Nucleic Acids and Proteins in Plants II

1 Nuclear Chromatin (With 16 Figures).- 1 Introduction.- 2 Chemistry of Chromatin.- 3 The Nucleosome.- 3.1 The Nucleosome Core Particle.- 3.2 The Nucleosomal DNA.- 3.3 Transcription, Replication, and Nucleosomes.- 4 Higher-Order Coiling: Chromatin Fibers.- 5 Domains and Mitotic Chromosomes.- 6 Interphase Chromatin: Heterochromatin.- 7 Interphase Chromatin: Euchromatin.- 8 Chromatin Organization and Genome Organization.- 9 Conclusions.- References.- 2 Chromosomal DNA Sequences and Their Organization (With 11 Figures).- 1 Introduction.- 2 Genome Analysis by Renaturation Kinetics.- 3 Proportions of Repeated and Non-Repeated DNA.- 4 Single-Copy and Repeated DNA Interspersion Patterns.- 5 Reverse Repeats.- 6 Genome Analysis by Equilibrium Centrifugation in Heavy Salt Gradients.- 7 Genome Analysis Using Restriction Endonucleases.- 7.1 Analysis of Whole Genome Digests After Electrophoresis and Ethidium Bromide Staining.- 7.2 Interspecies Comparisons of Major Families of Repeated Sequences.- 7.3 Sequence Analysis After Transfer to Nitrocellulose, Using Radioactive Probes.- 7.4 Analysis of Repeated DNA Families Using Restriction Endonucleases.- 7.5 Derivation of a Physical Map of the rDNA Repeat Unit in Soybean.- 8 The Properties and Arrangements of Repeated Sequences.- 9 The Structure of Nuclear Genes.- References.- 3 DNA Replication and the Cell Cycle (With 4 Figures).- 1 Introduction.- 2 Phases of the Cell Cycle.- 3 Methodology.- 3.1 Experimental Systems.- 3.1.1 Synchronous Populations of Cells.- 3.1.2 Non-Synchronous Populations of Cells.- 3.2 Techniques.- 3.2.1 Cytological Techniques.- 3.2.2 Genetic Techniques.- 3.2.3 Biochemical Techniques.- 4 Biochemistry of DNA Replication.- 4.1 General Features.- 4.2 Enzymology of DNA Replication.- 4.2.1 Endodeoxyribonuclease.- 4.2.2 DNA-Unwinding Enzyme.- 4.2.3 DNA-Binding Proteins.- 4.2.4 RNA Polymerase.- 4.2.5 DNA Polymerase.- 4.2.6 Ribonuclease H.- 4.2.7 DNA Ligase.- 4.2.8 DNA Methylase.- 5 DNA Replication and Chromatin Structure.- 5.1 General Features.- 5.2 Chromatin Organization at the Replication Origins.- 5.3 Movement of the Replication Fork.- 5.4 Re-Assembly of Chromatin.- 6 Relationship Between DNA Replication and Cell Division.- 7 Regulation of the Cell Cycle.- 7.1 Biochemical Aspects of Regulation.- 7.1.1 Ribonucleotide Reductase.- 7.1.2 Endodeoxyribonuclease.- 7.1.3 DNA Polymerase.- 7.1.4 Histone Hl Phosphokinase.- 7.1.5 General Aspects of Biochemical Regulation.- 7.2 Physiological Aspects of Regulation.- 8 Concluding Remarks.- References.- 4 DNA Endoreduplication and Differential Replication (With 8 Figures).- 1 Introduction.- 2 Somatic Polyploidization Cycles.- 2.1 Polyenergid Cells.- 2.2 Nuclear Restitution Cycles.- 2.3 Endo-Cycles.- 3 Differential DNA Replication.- 4 Physiological Significance of Somatic DNA Increase.- 5 An Evolutionary Perspective.- 6 Conclusions.- References.- 5 RNA Polymerase and Regulation of Transcription (With 8 Figures).- 1 Introduction.- 2 RNA Polymerases from Prokaryotes and Eukaryotes.- 2.1 Structure and Function.- 2.2 Regulation.- 3 Plant RNA Polymerases.- 3.1 Nuclear RNA Polymerases.- 3.1.1 Isolation and Separation.- 3.1.2 Subunit Structure.- 3.1.3 General Properties.- 3.1.4 Localization and Function.- 3.2 Chloroplast RNA Polymerase.- 3.2.1 Isolation.- 3.2.2 Properties of the Enzyme.- 3.2.3 Subunit Composition.- 3.2.4 In Vitro Products.- 4 Regulation of Transcription.- 4.1 RNA Synthesis Düring Development.- 4.1.1 Seed Germination.- 4.1.2 Hormonal Response.- 4.1.3 Photomorphogenesis.- 4.2 Mechanisms of Control of Transcription.- 4.2.1 Selective Gene Recognition.- 4.2.2 Alterations in the Level of RNA Polymerases and Modulation of Polymerase Activity.- 4.2.3 Template Availability.- 4.2.4 Factors Influencing Polymerase Activity and Specificity.- 4.2.5 Chloroplast RNA Polymerase.- 5 Conclusions.- References.- 6 RNA Sequences (With 4 Figures).- 1 Introduction.- 2 Conventions for the Graphical Representation of RNA Sequences.- 3 Structure of tRNA.- 3.1 Specific Plant tRNA Sequences.- 3.1.1 Sequences of Cytosolic tRNA's.- 3.1.2 Sequences of Organelle tRNA's.- 4 mRNA Structure.- 4.1 Cytosolic mRNA.- 4.2 Specific Cytosolic mRNA Sequences.- 4.3 Organelle mRNA's.- 5 Types of Ribosomal RNA.- 5.1 High Molecular Weight Ribosomal RNA Sequences.- 5.2 Low Molecular Weight Ribosomal RNA Sequences.- 6 Prospects.- References.- 7 RNA Processing and Other Post-Transcriptional Modifications (With 14 Figures).- 1 Introduction.- 2 Methods of Studying RNA Processing.- 3 Synthesis and Processing of rRNA.- 3.1 Processing of rRNA Transcripts in Bacteria.- 3.2 Blue-Green Algae.- 3.3 Chloroplasts and Mitochondria.- 3.4 Processing of Cytoplasmic rRNA in Nucleoli of Eukaryotes.- 4 Processing of tRNA.- 4.1 Bacteria.- 4.2 Eukaryotes.- 5 Processing of mRNA.- 5.1 General Features.- 5.2 Capping.- 5.3 Polyadenylation.- 5.4 Splicing.- References.- 8 Ribonucleases and Ribonucleic Acid Breakdown.- 1 RNA-Splitting Enzymes.- 1.1 Definitions, Terminology, and Classification.- 1.2 Problems of Purification and Identification.- 1.2.1 Formation of Artifacts by Oxido-Reductive Processes.- 1.2.2 Formation of Artifacts Due to Proteolytic Effects.- 1.2.3 Dependence of the pH Optima on a Variety of Factors.- 1.2.4 The Use of Homopolymers for the Assay of Base Specificity.- 1.2.5 Electrophoretic Variants.- 1.3 Types of RNA-Splitting Enzymes in Plants.- 1.4 Subcellular Localization.- 1.4.1 Soluble Enzymes.- 1.4.2 Particle-Bound Enzymes.- 1.4.3 Lysosomal Localization.- 1.5 RNA-Splitting Enzymes in Relation to Development.- 1.5.1 Seed Germination.- 1.5.2 Seed Maturation.- 1.5.3 Root Growth and Differentiation.- 1.5.4 Senescence.- 1.6 RNA-Splitting Enzymes and the Environment.- 1.6.1 Effect of Cellular Injury.- 1.6.2 Nucleolytic Enzymes in the Diseased Plant.- 1.6.3 Light Effects.- 1.6.4 Water Stress.- 1.7 Control ofRNase Activity.- 1.7.1 Genetic Control.- 1.7.2 Hormonal Control.- 2 Ribonucleic Acid Degradation.- 2.1 RNA "Level", "Breakdown", and "Turnover", Use and Mis-Use of the Terms and Methods.- 2.2 RNA Breakdown During Specific Physiological Processes.- 2.2.1 Seed Germination.- 2.2.2 Senescence.- 2.2.3 Pathological Processes.- 2.3 Regulation of RNA Breakdown.- 2.3.1 Hormonal Regulation.- 2.3.2 Light Effects.- References.- 9 Metabolism of Pyrimidines and Purines (With 10 Figures).- 1 Introduction.- 2 Occurrence of Pyrimidines and Purines in Plants.- 3 Formation of Pyrimidines and Purines.- 3.1 Pyrimidines.- 3.1.1 Pathway Reactions.- 3.1.2 Enzymes.- 3.2 Purines.- 4 Salvage Reactions of Pyrimidines and Purines.- 4.1 Pyrimidines.- 4.2 Purines.- 5 Interconversions of Nucleotides.- 6 Free Nucleotides in Relation to Nucleic Acid Synthesis.- 7 Degradation of Pyrimidines and Purines.- 7.1 Pyrimidines.- 7.2 Purines.- 8 Concluding Remarks.- References.- 10 Structure of Plant Viral Genomes (With 17 Figures).- 1 Introduction.- 2 DNA Viruses.- 2.1 Organization of the Genome of Cauliflower Mosaic Virus (CaMV).- 2.1.1 General Properties of the Virus.- 2.1.2 Structure of the CaMV Capsid.- 2.1.3 DNA Interruptions.- 2.1.4 Interaction DNA - Coat Protein.- 2.2 Structure of the Genome.- 2.2.1 Viral DNA.- 2.2.2 Restriction Map of the CaMV DNA.- 2.2.3 Sequence of CaMV DNA.- 3 RNA Viruses.- 3.1 Distribution of the Genes.- 3.1.1 The RNA's of Monopartite Plant Viruses.- 3.1.2 RNA's of Multipartite Plant Viruses.- 3.1.3 Satellite Viruses.- 3.2 Structure of RNA of Plant Viruses.- 3.2.1 Categories of 5' and 3' Termini of Plant Virus RNA's.- 3.2.2 Considerations on the Role of 5' and 3' Ends of Plant Virus RNA's.- 3.3 Plant Viral RNA's and Binding to Eukaryotic Ribosomes.- References.- 11 Translation of Plant Virus RNA's (With 5 Figures).- 1 Introduction.- 2 Virus RNA Structures.- 2.1 Structure at the 5' Terminus.- 2.1.1 m7 G5' ppp5' X(m) pY(m) p.... = "cap".- 2.1.2 Genome-Linked Protein.- 2.1.3 (p)ppX.- 2.2 Structure at the 3' Terminus.- 2.2.1 Poly(A)Tail.- 2.2.2 "tRNA-Like" Structure.- 2.2.3 pXOH.- 3 Fidelity of Translation.- 3.1 Comparison of in Vitro Products with in Vivo Products.- 3.2 Comparison of Products Formed in Different Cell-Free Systems.- 4 Strategy of Expression of the Information.- 4.1 Functionally Monocistronic: Expression of the Internal Cistron is Mediated by a Subgenomic mRNA.- 4.2 Monocistronic: The Primary Product is a "Polyprotein".- 4.3 Di- or Polycistronic.- 5 Competition Between Host and Viral mRNA's.- 6 Regulation of Expression of Virus Information.- 6.1 Regulation by Preferential Initiation.- 6.2 Regulation by the Use of Leaky Termination Codons.- 7 Function of Virus-Coded Proteins.- References.- 12 Biology, Structure, Functions and Possible Origin of Viroids (With 36 Figures).- 1 Introduction.- 2 The Biology of Viroids.- 2.1 Viroid Diseases.- 2.2 Economic Importance.- 2.3 Experimental Transmission.- 2.4 Experimental Host Range.- 2.5 Transmission Under Natural Conditions.- 2.6 Expression of Symptoms.- 2.7 Cytopathic Effects of Viroid Infection.- 2.8 Interference Between Viroids.- 2.9 Control Measures.- 3 The Structure of Viroids.- 3.1 Viroid Purification and Properties of Purified Viroids.- 3.2 The Primary Structure of PSTV.- 3.3 The Secondary Structure of PSTV.- 3.4 Absence of Tertiary Structure Folding in PSTV.- 3.5 Properties of the RNA Molecule Complementary to PSTV.- 3.6 Origin and Properties of Linear Viroid Molecules.- 3.7 Structure Formation, Conformers and Multiple Forms of PSTV.- 3.8 Structural Differences Between the Pathogenic PSTV "Type Strain" and a "Mild" PSTV Isolate.- 3.9 The Problem of Different Viroid "Species".- 3.10 The Complexity of the CCCV System.- 3.11 Structural Homologies and Differences Between the Viroid "Species" PSTV, CSV, CEV, CCCV and ASBV.- 4 The Functions of Viroids.- 4.1 Translation Properties of Viroids.- 4.2 The Problems of Viroid Replication.- 4.3 Replication of Viroids in Protoplasts and Cell Cultures.- 4.4 The Presumed DNA-Dependence of Viroid Replication.- 4.5 In Vitro Transcription of Viroid RNA by DNA-Dependent RNA Polymerase II of Plant Origin.- 4.6 In Vitro Transcription of Viroid RNA by RNA-Dependent RNA Polymerase Purified from Healthy Host Tissue.- 4.7 Properties of RNA Intermediates of Viroid Replication.- 4.8 Possible Mechanisms of Viroid Pathogenesis.- 5 The Possible Origin of Viroids.- 6 Viroid-Like RNA's Encapsidated in Virions (Virusoids).- 7 Viroids, "Prions" and "Virinos".- 8 Concluding Remarks.- References.- 13 The Ti-Plasmids of Agrobacterium tumefaciens (With 3 Figures).- 1 Introduction.- 2 Ti-Plasmids Are Catabolic Plasmids and Natural Gene Vectors for Plants.- 2.1 Genetic and Functional Organization of Octopine and Nopaline Ti-Plasmids.- 2.2 Generality of the Opine and Genetic Colonization Concepts.- 2.3 The Transfer of the T-Region to Plant Cells.- 3 Expression of T-DNA in Plant Cells.- 3.1 Transcription of T-DNA Sequences.- 3.2 Translation of T-DNA-Derived mRNA.- 4 The Development of the Ti-Plasmid as an Experimental Gene Vector.- 4.1 Are Genes, Inserted in the T-Region, Contrasferred to the Plant Nucleus?.- 4.2 Can Genes, Inserted via T-DNA into Plant Nuclei, Be Expressed?.- 4.3 Can Normal Plants Be Regenerated from T-DNA-Containing Plant Cells?.- 5 General Conclusions.- References.- 14 Organization and Expression of Plastid Genomes (With 5 Figures).- 1 Introduction.- 2 Physicochemical Properties and Structural Aspects of Plastid DNAs.- 2.1 Nucleotide Compositum of Plastid DNAs.- 2.2 Kinetic Complexity.- 2.3 Size, Uniformity and Intramolecular Heterogeneity of Plastid DNAs.- 2.4 Amount and Structural Arrangement of DNA Within Plastids.- 3 Physical Maps of Plastid DNAs.- 3.1 Gross Morphology of Plastid DNAs.- 3.2 Insertions, Deletions and Rearrangements.- 4 Gene Mapping.- 4.1 Genes on Plastid DNAs.- 4.1.1 Genes for rRNas.- 4.1.2 Genes for tRNAs.- 4.1.3 Genes Coding for Proteins.- 4.2 Gene Structure.- 4.3 Interspecies Conservation of Gene Structure and Sequence Among Plastid DNAs.- 4.4 Comparison of Eubacterial and Plastid Genes.- 5 Transcription of Plastid Genes.- 5.1 Transcription of rRNA Genes.- 5.2 Transcription of tRNA Genes.- 5.3 Transcription of Protein Genes.- 5.4 Control of Transcription.- 6 Replication of Plastid DNAs.- 7 Conclusions.- References.- 15 The Biosynthesis of Chloroplast Proteins (With 8 Figures).- 1 Introduction.- 2 The Protein-Synthesizing System of the Cytoplasm and the Chloroplast...- 2.1 The Ribosomes.- 2.2 Transfer RNA.- 2.3 Aminoacyl-tRNA-Synthetases.- 2.4 Regulatory Factors.- 2.5 Messenger RNA.- 3 Techniques Used for the Study of the Biosynthesis of Chloroplast Polypeptides.- 3.1 Synthesis of Chloroplast Proteins in Vivo.- 3.2 Protein Synthesis in Isolated Chloroplasts.- 3.3 In Vitro Polypeptide Synthesis.- 3.3.1 Polysomal Run-Off System.- 3.3.2 Heterologous in Vitro Synthesis of Chloroplast Proteins.- 4 The Site of Synthesis of Chloroplast Proteins.- 4.1 RuBP Carboxylase.- 4.2 Proton-Translocating ATPase.- 4.3 Cytochromes.- 4.4 Elongation Factors EF-GChl and EF-TChl.- 4.5 32,000 Mr Membrane Protein.- 4.6 Light-Harvesting Chlorophyll a/b Protein.- 4.7 P-700 Chlorophyll a-Complex Proteins.- 4.8 Ferredoxin.- 4.9 Other Thylakoid Membrane Proteins.- 4.10 Chloroplast Ribosomal Proteins.- 4.11 Aminoacyl-tRNA-Synthetases.- 5 Transport of Cytoplasmically Synthesized Proteins into the Chloroplast.- 6 Location of the Genes Specifying Chloroplast Polypeptides.- 7 Synthesis of Chloroplast Proteins During Development.- 7.1 RuBP Carboxylase.- 7.2 32,000-Mr Membrane Protein.- 7.3 Light-Harvesting Chlorophyll a/b Protein.- 7.4 Cytochromes.- 8 Conclusions.- References.- 16 Use of Mutants in the Study of Chloroplast Biogenesis (With 14 Figures).- 1 Introduction.- 2 Induction, Detection, and Characterization of Mutants Defective in Plastid Development.- 3 Structural Organization of Plastid Membranes.- 3.1 Developing Plastid Membranes.- 3.2 Mutants Affecting Structural Organization of Plastid Membranes in Relation to Photosynthetic Capacity.- 3.2.1 Mutants Defective in Dark Development.- 3.2.2 Mutants Defective in the Initial Steps of Greening.- 3.2.3 Mutants Defective in Differentiation of Lamellar Membranes into Grana and Stroma Regions.- 4 Synthesis of the Components of the Photosythetic Membranes.- 4.1 Genetic Control of Chlorophyll Synthesis.- 4.2 Genetic Control of Carotenoid Synthesis.- 4.3 Genetic Control of Thylakoid Protein Synthesis.- 5 Genetic Control of the Protein-Synthesizing System of Plastids.- 6 Coordinated Expression of the Nuclear and Plastid Genomes.- References.- 17 Interrelationship Between Chloroplasts and the Nucleo-Cytosol Compartment in Acetabularia (With 6 Figures).- 1 Introduction.- 2 Acetabularia.- 2.1 Morphology.- 2.2 Life Cycle.- 2.3 Ultrastructure.- 2.4 Compartmentation.- 2.4.1 The Nucleo-Cytosol Compartment.- 2.4.2 The Chloroplast.- 3 Chloroplast Gene Expression.- 3.1 Chloroplast DNA.- 3.2 Chloroplast Transcription.- 3.3 Translation of Chloroplast Proteins as Revealed by Nuclear Exchange Experiments.- 3.3.1 Malic Dehydrogenase.- 3.3.2 Chloroplast Ribosomal Proteins.- 3.4 Chloroplast Translation.- 3.5 80S Ribosomes Associated with Chloroplasts.- 4 Regulation of Enzyme Activity.- 4.1 Thymidine Kinase.- 4.2 Other Enzymes.- 5 Circadian Rhythms.- 5.1 O2 Evolution Rhythm.- 5.2 Coupled Translation - Membrane Model.- 5.3 Generalization of the Model.- References.- 18 Use (and Misuse) of Inhibitors in Gene Expression (With 4 Figures).- 1 Introduction.- 2 Mode of Action of Various Inhibitors.- 2.1 General Scheme of the Molecular Biology of Plant Cells.- 2.2 Inhibitors of Transcription.- 2.3 Inhibitors of Translation.- 3 Action of Inhibitors in Vivo.- 4 Possible Errors in Interpretation.- 4.1 Secondary Effects of Antibiotics.- 4.2 Interactions of the Genetic Systems.- 5 Conclusions.- References.- Author Index.- Plant Name Index.