DOCSLIB.ORG

Chemical Biomarkers in Aquatic Ecosystems

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chemical Biomarkers in Aquatic Ecosystems December 28, 2010 Time: 10:31am fm.tex Chemical Biomarkers in Aquatic Ecosystems i This page intentionally left blank December 28, 2010 Time: 10:31am fm.tex Chemical Biomarkers in Aquatic Ecosystems THOMAS S. BIANCHI AND ELIZABETH A. CANUEL PRINCETON UNIVERSITY PRESS PRINCETON AND OXFORD iii December 28, 2010 Time: 10:31am fm.tex Copyright c 2011 by Princeton University Press Published by Princeton University Press, 41 William Street, Princeton, New Jersey 08540 In the United Kingdom: Princeton University Press, 6 Oxford Street, Woodstock, Oxfordshire OX20 1TW press.princeton.edu All Rights Reserved Library of Congress Cataloging-in-Publication Data Bianchi, Thomas S. Chemical biomarkers in aquatic ecosystems/Thomas S. Bianchi and Elizabeth A. Canuel. p. cm. Includes bibliographical references and index. ISBN 978-0-691-13414-7 (cloth : alk. paper) 1. Aquatic ecology. 2. Biochemical markers. I. Canuel, Elizabeth A., 1959– II. Title. QH541.5.W3B53 2011 577.6—dc22 2010029921 British Library Cataloging-in-Publication Data is available This book has been composed in Sabon and Din Pro Printed on acid-free paper. ∞ Typeset by S R Nova Pvt Ltd, Bangalore, India Printed in the United States of America 10987654321 iv December 28, 2010 Time: 10:31am fm.tex We dedicate this book to our spouses, Jo Ann Bianchi and Emmett Duffy, and our children, Christopher Bianchi and Conor Duffy, for their unending support and patience, without which we could never have completed this book. v This page intentionally left blank December 28, 2010 Time: 10:31am fm.tex Several current characteristics of organic geochemical research serve to limit advances toward a deeper understanding of global biogeochemical cycles. For the most part, these problems are shared by all organic geochemists (author included), but are not unique to our guild. The first of these is that geochemical research is decidedly provincial. That is, functionally similar processes occurring in weathering rocks, soils, lakes, rivers and the ocean tend to be studied by different types of geochemists with dissimilar backgrounds, terminologies and methodologies. This geographic specialization has limited the scope of both our fieldwork and insight, and has resulted in lost research and interpretive opportunities. At present, there is insufficient information to obtain unique solutions at the global scale, even for bulk carbon. The main constraint is that meaningful rate constants for in situ degradation within key environment are not known. — John I. Hedges, 1992 vii This page intentionally left blank December 28, 2010 Time: 10:31am fm.tex Contents Preface xi Acknowledgments xix 1. Metabolic Synthesis 1 2. Chemical Biomarker Applications to Ecology and Paleoecology 19 3. Stable Isotopes and Radiocarbon 30 4. Analytical Chemical Methods and Instrumentation 49 5. Carbohydrates: Neutral and Minor Sugars 79 6. Proteins: Amino Acids and Amines 98 7. Nucleic Acids and Molecular Tools 127 8. Lipids: Fatty Acids 144 9. Isoprenoid Lipids: Steroids, Hopanoids, and Triterpenoids 169 10. Lipids: Hydrocarbons 185 11. Lipids: Alkenones, Polar Lipids, and Ether Lipids 207 12. Photosynthetic Pigments: Chlorophylls, Carotenoids, and Phycobilins 221 13. Lignins, Cutins, and Suberins 248 14. Anthropogenic Markers 267 Appendix I. Atomic Weights of Elements 287 Appendix II. Useful SI Units and Conversion Factors 291 Appendix III. Physical and Chemical Constants 293 Glossary 295 Bibliography 309 Index 385 This page intentionally left blank Preface Due to the complexity of organic matter sources in aquatic systems, the application of chemical biomarkers has become widespread in limnology and oceanography. We define biomarker molecules in this book as compounds that characterize certain biotic sources and selectively retain their source information, even after stages of decomposition and diagenesis (after Meyers, 2003). Hence, the term biomarker molecule should not be confused with the terms commonly used by ecotoxicologists or molecular biologists (see Timbrell, 1998; Wilson and Suk, 2002; Decaprio, 2006, and references therein). Early definitions of biological markers, or simply biomarkers or chemical biomarkers, described these compounds as molecular fossils derived from formerly living organisms (Eglinton et al., 1964; Eglinton and Calvin, 1967). More recently, biomarkers have been defined as complex organic compounds composed of carbon, hydrogen, and other elements, which occur in sediments, rocks, and crude oils, and show little to no change in their chemical structure from their precursor molecules that once existed in living organisms (Hunt et al., 1996; Peters et al., 2005; Gaines et al., 2009). Biomarkers have also been defined recently as lipid components found within bitumen in coal as well as kerogens that provide an unambiguous link to biological precursor compounds, because of their stability through diagenesis and catagenesis (Killops and Killops, 2005; Gaines et al., 2009). Additionally, the term geolipid has commonly been used to describe decay-resistant biomarkers in sediments because lipids are typically recalcitrant compared with other biochemical components of organic matter, making them more long- lived in the sedimentary record (Meyers, 1997). The first convincing linkage made between geolipids and living organisms was made by Treibs (1934), when a correlation was made between chlorophyll a in photosynthetic organisms and porphyrins in petroleum. This important discovery essentially marked the beginning of organic geochemistry. Chemical biomarkers have provided numerous insights about present and past aspects of Earth history, including (1) the food and energy sources available to microbes and higher organisms, (2) microbial chemotaxonomy, (3) sources of fossil fuels, and (4) the evolution of life on Earth. A greater knowledge of the biogeochemical cycling of organic matter, which involves the transformation, fate, and transport of chemical substances, is critical in understanding the effects of natural and human- induced environmental changes—from a regional and global context. Approaching aquatic sciences from a biogeochemical perspective requires a fundamental understanding in the biochemistry of organic matter. Our motivation for writing this book is that many of the books on chemical biomarkers are edited volumes, too diffuse and difficult to use as textbooks for advanced undergraduate and graduate courses. We also wanted to develop a book with examples of the applications of biomarkers to a range of aquatic environments, including riverine, estuarine, and oceanic ecosystems. December 28, 2010 Time: 10:31am fm.tex xii I Preface This book is designed for advanced undergraduate and graduate level classes in aquatic and marine biogeochemistry, organic geochemistry, and global ecosystem dynamics. Prerequisites for such a course may include introductory courses in inorganic and organic chemistry, oceanography and/or limnology, and environmental and/or ecosystem ecology. The book should also prove to be a valuable resource for researchers in limnological, estuarine, marine, and environmental sciences. The basic organization of the book is derived from classes we have taught in global biogeochemistry, organic geochemistry, and marine/estuarine biogeochemistry. It is structured around individual classes of biomarkers, with each chapter describing the structure and synthesis of each class of compounds, their reactivity, and examples of specific applications for each class of biomarkers. In chapter 1, we provide a general background on the synthesis of chemical biomarkers and their association with key metabolic pathways in organisms, as related to differences in cellular structure and function across the three domains of life. We discuss photosynthesis, the dominant pathway by which biomass is synthesized. Additionally, we present information about chemoautotrophic and microbial heterotrophic processes. The holistic view of biosynthetic pathways of chemical biomarkers here also provides a roadmap for other chapters in the book, where more specific details on chemical pathways are presented for each of the respective biomarker groups. While other organic geochemistry books have generally introduced the concepts of chemical biomarkers in the context of physical and chemical gradients found in natural ecosystems (e.g., anaerobic, aerobic), we begin by examining biosynthetic pathways at the cellular level of differentiation. Chapter 2 provides a brief historical account of the success and limitations of using chemical biomarkers in aquatic ecosystems. This chapter also introduces the general concepts of chemical biomarkers as they relate to global biogeochemical cycling. The application of chemical biomarkers in modern and/or ancient ecosystems is largely a function of the inherent structure and stability of the molecule, as well as the physicochemical environment of the system wherein it exists. In some cases, redox changes in sediments have allowed for greater preservation of biomarker compounds; in well- defined laminated sediments, for example, a strong case can be made for paleo-reconstruction of past organic matter composition sources. However, many of the labile chemical biomarkers may be lost or transformed within minutes to hours of being released from the cell from processes such as bacterial and/or metazoan grazing, cell lysis, and photochemical breakdown, just to name a few. The role of trophic effects versus large-scale physiochemical gradients in preserving or destroying the integrity of chemical
Load more

Recommended publications
  • Chlorophyll Biosynthesis
    Chlorophyll Biosynthesis: Various Chlorophyllides as Exogenous Substrates for Chlorophyll Synthetase Jürgen Benz and Wolfhart Rüdiger Botanisches Institut, Universität München, Menziger Str. 67, D-8000 München 19 Z. Naturforsch. 36 c, 51 -5 7 (1981); received October 10, 1980 Dedicated to Professor Dr. H. Merxmüller on the Occasion of His 60th Birthday Chlorophyllides a and b, Protochlorophyllide, Bacteriochlorophyllide a, 3-Acetyl-3-devinylchlo- rophyllide a, Pyrochlorophyllide a, Pheophorbide a The esterification of various chlorophyllides with geranylgeranyl diphosphate was investigated as catalyzed by the enzyme chlorophyll synthetase. The enzyme source was an etioplast membrane fraction from etiolated oat seedlings ( Avena sativa L.). The following chlorophyllides were prepared from the corresponding chlorophylls by the chlorophyllase reaction: chlorophyllide a (2) and b (4), bacteriochlorophyllide a (5), 3-acetyl-3-devinylchlorophyllide a (6), and pyro­ chlorophyllide a (7). The substrates were solubilized with cholate which reproducibly reduced the activity of chlorophyll synthetase by 40-50%. It was found that the following compounds were good substrates for chlorophyll synthetase: chlorophyllide a and b, 3-acetyl-3-devinylchloro- phyllide a, and pyrochlorophyllide a. Only a poor or no reaction was found with protochloro­ phyllide, pheophorbide a, and bacteriochlorophyllide. This difference of reactivity was not due to distribution differences of the substrates between solution and pelletable membrane fraction. Furthermore, no interference between good and poor substrate was detected. Structural features necessary for chlorophyll synthetase substrates were discussed. Introduction Therefore no exogenous 2 was applied. The only substrate was 2 formed by photoconversion of endo­ The last steps of chlorophyll a (Chi a) biosynthe­ genous Protochlide (1) in the etioplast membrane.
    [Show full text]
  • Antibacterial Photosensitization Through Activation of PNAS PLUS Coproporphyrinogen Oxidase
    Antibacterial photosensitization through activation of PNAS PLUS coproporphyrinogen oxidase Matthew C. Surdela, Dennis J. Horvath Jr.a, Lisa J. Lojeka, Audra R. Fullena, Jocelyn Simpsona, Brendan F. Dutterb,c, Kenneth J. Sallenga, Jeremy B. Fordd, J. Logan Jenkinsd, Raju Nagarajane, Pedro L. Teixeiraf, Matthew Albertollec,g, Ivelin S. Georgieva,e,h, E. Duco Jansend, Gary A. Sulikowskib,c, D. Borden Lacya,d, Harry A. Daileyi,j,k, and Eric P. Skaara,1 aDepartment of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232; bDepartment of Chemistry, Vanderbilt University, Nashville, TN 37232; cVanderbilt Institute for Chemical Biology, Nashville, TN 37232; dDepartment of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232; eVanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232; fBiomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203; gDepartment of Biochemistry, Vanderbilt University, Nashville, TN 37232; hDepartment of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232; iBiomedical and Health Sciences Institute, University of Georgia, Athens, GA 30602; jDepartment of Microbiology, University of Georgia, Athens, GA 30602; and kDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 Edited by Ferric C. Fang, University of Washington School of Medicine, Seattle, WA, and accepted by Editorial Board Member Carl F. Nathan June 26, 2017 (received for review January 10, 2017) Gram-positive bacteria cause the majority of skin and soft tissue Small-molecule VU0038882 (‘882) was previously identified in infections (SSTIs), resulting in the most common reason for clinic a screen for activators of the S. aureus heme-sensing system two- visits in the United States.
    [Show full text]
  • Impacts of Desulfobacterales and Chromatiales on Sulfate Reduction in The
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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-ND 4.0 International license. 1 Impacts of Desulfobacterales and Chromatiales on sulfate reduction in the 2 subtropical mangrove ecosystem as revealed by SMDB analysis 3 Shuming Mo 1, †, Jinhui Li 1, †, Bin Li 2, Ran Yu 1, Shiqing Nie 1, Zufan Zhang 1, Jianping 4 Liao 3, Qiong Jiang 1, Bing Yan 2, *, and Chengjian Jiang 1, 2 * 5 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro- 6 bioresources, Guangxi Research Center for Microbial and Enzyme Engineering 7 Technology, College of Life Science and Technology, Guangxi University, Nanning 8 530004, China. 9 2 Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove 10 Research Center, Guangxi Academy of Sciences, Beihai 536000, China. 11 3 School of Computer and Information Engineering, Nanning Normal University, 12 Nanning 530299, China. 13 † These authors contributed equally to this work. 14 *: Corresponding Author: 15 Tel: +86-771-3270736; Fax: +86-771-3237873 16 Email: [email protected] (CJ); [email protected] (BY) 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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.
    [Show full text]
  • Rodríguez-Concepción, M. Et Al. a Global Perspective on Carotenoids
    This is the accepted version of the following article: Rodríguez-Concepción, M. et al. A global perspective on carotenoids: metabolism, biotechnology, and benefits for nutrition and health in Progress in lipid research (Ed. Elsevier), vol. 70 (April 2018), p. 62-93 Which has been published in final form at DOI 10.1016/j-plipres.2018.04.004 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ A global perspective on carotenoids: metabolism, biotechnology, and benefits for nutrition and health. Manuel RODRIGUEZ CONCEPCIONa,*, Javier AVALOSb, M. Luisa BONETc, Albert BORONATa,d, Lourdes GOMEZ-GOMEZe, Damaso HORNERO-MENDEZf, M. Carmen LIMONb, Antonio J. MELÉNDEZ-MARTÍNEZg, Begoña OLMEDILLA-ALONSOh, Andreu PALOUc, Joan RIBOTc, Maria J. RODRIGOi, Lorenzo ZACARIASi, Changfu ZHUj a, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain. b, Department of Genetics, Universidad de Sevilla, 41012 Seville, Spain. c, Laboratory of Molecular Biology, Nutrition and Biotechnology, Universitat de les Illes Balears; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn); and Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain. d, Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain e, Instituto Botánico, Universidad de Castilla-La Mancha, 02071 Albacete, Spain. f, Department of Food Phytochemistry, Instituto de la Grasa (IG-CSIC), 41013 Seville, Spain. g, Food Color & Quality Laboratory, Area of Nutrition & Food Science, Universidad de Sevilla, 41012 Seville, Spain. h, Institute of Food Science, Technology and Nutrition (ICTAN-CSIC), 28040 Madrid, Spain. i, Institute of Agrochemistry and Food Technology (IATA-CSIC), 46980 Valencia, Spain.
    [Show full text]
  • Phyllobilins – the Abundant Bilin-Type Tetrapyrrolic Catabolites Of
    Chemical Society Reviews Phyllobilins – the Abundant Bilin -Type Tetrapyrrolic Catabolites of the Green Plant Pigment Chlorophyll Journal: Chemical Society Reviews Manuscript ID: CS-TRV-02-2014-000079.R1 Article Type: Tutorial Review Date Submitted by the Author: 02-May-2014 Complete List of Authors: Krautler, Bernhard; University of Innsbruck, Institute of Organic Chemistry Page 1 of 30 Chemical Society Reviews Phyllobilins-TutRev-BKräutler 2-May-14 1 Phyllobilins – the Abundant Bilin-type Tetrapyrrolic Catabolites of the Green Plant Pigment Chlorophyll Bernhard Kräutler Institute of Organic Chemistry and Centre of Molecular Biosciences, University of Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria E-mail: [email protected] Abstract . The seasonal disappearance of the green plant pigment chlorophyll in the leaves of deciduous trees has long been a fascinating biological puzzle. In the course of the last two and a half decades, important aspects of the previously enigmatic breakdown of chlorophyll in higher plants were elucidated. Crucial advances in this field were achieved by the discovery and structure elucidation of tetrapyrrolic chlorophyll catabolites, as well as by complementary biochemical and plant biological studies. Phyllobilins, tetrapyrrolic, bilin-type chlorophyll degradation products, are abundant chlorophyll catabolites, which occur in fall leaves and in ripe fruit. This tutorial review outlines ‘how’ chlorophyll is degraded in higher plants, and gives suggestions as to ‘why’ the plants dispose of their valuable green pigments during senescence and ripening. Insights into chlorophyll breakdown help satisfy basic human curiosity and enlighten school teaching. They contribute to fundamental questions in plant biology and may have practical consequences in agriculture and horticulture.
    [Show full text]
  • Exploring the Lipidomes of Shallow-Water and Deep-Sea Hydrothermal Systems
    Exploring the lipidomes of shallow-water and deep-sea hydrothermal systems Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - Am Fachbereich Geowissenschaften der Universität Bremen vorgelegt von Miriam Sollich Bremen Mai 2018 1. Gutachter: Dr. Solveig I. Bühring 2. Gutachter: Associate Prof. Dr. Eoghan P. Reeves Tag des Promotionskolloquiums:16. Februar 2018 Den Wissenschaftlern geht es wie den Chaoten. Es ist alles da, man muss es nur suchen. - Franz Kern - CONTENTS Abstract Zusammenfassung Acknowledgements List of Abbreviations Chapter I 1 Introduction and Methods Chapter II 37 Scope and Outline Chapter III 43 Heat stress dictates the microbial lipid composition along a thermal gradient in marine sediments Chapter IV 91 Shallow-water hydrothermal systems offer ideal conditions to study archaeal lipid membrane adaptations to environmental extremes Chapter V 113 Transfer of chemosynthetic fixed carbon and its ecological significance revealed by lipid analysis of fluids at diffuse flow deep-sea vents (East Pacific Rise 9°50’N) Chapter VI 143 Concluding Remarks and Future Perspectives ABSTRACT Shallow-water and deep-sea hydrothermal systems are environments where seawater percolates downward through fractures in the oceanic crust, and becomes progressively heated and chemically altered. Finally, the entrained water is expelled into the overlying water column as a hydrothermal fluid. Hydrothermal circulation occurs at all active plate boundaries like mid-ocean ridges, submarine volcanic arcs and backarc basins. They represent one of the most extreme and dynamic ecosystems on the planet with steep physico-chemical gradients. Nevertheless, these environments are characterized by exceptional high biomass representing hotspots of life in the mostly hostile and desolated deep sea.
    [Show full text]
  • High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-Methylalkyl)Succinate Synthase Genes
    ORIGINAL RESEARCH published: 07 January 2016 doi: 10.3389/fmicb.2015.01511 High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes Marion H. Stagars1,S.EmilRuff1,2† , Rudolf Amann1 and Katrin Knittel1* 1 Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany, 2 HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany Edited by: Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. Hans H. Richnow, These environments are typically anoxic and host diverse microbial communities that Helmholtz Centre for Environmental Research, Germany grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation Reviewed by: is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here Beth Orcutt, we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine Bigelow Laboratory for Ocean sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well Sciences, USA Zhidan Liu, as to identify factors structuring the alkane-degrading community. Using next generation China Agricultural University, China sequencing we obtained a total of 420 MasD species-level operational taxonomic units *Correspondence: (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and Katrin Knittel [email protected] evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD †Present address: community structure is clearly driven by the hydrocarbon source available at the various S.
    [Show full text]
  • Advance View Proofs
    M&E Papers in Press. Published online on March 23, 2012 doi:10.1264/jsme2.ME11357 1 2 Revised ME11357 3 4 Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of 5 Anaerobic Degradation of p-Xylene 6 * 7 YURIKO HIGASHIOKA, HISAYA KOJIMA , AND MANABU FUKUI 8 9 The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, 10 Kita-ku, Sapporo, Hokkaido 060-0819, Japan 11 Proofs 12 (Received December 21, 2011-Accepted February 2, 2012) 13 View 14 Running headline: p-Xylene-Degrading Sulfate Reducer 15 16 * Corresponding author. E-mail: [email protected]; Tel: 17 +81-11-706-5460;Advance Fax: +81-11-706-5460. 18 19 20 21 1 Copyright 2012 by the Japanese Society of Microbial Ecology / the Japanese Society of Soil Microbiology 22 A novel strain of p-xylene-degrading sulfate reducer was isolated in pure culture. 23 Strain PP31 was obtained from a p-xylene-degrading enrichment culture established 24 from polluted marine sediment. Analyses of the 16S rRNA gene and two functional 25 genes involved in sulfate respiration and anaerobic degradation of aromatic compounds 26 revealed that the isolate was closely related to members of the genus Desulfosarcina. 27 Strain PP31 was capable of growing on p-xylene under sulfate-reducing conditions, and 28 the ratio of generated sulfide and consumed p-xylene suggested complete oxidation by 29 the novel isolate. The strain could not grow on benzene, toluene, ethylbenzene, 30 m-xylene o-xylene, or n-hexane as an electron donor. Strain PP31 is the first isolated 31 bacterium that degrades p-xylene anaerobically, and will be useful to understanding the 32 mechanism of anaerobic degradation of p-xylene.
    [Show full text]
  • Carotenoids in Algae: Distributions, Biosyntheses and Functions
    Mar. Drugs 2011, 9, 1101-1118; doi:10.3390/md9061101 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Review Carotenoids in Algae: Distributions, Biosyntheses and Functions Shinichi Takaichi Department of Biology, Nippon Medical School, Kosugi-cho, Nakahara, Kawasaki 211-0063, Japan; E-Mail: [email protected]; Tel.: +81-44-733-3584; Fax: +81-44-733-3584 Received: 2 May 2011; in revised form: 31 May 2011 / Accepted: 8 June 2011 / Published: 15 June 2011 Abstract: For photosynthesis, phototrophic organisms necessarily synthesize not only chlorophylls but also carotenoids. Many kinds of carotenoids are found in algae and, recently, taxonomic studies of algae have been developed. In this review, the relationship between the distribution of carotenoids and the phylogeny of oxygenic phototrophs in sea and fresh water, including cyanobacteria, red algae, brown algae and green algae, is summarized. These phototrophs contain division- or class-specific carotenoids, such as fucoxanthin, peridinin and siphonaxanthin. The distribution of α-carotene and its derivatives, such as lutein, loroxanthin and siphonaxanthin, are limited to divisions of Rhodophyta (macrophytic type), Cryptophyta, Euglenophyta, Chlorarachniophyta and Chlorophyta. In addition, carotenogenesis pathways are discussed based on the chemical structures of carotenoids and known characteristics of carotenogenesis enzymes in other organisms; genes and enzymes for carotenogenesis in algae are not yet known. Most carotenoids bind to membrane-bound pigment-protein complexes, such as reaction center, light-harvesting and cytochrome b6f complexes. Water-soluble peridinin-chlorophyll a-protein (PCP) and orange carotenoid protein (OCP) are also established. Some functions of carotenoids in photosynthesis are also briefly summarized. Keywords: algal phylogeny; biosynthesis of carotenoids; distribution of carotenoids; function of carotenoids; pigment-protein complex 1.
    [Show full text]
  • Pigment-Based Chloroplast Types in Dinoflagellates
    Vol. 465: 33–52, 2012 MARINE ECOLOGY PROGRESS SERIES Published September 28 doi: 10.3354/meps09879 Mar Ecol Prog Ser Pigment-based chloroplast types in dinoflagellates Manuel Zapata1,†, Santiago Fraga2, Francisco Rodríguez2,*, José L. Garrido1 1Instituto de Investigaciones Marinas, CSIC, c/ Eduardo Cabello 6, 36208 Vigo, Spain 2Instituto Español de Oceanografía, Subida a Radio Faro 50, 36390 Vigo, Spain ABSTRACT: Most photosynthetic dinoflagellates contain a chloroplast with peridinin as the major carotenoid. Chloroplasts from other algal lineages have been reported, suggesting multiple plas- tid losses and replacements through endosymbiotic events. The pigment composition of 64 dino- flagellate species (122 strains) was analysed by using high-performance liquid chromatography. In addition to chlorophyll (chl) a, both chl c2 and divinyl protochlorophyllide occurred in chl c-con- taining species. Chl c1 co-occurred with chl c2 in some peridinin-containing (e.g. Gambierdiscus spp.) and fucoxanthin-containing dinoflagellates (e.g. Kryptoperidinium foliaceum). Chl c3 occurred in dinoflagellates whose plastids contained 19’-acyloxyfucoxanthins (e.g. Karenia miki- motoi). Chl b was present in green dinoflagellates (Lepidodinium chlorophorum). Based on unique combinations of chlorophylls and carotenoids, 6 pigment-based chloroplast types were defined: Type 1: peridinin/dinoxanthin/chl c2 (Alexandrium minutum); Type 2: fucoxanthin/ 19’-acyloxy fucoxanthins/4-keto-19’-acyloxy-fucoxanthins/gyroxanthin diesters/chl c2, c3, mono - galac to syl-diacylglycerol-chl c2 (Karenia mikimotoi); Type 3: fucoxanthin/19’-acyloxyfucoxan- thins/gyroxanthin diesters/chl c2, c3 (Karlodinium veneficum); Type 4: fucoxanthin/chl c1, c2 (K. foliaceum); Type 5: alloxanthin/chl c2/phycobiliproteins (Dinophysis tripos); Type 6: neoxanthin/ violaxanthin/a major unknown carotenoid/chl b (Lepidodinium chlorophorum).
    [Show full text]
  • Uva-DARE (Digital Academic Repository)
    UvA-DARE (Digital Academic Repository) Pharmacological and physiological functions of polyspecific drug transporters Jonker, J.W. Publication date 2003 Link to publication Citation for published version (APA): Jonker, J. W. (2003). Pharmacological and physiological functions of polyspecific drug transporters. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:01 Oct 2021 Chapterr 4 Thee breast cancer resistance protein protects against a major chlorophyll-derivedd dietary phototoxin andd protoporphyria Johann W. Jonker, Marije Buitelaar, Els Wagenaar, Martin A. van der Valk, Georgee L. Scheffer, Rik J. Scheper, Torsten Plösch, Folkert Kuipers, Ronaldd P.J. Oude Elferink, Hilde Rosing, Jos H. Beijnen and Alfred H. Schinkel Proc.Proc. Natl. Acad. Set. USA (2002) 99: 15649-J5654 BCRPBCRP protects against a dietary phototo.xin Thee breast cancer resistance protein protects against aa major chlorophyll-derived dietary phototoxin andd protoporphyria Johann W.
    [Show full text]
  • Advances on Antioxidants in Research and Applications
    E3S Web of Conferences 131, 01009 (2019) https://doi.org/10.1051/e3sconf/201913101009 ChinaBiofilms 2019 Advances on antioxidants in research and applications Ruirui Song1, Qi Wu1,a, Lin Zhao1 and Zhenyu Yun1 1 China National Institute of Standardization, Institute of Food and Agriculture Standardization, No.4 Zhi Chun Road, Haidian District, Beijing, China Abstract. Antioxidants play a significant role in the prevention and treatment of numerous chronic diseases as they prevent oxidative stress and maintain reduction-oxidation (redox) equilibrium in the human body by eliminating reactive free radicals effectively. This study focused on the types and applications of antioxidants and discussed the existing problems with regard to the practical applications of antioxidants. Also, it presented a review of the latest research on antioxidants in China and abroad and performed a comprehensive, objective analysis of relevant research on antioxidants. 1 Introduction related cell functions and bring cardiovascular plaques to the heart. Fruit and vegetables are good sources of As the standard of living improves, the global average dietary fiber, minerals, and trace elements and contain a life expectancy has increased and yet, there are still a variety of active antioxidants. An adequate intake of huge number of deaths in relation to noninfectious high-antioxidants fruit and vegetables is a major diseases such as cardiovascular disease, stroke, diabetes, approach to maintain redox balance in the body [6]. The and cancer [1]. A previous study shows that these WHO recommends a minimum of 400 g of fruit and chronic diseases are associated with oxidative stress vegetables per day for the prevention of chronic diseases caused by free radicals, and antioxidants allow for the and supplement of trace elements [7].
    [Show full text]