Table Of Content

Klaus Urich Comparative Animal Biochemistry Translated from the German by Patrick J. King With 248 Illustrations by Charlotte Urich and 87 Tables Springer-Verlag Berlin Heidelberg GmbH Author Professor Dr. Klaus Urich Universităt Mainz Institut rur Zoologie Niklas-Vogt-StraBe 25 D-55131 Mainz Translator Dr. Patrick J. King Stutzackerweg 8 CH-3110 Miinsingen TItie of the German Edition Klaus Urich, Vergleichende Biochemie der Tiere ISBN 978-3-642-08181-1 © Gustav Fischer Verlag . Stuttgart . New York 1990 Illustration: Dr. Charlotte Urich, Niklas-Vogt-StraBe 25, D-55131 Mainz Cover Illustration: The illustration on the front cover shows the symbiosis between the sea anemone Radianthus kueckenthali and the fish Amphiprion peri deraion: The signal substance amphikuemine that is produced by the sea anemone attracts the fish even at a concentration of 10-10 mollL. Library of Congress Cataloging-in-Publication Data Urich, Klaus, 1926- [Vergleichende Biochemie der Tiere. English] Comparative animal biochemistry I Klaus Urich ; translated'from the German by Patrick J. King. p. cm. Inc1udes bibliographical references and index. ISBN 978-3-642-08181-1 ISBN 978-3-662-06303-3 (eBook) DOI 10.1007/978-3-662-06303-3 1. Biochemistry. 2. Physiology, Comparative. I. Title. QP514.2.U7513 1994 591.19'2-dc20 94-7808 This work is subject to copyright. Ali rights are reserved, whether the whole or part of the material is con cemed, specifically the rights of translation, reprinting, reuse of illustrations, recitations, broadcasting, repro duction on microfilms or in other ways, and storage in data banks. Duplication of this publication or parts thereof is only permitted under the provisions of the German Copyright Law of September 9,1965, in its ver sion of June 24, 1985, and a copyright fee must always be paid, Violations fali under the prosecution act of the German Copyright Law. © Springer-Verlag Berlin Heidelberg 1994 Originally published by Springer-Verlag Berlin Heidelberg New York in 1994 Softcover reprint of the hardcover l st edition 1994 The use of registered names, trademarks, etc. in the publication does not imply, even in the absence of a spe cific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Product Liability: The publisher can give no guarantee for information about drug dosage and application thereof contained in this book. In every individual case the respective user must check its accuracy by consult ing other pharmaceuticalliterature. Cover: E. Kirchner, Heidelberg Typesetting: Mitterweger Werksatz GmbH, Plankstadt bei Heidelberg SPIN 10041846 3113130 - 5 4 3 2 1 O - Printed on acid-free paper Dedicated to the memory of Prof. Dr. Bernt Linzen (8.6.1931 - 5.8.1988) Preface The plan for this book goes back almost 20 years. tribute greatly to understanding the origins of Already, at that time, it was possible to recognize organisms. an extraordinary variation in metabolites and To provide the biochemist with a ready over processes superimposed upon the basic biochem view of the structural diversity of animals, the ical system of animals. Each species, each indi book includes a simplified version of animal sys vidual, in fact each type of cell of the multicellu tematics; for further information on the classifica lar organism possesses its own biochemical char tion, structure and life of particular animal spe acter, and this molecular variety, its biological sig cies, the reader should consult the relevant text nificance, and its evolutionary development books. It is assumed that the zoologist reader has throw up many interesting questions. The com a basic knowledge of biochemistry; important parative approach that has been so productive at general biochemical facts are in any case given for the higher levels of complexity of morphology many of the subjects covered. and physiology can also be used to great effect at I had already completed several chapters of the molecular level. this book by the beginning of the 1970s. Because There are countless papers, reviews and other of far-reaching changes in my employment condi articles on the subject of comparative biochem tions and duties as a high-school teacher, my istry and evolution, but no actual textbook. This transfer from Berlin to Mainz, and the task of set is remarkable in so far as each area of science is ting up a working group there, work on this book only really defined by its comprehensive repre was interrupted and could only be resumed in the sentation in the literature. In the present book, I 1980s. In the meantime, the data to be considered have given my view of the starting points and the had increased enormously; molecular biology, in content of comparative biochemistry. I would be particular, had produced a gigantic body of rele glad if further, related efforts by other authors vant data. Today, a single person can no longer would follow this attempt at a definition of the keep track of all aspects of comparative bio subject. In the widest sense, a comparative bio chemistry. chemistry should consider all organisms, but my And so arises the well-known dilemma: the knowledge of the biochemistry of the bacteria, portrayal of a large area of science by one or a algae, lower fungi and higher plants is unfortun few authors inevitably leaves gaps and deficien ately not sufficient for this purpose. In any case, cies; one book with contributions from many most of the available comparative biochemistry authors generally leaves much to be desired in data refer to animals. uniformity and consistency. When I decided, This book is directed at zoologists as well as according to the original plan, to attempt as a biochemists. Biochemists may discover that mo single author to bring together the whole of com lecular variation, though perhaps a complication parative biochemistry, the unavoidable deficien for general biochemical research, is in itself a fas cies were very clear to me. I would be very grate cinating scientific problem. Zoologists will find ful for any critical comments on gaps and mis that the molecular building blocks of animals dis takes in this presentation, but I would ask play just as much colourful variation as do micros biochemically oriented readers to judge the copic or macroscopic structures. They will see whole work· and not only those sections most that molecular variants can be understood partly familiar to them. I have researched the literature as adaptations to particular environmental condi up to the middle of 1988, but the reference lists tions and partly as the result of diversification given for each chapter do not include the whole along separate evolutionary lines. Finally, it will of the consulted literature; this would require too be seen that biochemical characters can con- much space. Rather, I have referred to the latest VIII Preface works and this should allow the reader access to Finally, I would like to thank all those who earlier and original papers. directly or indirectly have contributed to the pro There are particular problems associated with duction of this book. My family, my students and biochemical terminology and the names of or my examination candidates have shown much ganisms, as well as with the use of abbreviations patience with me during the years of work on the and symbols. Here, I have attempted on the one manuscript. My wife has, in addition, contrib hand to be consistent, but on tlie other hand to uted directly to the book by preparing the fig diverge as little as possible from the terminology ures. Particular thanks go to my secretary, Inge of the original authors. Some remarks on bio Pullig, and to Dr. Jens Beyer and Prof. Erhard chemical nomenclature and the use of abbrevi Thomas, who took over many of my duties to ations are to be found at the end of the book; the allow me time for this literary effort. I would also letter symbols for amino acids, other common like to thank the many colleagues who have given abbreviations, and the genetic code are repro me reprints or who have critically read parts of duced on the bookmark. the manuscript. Many areas of comparative biochemistry are Prof. Bernt Linzen played a decisive role in the still in the fact-collecting stage, and the present creation of the book through his constructive book is a compromise between the desires to criticism, intelligent advice and encouraging com achieve a certain completeness and to avoid boring ments but did not live to see its completion. I lists. The reader will notice that special cases, out dedicate this work to the memory of this eminent side of the norm, and entertaining exceptions give researcher who contributed so much to compara me particular pleasure. The colourful diversity of tive biochemistry. molecular structures and processes in animals has always fascinated me. If I succeed in conveying just a part of this fascination to the reader, then this book will have fulfilled its purpose. Mainz, Autumn 1989 KLAUS URICH Preface to the English Edition The basic idea of the book and the disposition of than July 1988 and so were not contained in the chapters has not been changed from that of the German version. As it was not possible to aug German edition of 1990. The rapid progress in ment the total number of references, because of general and comparative biochemistry, however, space limitations, a corresponding number of had made it necessary to actualize the text and older references have been omitted. incorporate the many new facts and ideas that I wish to thank Springer Verlag for generous have emerged since summer 1988 when the Ger cooperation during the preparation of the English man edition was completed. edition. I feel particulary grateful to Dr. Patrick J. In preparing the revised version, I have King who has succeded admirably in translating researched completely the original literature up the author's sometimes rather individual German to the end of 1991. As in the German edition, the into good English and so has helped to propagate references given in each chapter always refer to further ideas of comparative biochemistry. the latest works, and this could allow the reader access to earlier papers. Of a total of more than 4600 references, about 2100 were published later Mainz, Spring 1993 KLAUS URICH Contents Preface . . . . . . . . . . . . . . . . . . . . . . . VII 2.3.5 The Retroposons of Vertebrates . .. 23 Preface to the English Edition . . . . . . . . IX 2.3.6 Retropseudogenes . . . . . . . . . . .. 25 2.4 Size of the Genome . . . . . . . . . .. 25 2.4.1 The DNA Content of Haploid 1 The Subject Matter and Methods Genomes (the C Value). . . . . . . .. 25 of Comparative Biochemistry. . .. 1 2.4.2 Increase and Decrease in the DNA 1.1 Historical Development of the Content of Individual Cells . . . . .. 27 Comparative Approach in Biology.. 1 2.5 Chromatin Proteins . . . . . . . . . .. 28 1.2 Uniformity and Diversity 2.5.1 Structure and Evolution in Biochemistry . . . . . . . . . . . . .. 2 of the Histones . . . . . . . . . . . . .. 29 1.3 The Subjects of Comparative 2.5.2 The Histone Genes . . . . . . . . . .. 30 Biochemistry. . . . . . . . . . . . . . .. 3 2.5.3 Variability of the Histones . . . . . .. 32 1.3.1 Comparison of Low Molecular 2.5.4 Protamines . . . . . . . . . . . . . . . .. 33 Weight Substances . . . . . . . . . . .. 4 2.5.5 Non-Histone Proteins. . . . . . . . .. 34 1.3.2 Comparison of Information- 2.6 DNA Replication and Repair. . . .. 35 Carrying Macromolecules . . . . . .. 4 2.7 Transcription and RNA 1.4 Chance and Necessity Maturation. . . . . . . . . . . . . . . .. 37 in Molecular Evolution . . . . . . . .. 5 2.7.1 RNA Polymerases . . . . . . . . . . .. 37 1.4.1 Non-Adaptive ("Neutral") 2.7.2 Transcription. . . . . . . . . . . . . . .. 37 Differences. . . . . . . . . . . . . . . .. 5 2.7.3 Maturation of the Primary 1.4.2 Molecular Adaptation. . . . . . . . .. 6 Transcripts (RNA Processing). . . .. 38 References . . . . . . . . . . . . . . . .. 7 2.7.4 Production of Multiple Transcripts of a Gene .................. 40 2.7.5 Regulation of Transcription . . . . .. 41 2 Nucleic Acids 2.7.6 Heat-Shock Genes and Heat-Shock and Nuclear Proteins . . . . . . . .. 9 Proteins. . . . . . . . . . . . . . . . . .. 43 2.1 The Structure of Chromosomal 2.8 Ribonucleic Acids DNA ..................... 9 and Ribonucleoproteins . . . . . . .. 44 2.1.1 Conformation and Composition. .. 10 2.8.1 The rRNA Genes 2.1.2 Base Sequence and Their Transcription . . . . . . . .. 45 and Gene Structure . . . . . . . . . .. 11 2.8.2 Structure of rRNAs . . . . . . . . . .. 47 2.1.3 The Genetic Code. . . . . . . . . . .. 13 2.8.3 The 5S rRNAs and Their Genes. .. 49 2.1.4 Introns.................... 14 2.8.4 Ribosomal Proteins . . . . . . . . . .. 49 2.2 Multiple Genes and Pseudo genes .. 16 2.8.5 The Transfer RNAs 2.3 Repetitive Sequences and Their Genes . . . . . . . . . . . .. 51 and Mobile Elements. . . . . . . . .. 17 2.8.6 The Small Nuclear RNAs 2.3.1 Satellite DNA. . . . . . . . . . . . . .. 18 and Their Genes . . . . . . . . . . . .. 52 2.3.2 Middle Repetitive DNA 2.9 Mitochondrial DNA. . . . . . . . . .. 52 and Genome Organization. . . . . .. 19 2.9.1 The mtDNA of Vertebrates . . . . .. 52 2.3.3 Transposition of Middle Repetitive 2.9.2 The mtDNA of Invertebrates. . . .. 54 Sequences . . . . . . . . . . . . . . . .. 19 2.9.3 The mtDNA of Ciliates. . . . . . . .. 55 2.3.4 Mobile Sequences 2.9.4 Kinetoplast DNA. . . . . . . . . . . .. 55 ofInvertebrates. . . . . . . . . . . . .. 21 References . . . . . . . . . . . . . . . .. 56 XII Contents 3 The Structural Variety 4.3.2 Methodological Problems and Metabolism of Proteins. . . .. 70 in the Determination of Protein Polymorphism. . . . . . . . . . . . . . . 133 3.1 Structural Variety. . . . . . . . . . . .. 70 4.3.3 Dependence of Protein 3.1.1 Protein Constituents. . . . . . . . . .. 70 Polymorphism on Protein Type . . . . 134 3.1.2 Phosphorylation 4.3.4 Differences in Protein and Dephosphorylation. . . . . . . .. 73 Polymorphism Between 3.1.3 Analysis and Comparison Different Animal Groups of Protein Sequences . . . . . . . . .. 76 and Habitats. . . . . . . . . . . . . . . . 135 3.1.4 Folding of the Polypeptide Chain .. 77 4.3.5 Dependence of Protein 3.1.5 Multiple Forms of Proteins .. . . .. 78 Polymorphism on the Size 3.2 Protein Synthesis . . . . . . . . . . . .. 80 and History of a Population . . . . . . 136 3.2.1 Aminoacyl-tRNA Synthetases .. .. 81 4.3.6 Quantitative Genetic Variability . . . 136 3.2.2 Initiation, Elongation 4.3.7 DNA Polymorphism. . . . . . . . . . . 137 and Termination . . . . . . . . . . . .. 81 4.4 The Causes 3.2.3 Transport of Newly Synthesized of Genetic Polymorphism ....... 140 Proteins to Their Correct 4.4.1 Neutral Theories Destinations in the Cell. . . . . . . .. 83 of Molecular Evolution ......... 140 3.3 Proteolysis . . . . . . . . . . . . . . . .. 86 4.4.2 Selection Theories 3.3.1 Exopeptidases. . . . . . . . . . . . . .. 89 of Polymorphism ............. 142 3.3.2 Serine Proteinases . . . . . . . . . . .. 90 4.4.3 The Controversy Between 3.3.3 Cysteine Proteinases. . . . . . . . . .. 94 Neutralism and Selectionism 143 3.3.4 Aspartate Proteinases. . . . . . . . .. 95 4.5 Methods and Problems 3.3.5 Metalloproteinases. . . . . . . . . . .. 96 in the Molecular Approach 3.4 Proteinase Inhibitors ... . . . . . .. 97 to Evolutionary Relationships ..... 147 3.4.1 Serine-Proteinase Inhibitors. . . . .. 97 4.5.1 The Evolutionary Distance 3.4.2 Cysteine-Proteinase Inhibitors .... 101 Between Amino Acid or Nucleotide 3.4.3 uz-Macroglobulins ............ 102 Sequences ................. 148 References . . . . . . . . . . . . . . . . . 103 4.5.2 Determination of Evolutionary Distance from the Amino Acid Composition of Proteins . . . . . . . . 150 4.5.3 Immunological Distance 4 Molecular Evolution . . . . . . . . . 111 Between Proteins. . . . . . . . . . . . . 151 4.1 The Determination of Homology 4.5.4 Genetic Distance Given Between Protein or DNA by Electrophoretic Data . . . . . . . . 152. Sequences ................. 114 4.5.5 Comparison of DNA Sequences 4.2 The Mechanisms from the Thermostability of Molecular Evolution. . . . . . . . . 117 of Heteroduplices . . . . . . . . . . . . 153 4.2.1 Nucleotide Substitution. . . . . . . . . 118 4.5.6 DNA Restriction Analysis ....... 154 4.2.2 Deletion, Insertion and Duplication 4.5.7 Construction of Phylogenetic Trees of DNA Sequences. . . . . . . . . . . . 121 from Molecular Data . . . . . . . . . . 155 4.2.3 Gene Fusion and Exon Shuffling. . . 122 4.6 The Rate of Molecular Evolution . . 160 4.2.4 Transposition of DNA Sequences .. 122 4.6.1 The Rate of Protein Evolution . . . . 160 4.2.5 The Evolution of Multi-Gene 4.6.2 The Rate of Evolution Families. . . . . . . . . . . . . . . . . . . 123 of the Nucleic Acids . . . . . . . . . . . 162 4.2.6 Polyploidization. . . . . . . . . . . . . . 125 4.6.3 Is There a Molecular Clock? 163 4.2.7 Gene Transfer Between Species 4.7 Some Results of Molecular and "Molecular Lamarckism". . . . . 127 Research into Evolutionary 4.2.8 Adaptive and Innovative Protein Relationships . . . . . . . . . . . . . . . 164 Evolution. . . . . . . . . . . . . . . . . . 127 4.7.1 Molecular Phylogenetic Trees . . . . . 165 4.2.9 Molecular Mechanisms in the 4.7.2 Species Systematics . . . . . . . . . . . 165 Evolution of Complex Characters . . 129 4.7.3 Molecular Taxonomy Above 4.3 Protein and Nucleic Acid the Species Level. . . . . . . . . . . . . 168 Polymorphism. . . . . . . . . . . . . . . 130 4.7.4 Molecular Data and the Large-Scale 4.3.1 Definitions and Concepts ........ 131 Classification of Organisms ...... 170 Contents XIII 4.8 Palaeobiochemistry ........... 170 6.5 Cytokines and Interferons . . . . . . . 230 References . . . . . . . . . . . . . . . . . 171 6.6 The Complement System. . . . . . . . 232 6.7 Lectins . . . . . . . . . . . . . . . . . . . 233 6.8 Humoral Defence in Invertebrates .. 236 5 Plasma Proteins, Yolk Proteins 6.9 Immune-Reactive Proteins and Metal-Binding Proteins . .... 184 of the Cell Surface . . . . . . . . . . . . 237 5.1 The Variety of Plasma Proteins. . . . 184 6.9.1 Cell-Adhesion Molecules 5.1.1 Plasma Proteins of Vertebrates . . . . 184 of Vertebrates . . . . . . . . . . . . . . . 237 5.1.2 Plasma Proteins of Invertebrates. . . 186 6.9.2 Cell-Binding Proteins 5.2 Serum Albumin ofInvertebrates .............. 239 and u-Fetoprotein . . . . . . . . . . . . 186 6.9.3 The Variable Surface Glycoproteins 5.3 Plasma Proteins with Special of the Trypanosomes. . . . . . . . . . . 240 Binding and Transport Functions. . . 188 6.9.4 Surface Proteins of Other 5.3.1 Transferrin . . . . . . . . . . . . . . . . . 188 Protozoa . . . . . . . . . . . . . . . . . . 241 5.3.2 Haptoglobin and Haemopexin . . . . 189 References . . . . . . . . . . . . . . . . . 242 5.3.3 Caeruloplasmin and Pre-Albumins .. 190 5.4 Acute-Phase Proteins .......... 190 7 Respiratory Pigments. . . . . . . . . 249 5.5 Larval Haemolymph Proteins 7.1 The Haemoglobins and Myoglobins of Insects . . . . . . . . . . . . . . . . . . 191 of Vertebrates . . . . . . . . . . . . . . . 251 5.6 Plasma Lipoproteins. . . . . . . . . . . 192 7.1.1 The Structure of Haemoglobin . . . . 251 5.6.1 Plasma Lipoproteins 7.1.2 Ligand Binding and Cooperativity. . 253 of Vertebrates . . . . . . . . . . . . . . . 193 7.1.3 Heterotropic Interactions ........ 255 5.6.2 Plasma Lipoproteins of Insects 7.1.4 Temperature Effects and Other Invertebrates . . . . . . . . 195 and Adaptations . . . . . . . . . . . . . 260 5.7 Vitellogenins and Yolk Proteins. . . . 197 7.1.5 The Gene Families of Vertebrate 5.7.1 Vitellogenins and Yolk Proteins Haemoglobins ............... 260 of Vertebrates . . . . . . . . . . . . . . . 197 7.1.6 Myoglobins ................. 264 5.7.2 Vitellogenins and Yolk Proteins 7.1.7 Methaemoglobin Formation of Insects . . . . . . . . . . . . . . . . . . 200 and Reduction. . . . . . . . . . . . . . . 265 5.7.3 Vitellogenins and Yolk Proteins 7.2 Invertebrate Haemoglobins of Crustaceans and Other and Chlorocruorins . . . . . . . . . . . 265 Invertebrates ................ 201 7.2.1 Annelids, Pogonophora 5.8 Blood Clotting . . . . . . . . . . . . . . 202 and Echiurids . . . . . . . . . . . . . . . 267 5.8.1 Blood Clotting in Vertebrates . . . . . 202 7.2.2 Haemoglobins of the Molluscs . . . . 270 5.8.2 Blood Clotting in Arthropods. . . . . 206 7.2.3 Haemoglobins of the Crustaceans . . 272 5.9 Antifreeze Proteins . . . . . . . . . . . 207 7.2.4 Haemoglobins of the Insects . . . . . 273 5.10 Metallothioneins . . . . . . . . . . . . . 208 7.2.5 Haemoglobins of Other 5.11 Ferritins. . . . . . . . . . . . . . . . . . . 210 Invertebrates ................ 274 References . . . . . . . . . . . . . . . . . 211 7.3 Haemocyanins ............... 275 7.3.1 Haemocyanins of the Arthropods .. 276 6 Immunoproteins . . . . . . . . . . . . 220 7.3.2 Haemocyanins of the Molluscs . . . . 279 7.4 Haemerythrins . . . . . . . . . . . . . . 281 6.1 The Immunoglobulin References . . . . . . . . . . . . . . . . . 282 Super-Family ................ 221 6.2 Immunoglobulins. . . . . . . . . . . . . 222 8 Peptide Hormones. . . . . . . . . . . 288 6.2.1 Basic Structure of Immunoglobulins . . . . . . . . . . . 222 8.1 Hormones 6.2.2 The Variety of Immunoglobulins. . . 224 of the Neurohypophysis ......... 290 6.2.3 Comparative Biochemistry of 8.2 Hormones of the Hypothalamus Immunoglobulins. . . . . . . . . . . . . 225 and Urophysis ............... 292 6.2.4 Evolution 8.2.1 Release and Release-Inhibiting of the Immunoglobulins . . . . . . . . 227 Factors . . . . . . . . . . . . . . . . . . . 292 6.3 T Cell Receptors . . . . . . . . . . . . . 228 8.2.2 Peptides from the Hypothalamus, 6.4 MHC Antigens Gut and Frog Skin . . . . . . . . . . . . 293 and BrMicroglobulins .......... 228 8.2.3 Hormones of the Urophysis ...... 294