Encyclopedia of Plant Physiology New Series Volume 14A Editors A. Pirson, Gottingen M. H. Zimmermann, Harvard Nucleic Acids and Proteins in Plants I Structure, Biochemistry and Physiology of Proteins Edited by D. Boulter and B. Parthier Contributors L. Beevers J. D. Bewley D. D. Davies J. W Hart C. F. Higgins R. C. Huffaker P. J. Lea R. Manteuffel A. Marcus Ph. Matile M.-N.Miege B.J.Miflin K.Miintz D.H.Northcote B. Parthier J. W Payne P.1. Payne J. A. M. Ramshaw A. P. Rhodes D. D. Sabnis J. L. Stoddart H. Thomas J. H. Weil With 135 Figures Springer-Verlag Berlin Heidelberg New York 1982 Professor Dr. DONALD BOULTER University of Durham Department of Botany Science Laboratories, South Road Durham, DH1 3LEjUK Professor Dr. BENNO PARTHIER Akademie der Wissenschaften der DDR Institut fUr Biochemie der Pflanzen Halle Weinberg 3, Postfach 250 401 Halle (Saale)jGDR ISBN-13: 978-3-642-68239-1 e-ISBN-13 :978-3-642-6823 7-7 DOl: 10.1007/978-3-642-68237-7 Library of Congress Cataloging in Publication Data. Main entry under title: Nucleic acids and proteins in plants. (Encyclopedia of plant physiology; new ser.; v. 14, pt. A-). Bibliography: p. Includes index. Contents: pt. A. Structure, biochemistry, and physiology of proteins. I. Nucleic acids. 2. Plant proteins. 3. Botanical chemistry. I. Boulter, D. II. Parthier, Benno. III. Series. QK711.2.E5 new ser., vol. 14, pt. A, etc. 81-18256 [QK898.N81 581.1s [581.19'2451 AACR2. This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying machine or similar means, and storage in data banks. Under § 54 of the German Copyright Law where copies are made for other than private use, a fee is payable to "Verwertungsgesellschaft Wort" Munich. © by Springer-Verlag Berlin· Heidelberg 1982 Softcover reprint of the hardcover 1s t edition 1982 The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement that such names are exempt from the relevant protective laws and regulations and therefore free for general use. 2131/3130-543210 Contents Introduction D. BOULTER and B. PARlHIER I. Biosynthesis and Metabolism of Protein Amino Acids and Proteins 1 Ammonia Assimilation and Amino Acid Metabolism BJ. MIFLIN and P.J. LEA (With 8 Figures) 1 Introduction ............ 5 2 Ammonia Assimilation and Transamination 5 2.1 Introduction ............ 5 2.2 Enzymes Involved in the Glutamate Synthase Cycle 5 2.3 Evidence for the Glutamate Synthase Cycle 7 2.3.1 Assimilation in Leaves . . 7 2.3.2 Green Algae . . . . . . . . . . . 8 2.3.3 Roots and Tissue Culture ..... 9 2.3.4 Maturing Seeds ....................... 10 2.3.5 Legume Root Nodules ........ 10 2.4 Alternative Pathways of Ammonia Assimilation 11 2.5 Localization of Ammonia Assimilation 13 2.5.1 Enzyme Distribution 13 2.5.2 Studies with Isolated Organelles 14 2.6 Regulation ........... 15 3 Transamination . . . . . . . . . . . 16 4 Biosynthesis of the Other Amino Acids 16 4.1 Introduction .......... 16 4.2 Synthesis of Amino Acids Derived from Pyruvate 17 4.2.1 Enzymic Evidence . . . . . . . . . . . . 18 4.2.2 Subcellular Localization . . . . . . . . . 18 4.2.3 Regulation . . . . . . . . . . . . . . . 18 4.3 Synthesis of Amino Acids Derived from Glutamate 19 4.3.1 Enzymic Evidence . . . . 19 4.3.2 In Vivo Studies . . . . . 22 4.3.3 Sub-Cellular Localization 23 4.3.4 Regulation . . . . . . . 23 4.4 Synthesis of the Aspartate Family of Amino Acids 24 4.4.1 Enzymic Evidence . . . . . . . . 25 4.4.2 Subcellular Localization . . . . . 27 4.4.3 Regulation . . . . . . . . . . . 28 4.5 Synthesis of Glycine, Serine and Cysteine 32 4.5.1 Enzymic Evidence . . . . 33 4.5.2 Sub-Cellular Localization 35 4.5.3 Regulation . . . . . . . 35 VI Contents 4.6 Synthesis of the Aromatic Amino Acids 35 4.6.1 Enzymic Evidence .... 36 4.6.2 Sub-Cellular Localization 38 4.6.3 Regulation . . . 38 4.7 Synthesis of Histidine 39 5 Amino Acid Catabolism . 41 5.1 Photo respiration . . . 41 5.2 Nitrogen Transport Compounds 42 5.2.1 Asparagine 42 5.2.2 Ureides 44 5.2.3 Arginine 45 References 47 2 Transfer RNA and Aminoacyl-tRNA Synthetases in Plants J.H. WElL and B. PARTHIER (With 10 Figures) 1 Introduction ...................... 65 2 Transfer RNA's (tRNA's) ................ 66 2.1 Occurrence and Intracellular Localization of Plant tRNA's 66 2.2 Extraction, Fractionation and Purification of Plant tRNA's 72 2.2.1 Extraction of Plant tRNA's ........ 72 2.2.2 Fractionation and Purification of Plant tRNA's 72 2.3 Structure of Plant tRNA's ......... 74 2.3.1 New Methods for Sequence Determination . . 74 2.3.2 Structure of Plant Cytoplasmic tRNA's 76 2.3.3 Structure of Chloroplastic tRNA's ..... 76 2.4 Organization and Expression of tRNA Genes in Nuclear and Organellar Genomes . . . . . . . . . . . . . . . . . 78 2.4.1 tRNA Genes in the Nuclear Genome . . . . . 78 2.4.2 tRNA Genes in the Chloroplast Genome 78 2.4.3 tRNA Genes in the Plant Mitochondrial Genome 81 2.4.4 Biosynthesis of Plant tRNA's 82 2.5 Functions of tRNA's . . . . . . . . . . . 82 2.5.1 Role of tRNA's in Protein Biosynthesis 82 2.5.2 Other Biological Functions of tRNA's . 82 2.6 tRNA's and Plant Development . . . . . . 83 3 Aminoacyl-tRNA Synthetases . . . . . . . . . 84 3.1 Preparation, Fractionation and Purification of the Enzymes 84 3.2 Intracellular Localization and Enzyme Heterogeneity 86 3.3 Functional and Molecular Properties . 88 3.3.1 Assays of Activity ...... 88 3.3.2 Kinetic Parameters ...... 89 3.3.3 Molecular Structure and Stability 92 3.4 Substrate Specificities 93 3.4.1 Transfer RNA 93 3.4.2 Amino Acids . 97 3.4.3 ATP 98 3.5 Biosynthesis of Synthetases 99 3.6 Synthetases and Developmental Processes 101 References . . . . . . . . . . . . . . . . 103 3 Ribosomes, Polysomes and the Translation Process A. MARCUS (With 9 Figures) I Introduction 113 2 Ribosomes . . . . . . . 113 Contents VII 3 Translation 114 4 The Genetic Code and Messenger RNA 118 5 Synthesis of Aminoacyl-tRNA 121 6 Synthesis of the Protein Chain 122 6.1 Initiation 122 6.2 Elongation 129 6.3 Termination 129 7 Regulation of Protein Synthesis 130 8 Epilogue 131 References 131 4 Post-Translational Modifications L. BEEVERS (With 3 Figures) 1 Introduction 136 2 Cleavage of N-Terminal Amino Acids 136 3 Secondary and Tertiary Structure 137 3.1 Quaternary Structure 137 4 Modification of Protein Amino Acids 138 4.1 Methylation 138 4.2 Phosphorylation 140 4.3 ADP-Ribosylation 141 4.4 Hydroxylation 142 4.5 Acetylation 142 4.6 Non-Protein Amino Acids 143 5 Conjugated Proteins 143 5.1 Haemoproteins 143 5.2 Porphyroproteins 144 5.3 Flavoproteins 144 5.4 Metalloproteins 144 6 Metalloenzymes 145 7 Glycoproteins 147 7.1 O-Glycosidic Linkages 148 7.1.1 Arabinogalactan-Proteins 149 7.2 Yeast Mannan 149 7.3 N-Glycosidic Linkages 149 7.4 Miscellaneous Glycoproteins 150 7.5 Formation of the O-Glycopeptide Bonds 151 7.6 Formation of N-Glycopeptide Bonds 152 8 Compartmentalization and Organelle Biogenesis 154 8.1 Mitochondria 154 8.2 Chloroplasts 156 8.3 Glyoxysomes 156 8.4 Protein Bodies - Cereal Endosperm 158 8.4.1 Protein Bodies - Legume Seeds 158 8.5 Vacuolar Proteins 160 8.6 Secreted Proteins 160 9 Conclusions 160 References 161 5 Protein Degradation PH. MATILE 1 Introduction 169 2 Proteolysis in Germinating Seeds 170 2.1 The Role of Protein Bodies 170 VIII Contents 2.2 Localization of Proteases in Protein Bodies 171 2.3 Regulation of Proteolysis in Protein Bodies 172 2.4 Autophagic Function of Protein Bodies 173 3 Protein Degradation in Leaves ...... . 173 3.1 Leaf Proteases . . . . . . . . . . . . . 173 3.2 Proteases and the Degradation of Leaf Protein 174 3.3 Degradation of Chloroplastic Protein 176 4 Yeast ............ . 178 4.1 Proteolysis in Bakers' Yeast .. . 178 4.2 The Proteolytic System of Yeast . 179 4.3 Compartmentation of Proteolysis 181 5 Concepts of Protein Degradation 182 References ........... . 183 6 Physiological Aspects of Protein Turnover D.D. DAVIES (With 9 Figures) 1 Introduction ................ 189 2 The Measurement of Protein Turnover 190 2.1 The Measurement of Gross Protein Synthesis 191 2.2 The Measurement of Protein Degradation 192 2.2.1 Density Labelling . . . . . . . . . . 194 2.2.2 The Use of Tritiated Water eH 0) . . 194 2 2.2.3 The Double Isotope Method for Measuring Relative Rates of Protein Degradation .............. 197 3 The Contribution of Protein Turnover to Respiration 197 4 Protein Turnover During Seed Germination 199 4.1 Protein Degradation . . . . . . . . . . 199 4.1.1 Proteinase Inhibitiors ....... 199 4.1.2 Activation of Zymogens . . . . . . 200 4.1.3 De Novo Synthesis of Endopeptidases 201 4.2 Protein Synthesis ........ 201 5 Protein Turnover During Active Growth . . . 202 6 The Measurement of Enzyme Turnover 205 6.1 Determination of the Rate Constant of Degradation from Changes in Enzyme Activity . . . . . . . . . . . . . . . . . . . . . . . 205 6.2 Determination of the Rate of Enzyme Degradation by Density Labelling 207 6.3 Determination of the Rate of Enzyme Degradation by Immunology 208 7 Protein Turnover During Senescence 209 7.1 Protein Synthesis in Senescing Leaves 209 7.2 Protein Synthesis in Ripening Fruit 211 7.3 Protein Degradation During Senescence 211 8 The Specificity of Protein Degradation 213 8.1 Correlation with Size . . . . . 213 8.2 Correlation with Charge 214 8.3 Correlation with" Abnormality" 215 8.4 Correlation with Amide Concentration 215 8.5 Correlation with Disulphide Content . 216 8.6 Correlation with Thermodynamic Properties 216 8.7 Correlation with Glycosylation ..... 217 8.8 Correlation with Hydrophobicity 217 8.9 Interdependence or Independence of Correlates 218 9 Protein Degradation Under Stress 218 References . . . . . . . . . . . . . . . . . . . 219 Contents IX 7 Structures of Plant Proteins J.A.M. RAMSHAW (With 31 Figures) 1 Introduction ........ . 229 2 Enzymes .......... . 230 2.1 Ribulose 1,5-Bisphosphate Carboxylase 230 2.2 Proteases . . 231 2.3 Peroxidase 237 2.4 ATP Synthase 239 2.5 Phosphorylase 240 2.6 Glycolate Oxidase 240 3 Electron Transfer Proteins 241 3.1 Cytochrome c 241 3.2 Cytochrome C6 245 3.3 Ferredoxin 246 3.4 Plastocyanin 248 3.5 Stellacyanin 253 4 Toxic Proteins 254 4.1 Phytohaemagglutinins (Lectins) 254 4.1.1 Concanavalin A 254 4.1.2 Favin and Related Lectins 257 4.1.3 Wheat Germ Agglutinin . 258 4.1.4 Lectins from Ricinus communis 259 4.2 Protease Inhibitors . . . . . . . . 261 4.2.1 Protease Inhibitors from the Leguminosae 261 4.2.2 Protease Inhibitors from the Solanaceae 264 4.2.3 Protease Inhibitors from Other Sources 267 4.3 Other Toxic Proteins 267 4.3.1 Viscotoxin . 267 4.3.2 Purothionins . 268 5 Other Plant Proteins . . 269 5.1 Seed Storage Proteins 269 5.2 Histones 272 5.3 Leghaemoglobin . . 274 5.4 Sweet Proteins . . . 276 5.5 Pollen Allergens . . 278 5.6 Other Proteins and Recent Studies 278 References . . . . . . . . . . 279 8 Protein Types and Distribution M.-N. MffiGE (With 14 Figures) 1 Introduction ........................... 291 2 Protein Types with Regard to Their Chemistry, Physiology, Histology and Ontogeny ..... 291 2.1 Chemical Types 291 2.1.1 Holoproteins . . . . . . . . . . 291 2.1.2 Conjugated Proteins . . . . . . . 292 2.1.3 Protein Solubility . . . . . . . . 292 2.1.4 Protein Stability to Heat and Cold 292 2.2 Metabolic and Structural Proteins . . . 293 3 Storage Proteins of Mature Seeds: Nature, Function and Ultrastructural Localization ........... . 294 3.1 Storage Proteins in Legume Seeds . . . . . . . . . . . . . 294 3.1.1 Globulins ..................... 295 3.1.2 Nutritive Value of Leguminosae ........... 301 3.1.3 Taxonomic Applications of Protein Structure Comparisons 302 x Contents 3.2 Storage Proteins of Seeds with Endosperm: Cereals ........ 304 3.3 Cellular Localization of Storage Proteins in Seeds . . . . . . . .. 305 3.3.1 Protein Bodies in Seeds Without Endosperm (Legumes and Other Classes) ......................... 305 3.3.2 Protein Bodies in Seeds with Endosperm: Cereal Grains and Ricinus communis Seeds . . . . . . . . . . . . . 307 3.3.3 The Membranes Surrounding Protein Bodies 311 3.4 Albumins . . . . . . . 314 4 Distribution of Enzymes . . . . . . 315 4.1 Definition, Nomenclature . . . . 315 4.2 Cellular Localization of Enzymes 315 4.3 Multimolecular Forms of Enzymes: Isoenzymes 316 4.3.1 Isoenzymes in Relation to Subcellular Structure 316 4.3.2 Isoenzymes in Relation to Tissue Localization and to Ontogeny 316 4.3.3 Isoenzymes in Relation to Environment: Biological Significance 317 4.3.4 Isoenzymes in Relation to Taxonomy 317 5 Distribution of Protease Inhibitors in Plants 318 6 Lectins: Nature and Distribution 319 6.1 Occurrence in Plants and Definition 319 6.2 Structure . . . . . . . . . . . . 320 6.3 Glycoprotein Nature, Glycosylation Site, Lectin-Protein Linkages 321 6.4 Different Types of Lectins 322 6.4.1 Agglutinins . . . . 322 6.4.2 Mitogenic Lectisn . . 323 6.4.3 Lectins as Enzymes 323 6.4.4 Lectins as Toxins: Ricin and Abrin 324 6.4.5 p-Lectins . . 324 6.5 Lectin Distribution . . . . . . . . . . 325 6.5.1 Detection ........... 325 6.5.2 Distribution of Lectins in Different Tissues During Development 325 6.5.3 Subcellular Distribution 326 6.5.4 Taxonomical Distribution 327 6.5.5 Possible Roles for the Lectins 327 7 Tuber Proteins ....... 328 7.1 Tubers of Leguminosae . . 328 7.2 Solanum tuberosum Tubers 328 7.3 Ipomoea hatatas Tubers . 330 7.4 Dioscorea spp. Tubers 330 7.5 Manihot esculenta Tubers . 331 7.6 Colocasia esculenta, Xanthosoma sagittifolium, Canna edulis, Maranta arundinacea Tubers . . . . . 331 8 Proteins in Specialized Structures 331 8.1 Cell Wall Proteins 331 8.1.1 Extensin 331 8.1.2 Enzymes . . 333 8.2 Pollen Proteins 333 8.2.1 Intine Proteins 334 8.2.2 Exine Proteins 335 8.2.3 Nutritional Value of Pollen 335 References . . . . . . . . . . . . 335 9 Cereal Storage Proteins: Structure and Role in Agriculture and Food Technology P.I. PAYNE and A.P. RHODFS (With 3 Figures) I Introduction ................ 346 Contents XI 2 Anatomical Structure of the Cereal Grain; Protein Content and Protein Distribution .......... 346 3 Classification of the Cereal Proteins 347 4 The Protein Constituents . 348 4.1 Albumin and Globulin 348 4.2 Prolamin 350 4.3 Glutelin ...... 353 5 Agricultural Aspects . . . 357 5.1 Breeding High-Protein Wheats 357 5.2 High-Lysine Barley 358 5.3 High-Lysine Maize . . . . . 359 5.4 Protein Improvement in Rice 359 5.5 High-Lysine Sorghum 360 5.6 Triticale ........ 360 6 Technological Aspects . . . . 361 6.1 Milling Quality of Wheats 361 6.2 Bread ......... 361 6.3 Biscuits (Cookies) 362 6.4 Pasta Products (Macaroni, Spaghetti, Vermicelli and Noodles) 362 6.5 Breakfast Cereals from Wheat 363 6.6 Chapa tis .......... 363 6.7 Use of Zein Films . . . . . . 363 6.8 Identification of Cereal Varieties 363 References . . . . . . . . . . . . 365 10 Biochemistry and Physiology of Leaf Proteins R.C. HUFFAKER (With 10 Figures) 1 Introduction . . . . . . . . . . . . . . . . 370 2 Ribulose Bisphosphate Carboxylase (RuBPCase) 371 3 Proteinase Inhibitors 383 4 Nitrate Reductase (NR) . . . . . . 384 5 Nitrite Reductase (NiR) . . . . . . 392 6 Phenylalanine Ammonia-Lyase (PAL) 393 References . . . . . . . . . . . . . 394 11 Microtubule Proteins and P-Proteins D.D. SABNIS and J.W. HART (With 3 Figures) 1 General Introduction . . . . . 401 2 Tubulin and Associated Proteins 401 2.1 Introduction 401 2.2 Tubulin . . . . . 402 2.2.1 Methodology 402 2.2.2 Distribution . 403 2.2.3 Physical and Chemical Properties 403 2.3 Proteins Associated with Tubulin . 408 2.3.1 Introduction . . . . . . . . . . 408 2.3.2 Proteins Involved in Assembly . . 408 2.3.3 Enzymes Associated with Tubulin 409 2.4 Tubulin Assembly 410 2.4.1 Introduction . . . . . . . . . . 410