. PATENT AND TRADEMARK OFFICE CPC NOTICE OF CHANGES 89 DATE: JULY 1, 2015 PROJECT RP0098 The following classification changes will be effected by this Notice of Changes: Action Subclass Group(s) Symbols deleted: C12Y 101/01063 C12Y 101/01128 C12Y 101/01161 C12Y 102/0104 C12Y 102/03011 C12Y 103/01004 C12Y 103/0103 C12Y 103/01052 C12Y 103/99007 C12Y 103/9901 C12Y 103/99013 C12Y 103/99021 C12Y 105/99001 C12Y 105/99002 C12Y 113/11013 C12Y 113/12012 C12Y 114/15002 C12Y 114/99028 C12Y 204/01119 C12Y 402/01052 C12Y 402/01058 C12Y 402/0106 C12Y 402/01061 C12Y 601/01025 C12Y 603/02027 Symbols newly created: C12Y 101/01318 C12Y 101/01319 C12Y 101/0132 C12Y 101/01321 C12Y 101/01322 C12Y 101/01323 C12Y 101/01324 C12Y 101/01325 C12Y 101/01326 C12Y 101/01327 C12Y 101/01328 C12Y 101/01329 C12Y 101/0133 C12Y 101/01331 C12Y 101/01332 C12Y 101/01333 CPC Form – v.4 CPC NOTICE OF CHANGES 89 DATE: JULY 1, 2015 PROJECT RP0098 Action Subclass Group(s) C12Y 101/01334 C12Y 101/01335 C12Y 101/01336 C12Y 101/01337 C12Y 101/01338 C12Y 101/01339 C12Y 101/0134 C12Y 101/01341 C12Y 101/01342 C12Y 101/03043 C12Y 101/03044 C12Y 101/98003 C12Y 101/99038 C12Y 102/01083 C12Y 102/01084 C12Y 102/01085 C12Y 102/01086 C12Y 103/01092 C12Y 103/01093 C12Y 103/01094 C12Y 103/01095 C12Y 103/01096 C12Y 103/01097 C12Y 103/0701 C12Y 103/08003 C12Y 103/08004 C12Y 103/08005 C12Y 103/08006 C12Y 103/08007 C12Y 103/08008 C12Y 103/08009 C12Y 103/99032 C12Y 104/01023 C12Y 104/01024 C12Y 104/03024 C12Y 105/01043 C12Y 105/01044 C12Y 105/01045 C12Y 105/03019 C12Y 105/0302 -
Electronic Supplementary Information S10
Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2019 Electronic Supplementary Information S10. Up and downregulated genes of ACR3 and TIP-ACR3 compared to control roots all exposed to 0.1 mM As III . HYBRIDIZATION 4: LIST OF UP-REGULATED GENES Fold Change Probe Set ID ([0.1 ACR3] vs [0.1-HR]) Blast2GO description Genbank Accessions C228_s_at 48.018467 N.tabacum cysteine-rich extensin-like protein-4 mRNA EB683071 C1359_at 32.31786 Proteinase inhibitor I3, Kunitz legume, Kunitz inhibitor ST1-like DW004832 EB430244_x_at 22.426174 unknow EB430244 C10896_at 21.463442 dir1 (defective in induced resistance 1) lipid binding JF275847.1 BP528597_at 21.445984 Mitochondrial DNA BP528597 C10933_x_at 20.347004 Solanum nigrum clone 82 organ-specific protein S2 (OS) EB443218 TT31_B05_s_at 17.260008 Proteinase inhibitor I3, Kunitz legume, Kunitz inhibitor ST1-like C3546_s_at 17.171844 fasciclin-like arabinogalactan protein 2 EB451563 C8455_at 16.855278 Defective in induced resistance 2 protein (DIR2) BP530866 C11687_at 16.618454 galactinol synthase EB432401 BP136836_s_at 15.364014 Nicotiana tabacum mitochondrial DNA BP136836 BP525701_at 15.137816 Nicotiana tabacum mitochondrial DNA BP525701 EB682942_at 14.943408 Hop-interacting protein THI101 EB682942 BP133164_at 14.644844 Nicotiana tabacum mitochondrial DNA BP133164 AY055111_at 14.570147 Nicotiana tabacum pathogenesis-related protein PR10a AY055111 TT08_C02_at 14.375496 BP526999_at 14.374481 Nicotiana tabacum mitochondrial DNA BP526999 CV017694_s_at -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S. -
Metabolic Responses to Potassium Availability and Waterlogging in Two Oil- Producing Species: Sunflower and Oil Palm
Metabolic responses to potassium availability and waterlogging in two oil- producing species: sunflower and oil palm Jing Cui Supervisor: Prof. Guillaume Tcherkez A thesis submitted for the degree of Doctor of Philosophy The Australian National University Declaration Except where otherwise indicated, this thesis is my own original work. No portion of the work presented in this thesis has been submitted for another degree. Jing Cui Research School of Biology College of Medicine, Biology and Environment September, 2019 © Copyright by Jing Cui (2019). All Rights Reserved. 1 Acknowledgements Primarily my deepest thank goes to my principal supervisor Professor Guillaume Tcherkez (Research School of Biology, The Australian National University, Canberra), who has always given me help, advice and support throughout my PhD, Thank you very much for your enthusiasm, patience, efficience and guidance. One of the major motivations I committed to this PhD is your strong faith in me, I have been truly fortunate to work with you for the last three years. I thank my co-supervisor Dr. Emmanuelle Lamade (CIRAD, France), for your time, thoughtful comments and invaluable advice that they gave me along my project. Thank you also to my PhD committee members Dr. Adam Carroll (Research School of Chemistry and Biology Joint Mass Spectrometry Facility), Dr. Cyril Abadie, Dr. Hilary Stuart-Williams and Prof. Marilyn Ball (Research School of Biology, The Australian National University) for their help and guidance. I would like to thank Dr Thy Truong (Research School of Chemistry and Biology Joint Mass Spectrometry Facility) for taking the time to share with me her expertise in GC-MS, and look forward to working with her in LC/MSMS, also thank Dr.Marlène Davanture and Dr. -
Physiology of Deletion Mutants in the Anaerobic Β-Myrcene Degradation Pathway in Castellaniella Defragrans Frauke Lüddeke, Aytac Dikfidan and Jens Harder*
Lüddeke et al. BMC Microbiology 2012, 12:192 http://www.biomedcentral.com/1471-2180/12/192 RESEARCH ARTICLE Open Access Physiology of deletion mutants in the anaerobic β-myrcene degradation pathway in Castellaniella defragrans Frauke Lüddeke, Aytac Dikfidan and Jens Harder* Abstract Background: Monoterpenes present a large and versatile group of unsaturated hydrocarbons of plant origin with widespread use in the fragrance as well as food industry. The anaerobic β-myrcene degradation pathway in Castellaniella defragrans strain 65Phen differs from well known aerobic, monooxygenase-containing pathways. The initial enzyme linalool dehydratase-isomerase ldi/LDI catalyzes the hydration of β-myrcene to (S)-(+)-linalool and its isomerization to geraniol. A high-affinity geraniol dehydrogenase geoA/GeDH and a geranial dehydrogenase geoB/ GaDH contribute to the formation of geranic acid. A genetic system was for the first time applied for the betaproteobacterium to prove in vivo the relevance of the linalool dehydratase-isomerase and the geraniol dehydrogenase. In-frame deletion cassettes were introduced by conjugation and two homologous recombination events. Results: Polar effects were absent in the in-frame deletion mutants C. defragrans Δldi and C. defragrans ΔgeoA. The physiological characterization of the strains demonstrated a requirement of the linalool dehydratase-isomerase for growth on acyclic monoterpenes, but not on cyclic monoterpenes. The deletion of geoA resulted in a phenotype with hampered growth rate on monoterpenes as sole carbon and energy source as well as reduced biomass yields. Enzyme assays revealed the presence of a second geraniol dehydrogenase. The deletion mutants were in trans complemented with the broad-host range expression vector pBBR1MCS-4ldi and pBBR1MCS-2geoA, restoring in both cases the wild type phenotype. -
Supplementary Information
Supplementary Information The domain composition of sequences from Laurencia dendroidea that were annotated as terpene synthases and presented in Table 2 of the main manuscript were obtained through search for conserved domains using the NCBI Conserved Domain Database (CDD, [1]) and compared with the domain composition of corresponding sequences available in the SwissProt/UniProt and PlantCycDB databases. Analyzing the tables and figures below, we reinforce the Blast annotations presented in Table 2 of the main manuscript text, although biochemical and gene cloning approaches are necessary to prove these in silico identifications. For two of the 21 terpene synthase sequences from Laurencia (identified as nerolidol synthase and (+)-delta-cadinene synthase), we were not able to identify conserved domains, possibly because they were partial sequences. In the case of alpha-bisabolene synthase, we provide the domain composition of a reference sequence and the alignment of the sequence from L. dendroidea with this reference, showing a high similarity between them. Table S1. List of domain hits for a putative (3R)-linalool synthase gene from L. dendroidea. Name Accession Description Interval E-Value DNA repair protein (rad1); All proteins in this rad1 TIGR00596 1–51 1.04e-15 family for which functions are known are ... Figure S1. Conserved domains detected in a putative (3R)-linalool synthase gene from L. dendroidea (edited from the NCBI CDD database, [1]). Table S2. List of domain hits for the (3R)-linalool synthase gene from Zea mays mays (GDQC-116173-MONOMER—PlantCycDB). Name Accession Description Interval E-Value Plant Terpene Cyclases, Class 1; Terpene_cyclase_plant_C1 cd00684 This CD includes a diverse group of 1377–1833 9.57e-107 monomeric plant terpene ..