Encyclopedia of Plant Physiology New Series Volume 14B Editors A. Pirson, Gottingen M. H. Zimmermann, Harvard Nucleic Acids and Proteins in Plants II Structure, Biochemistry and Physiology of Nucleic Acids Edited by B. Parthier and D. Boulter Contributors H.1. Bohnert W Bottomley 1. A. Bryant E. 1. Crouse T. A. Dyer G. L. Farkas R. B.F lavell G. Galling D. Grierson K. W Henningsen L. Hirth W N agl L. N eeleman H. L. Sanger 1. Schell 1. M. Schmitt H. G.S chweiger B. M.S tummann L. van Vloten-Doting C. Wasternack R. Wollgiehn With 173 Figures Springer-Verlag Berlin Heidelberg New York 1982 Professor Dr. BENNO PARTHIER Akademie der Wissenschaften der DDR Institut fUr Biochemie der Pflanzen Halle Weinberg 3, Postfach 250 401 Halle (Saale)jGDR Professor Dr. DONALD BOULTER University of Durham Department of Botany Science Laboratories, South Road Durham, DH1 3LEjUK ISBN-13: 978-3-642-68349-7 e-ISBN-13: 978-3-642-68347-3 DOT: 10.1007/978-3-642-68347-3 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-B). Bibliography: p. Includes index. Contents: pt. A. Structure. biochemistry. and physiology of proteins I edited by D. Boulter and B. Parthier pt. B. Structure, biochemistry, and physiology of nucleic acids I edited by B. Parthier and D. Boulter. 1. 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.N8] 581.1s [581.19'24]. 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, fe-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 "Verwertungsge sellschaft Wort" Munich. © by Springer-Verlag Berlin-Heidelberg 1982 Softcover reprint of the hardcover I st 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. Typesetting, printing and bookbinding: Universitiitsdruckerei H. Sturtz AG, Wurzburg. 2131/3130-543210 Contents 1 Nuclear Chromatin W. NAGL (With 16 Figures) 1 Introduction . . . . . 1 2 Chemistry of Chromatin . 1 3 The Nucleosome 4 3.1 The Nucleosome Core Particle 6 3.2 The Nucleosomal DNA 8 3.3 Transcription, Replication, and Nucleosomes 12 4 Higher-Order Coiling: Chromatin Fibers 13 5 Domains and Mitotic Chromosomes 17 6 Interphase Chromatin: Heterochromatin 19 7 Interphase Chromatin: Euchromatin 22 8 Chromatin Organization and Genome Organization 30 9 Conclusions 32 References . . . . . . . . . . . . . . . . . . . 33 2 Chromosomal DNA Sequences and Their Organization R.B. FLAVELL (With 11 Figures) 1 Introduction . . . . . . . . . . . . . . . . . 46 2 Genome Analysis by Renaturation Kinetics 47 3 Proportions of Repeated and Non-Repeated DNA 50 4 Single-Copy and Repeated DNA Interspersion Patterns 51 5 Reverse Repeats ................. 54 6 Genome Analysis by Equilibrium Centrifugation in Heavy Salt Gradients 55 7 Genome Analysis Using Restriction Endonucleases .......... 56 7.1 Analysis of Whole Genome Digests After Electrophoresis and Ethidium Bromide Staining . . . . . . . . . . . . . . . . . . . . . .. 56 7.2 Interspecies Comparisons of Major Families of Repeated Sequences 59 7.3 Sequence Analysis After Transfer to Nitrocellulose, Using Radioactive Probes . . . . . . . . . . . . . . . . . . . . . . . . . . .. 59 7.4 Analysis of Repeated DNA Families Using Restriction Endonucleases 60 7.5 Derivation of a Physical Map of the rDNA Repeat Unit in Soybean 61 8 The Properties and Arrangements of Repeated Sequences 63 9 The Structure of Nuclear Genes 67 References . . . . . . . . . . . . . . . . . . . . . 70 3 DNA Replication and the Cell Cycle I.A. BRYANT (With 4 Figures) 1 Introduction . . . . . 75 2 Phases of the Cell Cycle . . 76 3 Methodology ...... 77 3.1 Experimental Systems 78 3.1.1 Synchronous Populations of Cells 78 3.1.2 Non-Synchronous Populations of Cells 79 VI Contents 3.2 Techniques . . . . . . . . 80 3.2.1 Cytological Techniques 80 3.2.2 Genetic Techniques . . 80 3.2.3 Biochemical Techniques 82 4 Biochemistry of DNA Replication 82 4.1 General Features . . . . . 82 4.2 Enzymology of DNA Replication 86 4.2.1 Endodeoxyribonuclease . 86 4.2.2 DNA-Unwinding Enzyme 87 4.2.3 DNA-Binding Proteins 87 4.2.4 RNA Polymerase 87 4.2.5 DNA Polymerase 88 4.2.6 Ribonuclease H 95 4.2.7 DNA Ligase . . 95 4.2.8 DNA Methylase 96 5 DNA Replication and Chromatin Structure 96 5.1 General Features . . . . . . . . . . 96 5.2 Chromatin Organization at the Replication Origins 96 5.3 Movement of the Replication Fork ...... . 97 5.4 Re-Assembly of Chromatin . . . . . . . . . . . 97 6 Relationship Between DNA Replication and Cell Division 98 7 Regulation of the Cell Cycle . . . . . 100 7.1 Biochemical Aspects of Regulation 101 7.1.1 Ribonucleotide Reductase . 101 7.1.2 Endodeoxyribonuclease . . . 101 7.1.3 DNA Polymerase . . . . . . 102 7.1.4 Histone Hl Phosphokinase 102 7.1.5 General Aspects of Biochemical Regulation 103 7.2 Physiological Aspects of Regulation 103 8 Concluding Remarks 104 References . . . . . . . . . . . . . . 105 4 DNA Endoreduplication and Differential Replication W. NAGL (With 8 Figures) 1 Introduction . . . . . . . . . 111 2 Somatic Polyploidization Cycles 111 2.1 Polyenergid Cells 112 2.2 Nuclear Restitution Cycles . 112 2.3 Endo-Cycles . . . . . . . 114 3 Differential DNA Replication 115 4 Physiological Significance of Somatic DNA Increase 119 5 An Evolutionary Perspective 120 6 Conclusions 121 References . . . . . . . . . . . . . . . . . . . 121 5 RNA Polymerase and Regulation of Transcription R. WOLLGlliHN (With 8 Figures) 1 Introduction . . . . . . . . . . . . . . . . . 125 2 RNA Polymerases from Prokaryotes and Eukaryotes 125 2.1 Structure and Function 125 2.2 Regulation . . . . . . . . . 128 3 Plant RNA Polymerases ..... 129 3.1 Nuclear RNA Polymerases . 129 3.1.1 Isolation and Separation 130 Contents VII 3.1.2 Subunit Structure 133 3.1.3 General Properties 135 3.1.4 Localization and Function 138 3.2 Chloroplast RNA Polymerase . 139 3.2.1 Isolation ....... 139 3.2.2 Properties of the Enzyme 140 3.2.3 Subunit Composition . . 140 3.2.4 In Vitro Products 141 4 Regulation of Transcription 141 4.1 RNA Synthesis During Development 141 4.1.1 Seed Germination 141 4.1.2 Hormonal Response ..... 143 4.1.3 Photomorphogenesis ..... 143 4.2 Mechanisms of Control of Transcription 145 4.2.1 Selective Gene Recognition 146 4.2.2 Alterations in the Level of RNA Polymerases and Modulation of Polymerase Activity . . . . . . . . . . . . . . . . 147 4.2.3 Template Availability . . . . . . . . . . . . . . . 152 4.2.4 Factors Influencing Polymerase Activity and Specificity 154 4.2.5 Chloroplast RNA Polymerase 157 5 Conclusions 158 References . . . . . . . . . . . . . . 159 6 RNA Sequences T.A. DYER (With 4 Figures) 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . 171 2 Conventions for the Graphical Representation of RNA Sequences 172 3 Structure of tRNA . . . . . . . . . 172 3.1 Specific Plant tRNA Sequences . . 174 3.1.1 Sequences ofCytosolic tRNA's 174 3.1.2 Sequences of Organelle tRNA's 175 4 mRNA Structure . . . . . . . . . . 175 4.1 Cytosolic mRNA . . . . . . . . 175 4.2 Specific Cytosolic mRNA Sequences 179 4.3 Organelle mRNA's ....... 181 5 Types of Ribosomal RNA . . . . . . 181 5.1 High Molecular Weight Ribosomal RNA Sequences 182 5.2 Low Molecular Weight Ribosomal RNA Sequences 186 6 Prospects 187 References . . . . . . . . . . . . . . . . . . . . . 187 7 RNA Processing and Other Post-Transcriptional Modifications D. GRIERSON (With 14 Figures) 1 Introduction . . . . . . . . . . . 192 2 Methods of Studying RNA Processing 193 3 Synthesis and Processing of rRNA 194 3.1 Processing of rRNA Transcripts in Bacteria 194 3.2 Blue-Green Algae . . . . . . . . . . . 197 3.3 Chloroplasts and Mitochondria . . . . . 198 3.4 Processing of Cytoplasmic rRNA in Nucleoli of Eukaryotes 201 4 Processing of tRNA 209 4.1 Bacteria . 209 4.2 Eukaryotes . . 211 VIII Contents 5 Processing of mRNA 211 5.1 General Features 211 5.2 Capping . . . 212 5.3 Polyadenylation 213 5.4 Splicing 214 References . . . . . 216 8 Ribonucleases and Ribonucleic Acid Breakdown G.L. FARKAS 1 RNA-Splitting Enzymes . . . . . . . . . . . 224 1.1 Definitions, Terminology, and Classification 224 1.2 Problems of Purification and Identification . 226 1.2.1 Formation of Artifacts by Oxido-Reductive Processes 227 1.2.2 Formation of Artifacts Due to Proteolytic Effects . . 227 1.2.3 Dependence of the pH Optima on a Variety of Factors 228 1.2.4 The Use of Homopolymers for the Assay of Base Specificity 228 1.2.5 Electrophoretic Variants . . . . . . 228 1.3 Types of RNA-Splitting Enzymes in Plants 229 1.4 Subcellular Localization 231 1.4.1 Soluble Enzymes . . . . . . . . . 231 1.4.2 Particle-Bound Enzymes . . . . . . 231 1.4.3 Lysosomal Localization . . . . . . 234 1.5 RNA-Splitting Enzymes in Relation to Development 235 1.5.1 Seed Germination ...... 235 1.5.2 Seed Maturation . . . . . . . 236 1.5.3 Root Growth and Differentiation 237 1.5.4 Senescence ......... 237 1.6 RNA-Splitting Enzymes and the Environment 239 1.6.1 Effect of Cellular Injury . . . . . . . 239 1.6.2 Nucleolytic Enzymes in the Diseased Plant 241 1.6.3 Light Effects . . . . 242 1.6.4 Water Stress . . . . 243 1.7 Control of RNase Activity 244 1.7.1 Genetic Control 244 1.7.2 Hormonal Control 245 2 Ribonucleic Acid Degradation 246 2.1 RNA "Level", "Breakdown", and "Turnover", Use and Mis-Use of the Terms and Methods . . . . . . . . . . . . . . . . 246 2.2 RNA Breakdown During Specific Physiological Processes 247 2.2.1 Seed Germination 247 2.2.2 Senescence ...... 248 2.2.3 Pathological Processes 250 2.3 Regulation of RNA Breakdown 251 2.3.1 Hormonal Regulation 251 2.3.2 Light Effects 253 References . . . . . . . . . . 254 9 Metabolism of Pyrimidines and Purines C. WASTERNACK (With 10 Figures) 1 Introduction . . . . . . . . . . . . 263 2 Occurrence of Pyrimidines and Purines in Plants 263 3 Formation of Pyrimidines and Purines 266 3.1 Pyrimidines .............. 266 Contents IX 3.1.1 Pathway Reactions . . . . . . . . 266 3.1.2 Enzymes . . . . . . . . 268 3.2 Purines .............. . 272 4 Salvage Reactions of Pyrimidines and Purines 274 4.1 Pyrimidines ............ . 274 4.2 Purines .............. . 277 5 Interconversions of Nucleotides . . . . . . . 279 6 Free Nucleotides in Relation to Nucleic Acid Synthesis 282 7 Degradation of Pyrimidines and Purines 284 7.1 Pyrimidines 284 7.2 Purines 285 8 Concluding Remarks 288 References . . . . . . 290 10 Structure of Plant Viral Genomes L. HIRTH (With 17 Figures) 1 Introduction ......................... 302 2 DNA Viruses . . . . . . . . . . . . . . . . . . . . . . . ., 302 2.1 Organization of the Genome of Cauliflower Mosaic Virus (CaMV) 302 2.1.1 General Properties of the Virus 302 2.1.2 Structure of the CaMV Capsid 303 2.1.3 DNA Interruptions ..... 303 2.1.4 Interaction DNA - Coat Protein 303 2.2 Structure of the Genome ..... 304 2.2.1 Viral DNA . . . . . . . . . 304 2.2.2 Restriction Map of the CaMV DNA 305 2.2.3 Sequence of CaMV DNA 305 3 RNA Viruses . . . . . . . . . . . . . . 309 3.1 Distribution of the Genes . . . . . . . 310 3.1.1 The RNA's of Monopartite Plant Viruses 310 3.1.2 RNA's of Multipartite Plant Viruses . . 312 3.1.3 Satellite Viruses . . . . . . . . . . . 312 3.2 Structure of RNA of Plant Viruses . . . . . 314 3.2.1 Categories of 5' and 3' Termini of Plant Virus RNA's 315 3.2.2 Considerations on the Role of 5' and 3' Ends of Plant Virus RNA's. . . . . . . . . . . . . . . . . . . . 326 3.3 Plant Viral RNA's and Binding to Eukaryotic Ribosomes 327 References ....................... 331 11 Translation of Plant Virus RNA's L. VAN VLOTEN-DOTING and L. NEELEMAN (With 5 Figures) 1 Introduction ......... 337 2 Virus RNA Structures ........... 339 2.1 Structure at the 5' Terminus . . . . . . . 339 2.1.1 m7 G5' ppp5' x(m) py(m) p .... ="cap" 339 2.1.2 Genome-Linked Protein 340 2.1.3 (p)ppX . . . . . . . . 340 2.2 Structure at the 3' Terminus . 341 2.2.1 Poly(A)Tail . . . . . . 341 2.2.2 "tRNA-Like" Structure 341 2.2.3 pXOH ..•••••• 342 3 Fidelity of Translation . . . . . 343 3.1 Comparison of in Vitro Products with in Vivo Products. 343 3.2 Comparison of Products Formed in Different Cell-Free Systems 344 X Contents 4 Strategy of Expression of the Information . . . . . . . . . . . . 346 4.1 Functionally Monocistronic: Expression of the Internal Cistron is Mediated by a Subgenomic mRNA . . . . . . . . . 347 4.2 Monocistronic: The Primary Product is a "Polyprotein" 348 4.3 Di- or Polycistronic .......... 349 5 Competition Between Host and Viral mRNA's 353 6 Regulation of Expression of Virus Information 354 6.1 Regulation by Preferential Initiation 354 6.2 Regulation by the Use of Leaky Termination Codons 354 7 Function of Virus-Coded Proteins 358 References ..................... 359 12 Biology, Structure, Functions and Possible Origin of Viroids H.L. SANGER (With 36 Figures) 1 Introduction ...... 368 2 The Biology of Viroids . . . 369 2.1 Viroid Diseases 369 2.2 Economic Importance 373 2.3 Experimental Transmission 373 2.4 Experimental Host Range . 374 2.5 Transmission Under Natural Conditions 374 2.6 Expression of Symptoms . . . . . . 375 2.7 Cytopathic Effects of Viroid Infection 378 2.8 Interference Between Viroids 382 2.9 Control Measures . . . . . . . . . 382 3 The Structure of Viroids ........ 383 3.1 Viroid Purification and Properties of Purified Viroids 384 3.2 The Primary Structure of PSTV . . . . . . . . . 386 3.3 The Secondary Structure of PSTV . . . . . . . . 387 3.4 Absence of Tertiary Structure Folding in PSTV 390 3.5 Properties of the RNA Molecule Complementary to PSTV 391 3.6 Origin and Properties of Linear Viroid Molecules 393 3.7 Structure Formation, Conformers and Multiple Forms of PSTV 396 3.8 Structural Differences Between the Pathogenic PSTV "Type Strain" and a "Mild" PSTV Isolate . . . . . . . . . . . . . . . . .. 400 3.9 The Problem of Different Viroid "Species" . . . . . . . . . .. 403 3.10 The Complexity of the CCCV System ............. 405 3.11 Structural Homologies and Differences Between the Viroid "Species" PSTV, CSV, CEV, CCCV and ASBV 410 4 The Functions of Viroids . . . . . . . . . . . . . . . 417 4.1 Translation Properties of Viroids ......... 417 4.2 The Problems of Viroid Replication ........ 419 4.3 Replication of Viroids in Protoplasts and Cell Cultures 420 4.4 The Presumed DNA-Dependence of Viroid Replication 424 4.5 In Vitro Transcription of Viroid RNA by DNA-Dependent RNA Polymerase II of Plant Origin . . . . . . . . . . . . . . .. 425 4.6 In Vitro Transcription of Viroid RNA by RNA-Dependent RNA Polymerase Purified from Healthy Host Tissue . . . . 429 4.7 Properties of RNA Intermediates of Viroid Replication 430 4.8 Possible Mechanisms of Viroid Pathogenesis . . . 431 5 The Possible Origin of Viroids . . . . . . . . . . . 435 6 Viroid-Like RNA's Encapsidated in Virions (Virusoids) 438 7 Viroids, "Prions" and "Virinos" 440 8 Concluding Remarks 443 References .......... 445 Contents XI 13 The Ti-Plasmids of Agrobacterium tumefaciens J. SCHELL (With 3 Figures) 1 Introduction ........................... 455 2 Ti-Plasmids Are Catabolic Plasmids and Natural Gene Vectors for Plants 457 2.1 Genetic and Functional Organization of Octopine and Nopaline Ti- Plasmids ...................... 459 2.2 Generality of the Opine and Genetic Colonization Concepts 462 2.3 The Transfer of the T-Region to Plant Cells 464 3 Expression of T-DNA in Plant Cells . . . . . . . . . . . . 465 3.1 Transcription of T -DNA Sequences . . . . . . . . . . . 465 3.2 Translation ofT-DNA-Derived mRNA . . . . . . . . . 467 4 The Development of the Ti-Plasmid as an Experimental Gene Vector 468 4.1 Are Genes, Inserted in the T-Region, Contrasferred to the Plant Nucleus? . . . . . . . . . . . . . . . . . . . . . . . . 468 4.2 Can Genes, Inserted via T-DNA into Plant Nuclei, Be Expressed? 468 4.3 Can Normal Plants Be Regenerated from T-DNA-Containing Plant Cells? 468 5 General Conclusions 469 References ..... 470 14 Organization and Expression of Plastid Genomes H.l. BOHNERT, E.l. CROUSE, and I.M. SCHMITT (With 5 Figures) 1 Introduction ..................... 475 2 Physicochemical Properties and Structural Aspects of Plastid DNAs 476 2.1 Nucleotide Composition of Plastid DNAs . . . . . . . . . . 477 2.2 Kinetic Complexity . . . . . . . . . . . . . . . . . . . . 481 2.3 Size, Uniformity and Intramolecular Heterogeneity of Plastid DNAs 481 2.4 Amount and Structural Arrangement of DNA Within Plastids 484 3 Physical Maps of Plastid DNAs . . . . . . 486 3.1 Gross Morphology of Plastid DNAs 486 3.2 Insertions, Deletions and Rearrangements 487 4 Gene Mapping ..... 490 4.1 Genes on Plastid DNAs . . . . 490 4.1.1 Genes for rRNas 490 4.1.2 Genes for tRNAs 493 4.1.3 Genes Coding for Proteins 495 4.2 Gene Structure ....... 497 4.3 Interspecies Conservation of Gene Structure and Sequence Among Plastid DNAs . . . . . . . . . . . . . . 503 4.4 Comparison of Eubacterial and Plastid Genes 504 5 Transcription of Plastid Genes . . 505 5.1 Transcription of rRNA Genes 505 5.2 Transcription of tRNA Genes 508 5.3 Transcription of Protein Genes 508 5.4 Control of Transcription 510 6 Replication of Plastid DNAs 513 7 Conclusions 514 References ......... 515 15 The Biosynthesis of Chloroplast Proteins W. BOTTOMLEY and H.J. BOHNERT (With 8 Figures) 1 Introduction ......................... 531 2 The Protein-Synthesizing System of the Cytoplasm and the Chloroplast 533