Nucleic Acids and Proteins in Plants I: Structure, Biochemistry and Physiology of Proteins

ISBN-13: 9783642682391 / Angielski / Miękka / 2011 / 770 str.

D. Boulter

Opis

D. BOULTER and B. PARTHIER At the time of the former edition of the Encyclopedia of Plant Physiology, approximately 25 years ago, no complete plant protein amino acid sequences or nucleic acid sequences had been determined. Although the structure of DNA and its function as the genetic material had just been reported, little detail was known of the mechanism of its action, and D. G. CATCHSIDE was to write in the first chapter of the first volume of the Encyclopedia: "There is a consider able body of evidence that the gene acts as a unit of physiological action through the control of individual enzymes." No cell-free transcription and pro tein-synthesizing systems were available and the whole range of powerful meth ods of recombinant DNA technology was still to be developed. Today for the first time with plant systems, it is possible not only to describe their molecular biology but also to manipulate it, i. e., to move from a description to a technological phase. The properties of living systems are inscribed by those of the proteins and nucleic acids which they synthesize. Proteins, due to their very large size, occur as macromolecules in colloidal solution or associated in supra-molecular colloi dal form. The colloidal state confers low thermal conductivity, low diffusion coefficients and high viscosity, properties which buffer a biological system from the effects of a changing environment. Biological systems not only have great stability, but also the capacity to reproduce."

Spis treści

I. Biosynthesis and Metabolism of Protein Amino Acids and Proteins.- 1 Ammonia Assimilation and Amino Acid Metabolism.- 1 Introduction.- 2 Ammonia Assimilation and Transamination.- 2.1 Introduction.- 2.2 Enzymes Involved in the Glutamate Synthase Cycle.- 2.3 Evidence for the Glutamate Synthase Cycle.- 2.3.1 Assimilation in Leaves.- 2.3.2 Green Algae.- 2.3.3 Roots and Tissue Culture.- 2.3.4 Maturing Seeds.- 2.3.5 Legume Root Nodules.- 2.4 Alternative Pathways of Ammonia Assimilation.- 2.5 Localization of Ammonia Assimilation.- 2.5.1 Enzyme Distribution.- 2.5.2 Studies with Isolated Organelles.- 2.6 Regulation.- 3 Transamination.- 4 Biosynthesis of the Other Amino Acids.- 4.1 Introduction.- 4.2 Synthesis of Amino Acids Derived from Pyruvate.- 4.2.1 Enzymic Evidence.- 4.2.2 Subcellular Localization.- 4.2.3 Regulation.- 4.3 Synthesis of Amino Acids Derived from Glutamate.- 4.3.1 Enzymic Evidence.- 4.3.2 In Vivo Studies.- 4.3.3 Sub-Cellular Localization.- 4.3.4 Regulation.- 4.4 Synthesis of the Aspartate Family of Amino Acids.- 4.4.1 Enzymic Evidence.- 4.4.2 Subcellular Localization.- 4.4.3 Regulation.- 4.5 Synthesis of Glycine, Serine and Cysteine.- 4.5.1 Enzymic Evidence.- 4.5.2 Sub-Cellular Localization.- 4.5.3 Regulation.- 4.6 Synthesis of the Aromatic Amino Acids.- 4.6.1 Enzymic Evidence.- 4.6.2 Sub-Cellular Localization.- 4.6.3 Regulation.- 4.7 Synthesis of Histidine.- 5 Amino Acid Catabolism.- 5.1 Photorespiration.- 5.2 Nitrogen Transport Compounds.- 5.2.1 Asparagine.- 5.2.2 Ureides.- 5.2.3 Arginine.- References.- 2 Transfer RNA and Aminoacyl-tRNA Synthetases in Plants.- 1 Introduction.- 2 Transfer RNA’s (tRNA’s).- 2.1 Occurrence and Intracellular Localization of Plant tRNA’s.- 2.2 Extraction, Fractionation and Purification of Plant tRNA’s.- 2.2.1 Extraction of Plant tRNA’s.- 2.2.2 Fractionation and Purification of Plant tRNA’s.- 2.3 Structure of Plant tRNA’s.- 2.3.1 New Methods for Sequence Determination.- 2.3.2 Structure of Plant Cytoplasmic tRNA’s.- 2.3.3 Structure of Chloroplastic tRNA’s.- 2.4 Organization and Expression of tRNA Genes in Nuclear and Organellar Genomes.- 2.4.1 tRNA Genes in the Nuclear Genome.- 2.4.2 tRNA Genes in the Chloroplast Genome.- 2.4.3 tRNA Genes in the Plant Mitochondrial Genome.- 2.4.4 Biosynthesis of Plant tRNA’s.- 2.5 Functions of tRNA’s.- 2.5.1 Role of tRNA’s in Protein Biosynthesis.- 2.5.2 Other Biological Functions of tRNA’s.- 2.6 tRNA’s and Plant Development.- 3 Aminoacyl-tRNA Synthetases.- 3.1 Preparation, Fractionation and Purification of the Enzymes.- 3.2 Intracellular Localization and Enzyme Heterogeneity.- 3.3 Functional and Molecular Properties.- 3.3.1 Assays of Activity.- 3.3.2 Kinetic Parameters.- 3.3.3 Molecular Structure and Stability.- 3.4 Substrate Specificities.- 3.4.1 Transfer RNA.- 3.4.2 Amino Acids.- 3.4.3 ATP.- 3.5 Biosynthesis of Synthetases.- 3.6 Synthetases and Developmental Processes.- References.- 3 Ribosomes, Polysomes and the Translation Process.- 1 Introduction.- 2 Ribosomes.- 3 Translation.- 4 The Genetic Code and Messenger RNA.- 5 Synthesis of Aminoacyl-tRNA.- 6 Synthesis of the Protein Chain.- 6.1 Initiation.- 6.2 Elongation.- 6.3 Termination.- 7 Regulation of Protein Synthesis.- 8 Epilogue.- References.- 4 Post-Translational Modifications.- 1 Introduction.- 2 Cleavage of N-Terminal Amino Acids.- 3 Secondary and Tertiary Structure.- 3.1 Quaternary Structure.- 4 Modification of Protein Amino Acids.- 4.1 Methylation.- 4.2 Phosphorylation.- 4.3 ADP-Ribosylation.- 4.4 Hydroxylation.- 4.5 Acetylation.- 4.6 Non-Protein Amino Acids.- 5 Conjugated Proteins.- 5.1 Haemoproteins.- 5.2 Porphyroproteins.- 5.3 Flavoproteins.- 5.4 Metalloproteins.- 6 Metalloenzymes.- 7 Glycoproteins.- 7.1 O-Glycosidic Linkages.- 7.1.1 Arabinogalactan-Proteins.- 7.2 Yeast Mannan.- 7.3 N-Glycosidic Linkages.- 7.4 Miscellaneous Glycoproteins.- 7.5 Formation of the O-Glycopeptide Bonds.- 7.6 Formation of N-Glycopeptide Bonds.- 8 Compartmentalization and Organelle Biogenesis.- 8.1 Mitochondria.- 8.2 Chloroplasts.- 8.3 Glyoxysomes.- 8.4 Protein Bodies — Cereal Endosperm.- 8.4.1 Protein Bodies — Legume Seeds.- 8.5 Vacuolar Proteins.- 8.6 Secreted Proteins.- 9 Conclusions.- References.- 5 Protein Degradation.- 1 Introduction.- 2 Proteolysis in Germinating Seeds.- 2.1 The Role of Protein Bodies.- 2.2 Localization of Proteases in Protein Bodies.- 2.3 Regulation of Proteolysis in Protein Bodies.- 2.4 Autophagic Function of Protein Bodies.- 3 Protein Degradation in Leaves.- 3.1 Leaf Proteases.- 3.2 Proteases and the Degradation of Leaf Protein.- 3.3 Degradation of Chloroplastic Protein.- 4 Yeast.- 4.1 Proteolysis in Bakers’ Yeast.- 4.2 The Proteolytic System of Yeast.- 4.3 Compartmentation of Proteolysis.- 5 Concepts of Protein Degradation.- References.- 6 Physiological Aspects of Protein Turnover.- 1 Introduction.- 2 The Measurement of Protein Turnover.- 2.1 The Measurement of Gross Protein Synthesis.- 2.2 The Measurement of Protein Degradation.- 2.2.1 Density Labelling.- 2.2.2 The Use of Tritiated Water (3H2O).- 2.2.3 The Double Isotope Method for Measuring Relative Rates of Protein Degradation.- 3 The Contribution of Protein Turnover to Respiration.- 4 Protein Turnover During Seed Germination.- 4.1 Protein Degradation.- 4.1.1 Proteinase Inhibitors.- 4.1.2 Activation of Zymogens.- 4.1.3 De Novo Synthesis of Endopeptidases.- 4.2 Protein Synthesis.- 5 Protein Turnover During Active Growth.- 6 The Measurement of Enzyme Turnover.- 6.1 Determination of the Rate Constant of Degradation from Changes in Enzyme Activity.- 6.2 Determination of the Rate of Enzyme Degradation by Density Labelling.- 6.3 Determination of the Rate of Enzyme Degradation by Immunology.- 7 Protein Turnover During Senescence.- 7.1 Protein Synthesis in Senescing Leaves.- 7.2 Protein Synthesis in Ripening Fruit.- 7.3 Protein Degradation During Senescence.- 8 The Specificity of Protein Degradation.- 8.1 Correlation with Size.- 8.2 Correlation with Charge.- 8.3 Correlation with “Abnormality”.- 8.4 Correlation with Amide Concentration.- 8.5 Correlation with Disulphide Content.- 8.6 Correlation with Thermodynamic Properties.- 8.7 Correlation with Glycosylation.- 8.8 Correlation with Hydrophobicity.- 8.9 Interdependence or Independence of Correlates.- 9 Protein Degradation Under Stress.- References.- 7 Structures of Plant Proteins.- 1 Introduction.- 2 Enzymes.- 2.1 Ribulose 1,5-Bisphosphate Carboxylase.- 2.2 Proteases.- 2.3 Peroxidase.- 2.4 ATP Synthase.- 2.5 Phosphorylase.- 2.6 Glycolate Oxidase.- 3 Electron Transfer Proteins.- 3.1 Cytochrome c.- 3.2 Cytochrome c6.- 3.3 Ferredoxin.- 3.4 Plastocyanin.- 3.5 Stellacyanin.- 4 Toxic Proteins.- 4.1 Phytohaemagglutinins (Lectins).- 4.1.1 Concanavalin A.- 4.1.2 Favin and Related Lectins.- 4.1.3 Wheat Germ Agglutinin.- 4.1.4 Lectins from Ricinus communis.- 4.2 Protease Inhibitors.- 4.2.1 Protease Inhibitors from the Leguminosae.- 4.2.2 Protease Inhibitors from the Solanaceae.- 4.2.3 Protease Inhibitors from Other Sources.- 4.3 Other Toxic Proteins.- 4.3.1 Visco toxin.- 4.3.2 Purothionins.- 5 Other Plant Proteins.- 5.1 Seed Storage Proteins.- 5.2 Histones.- 5.3 Leghaemoglobin.- 5.4 Sweet Proteins.- 5.5 Pollen Allergens.- 5.6 Other Proteins and Recent Studies.- References.- 8 Protein Types and Distribution.- 1 Introduction.- 2 Protein Types with Regard to Their Chemistry, Physiology, Histology and Ontogeny.- 2.1 Chemical Types.- 2.1.1 Holoproteins.- 2.1.2 Conjugated Proteins.- 2.1.3 Protein Solubility.- 2.1.4 Protein Stability to Heat and Cold.- 2.2 Metabolic and Structural Proteins.- 3 Storage Proteins of Mature Seeds: Nature, Function and Ultrastructural Localization.- 3.1 Storage Proteins in Legume Seeds.- 3.1.1 Globulins.- 3.1.2 Nutritive Value of Leguminosae.- 3.1.3 Taxonomic Applications of Protein Structure Comparisons.- 3.2 Storage Proteins of Seeds with Endosperm: Cereals.- 3.3 Cellular Localization of Storage Proteins in Seeds.- 3.3.1 Protein Bodies in Seeds Without Endosperm (Legumes and Other Classes).- 3.3.2 Protein Bodies in Seeds with Endosperm: Cereal Grains and Ricinus communis Seeds.- 3.3.3 The Membranes Surrounding Protein Bodies.- 3.4 Albumins.- 4 Distribution of Enzymes.- 4.1 Definition, Nomenclature.- 4.2 Cellular Localization of Enzymes.- 4.3 Multimolecular Forms of Enzymes: Isoenzymes.- 4.3.1 Isoenzymes in Relation to Subcellular Structure.- 4.3.2 Isoenzymes in Relation to Tissue Localization and to Ontogeny.- 4.3.3 Isoenzymes in Relation to Environment: Biological Significance.- 4.3.4 Isoenzymes in Relation to Taxonomy.- 5 Distribution of Protease Inhibitors in Plants.- 6 Lectins: Nature and Distribution.- 6.1 Occurrence in Plants and Definition.- 6.2 Structure.- 6.3 Glycoprotein Nature, Glycosylation Site, Lectin-Protein Linkages.- 6.4 Different Types of Lectins.- 6.4.1 Agglutinins.- 6.4.2 Mitogenic Lectisn.- 6.4.3 Lectins as Enzymes.- 6.4.4 Lectins as Toxins: Ricin and Abrin.- 6.4.5 ?-Lectins.- 6.5 Lectin Distribution.- 6.5.1 Detection.- 6.5.2 Distribution of Lectins in Different Tissues During Development.- 6.5.3 Subcellular Distribution.- 6.5.4 Taxonomical Distribution.- 6.5.5 Possible Roles for the Lectins.- 7 Tuber Proteins.- 7.1 Tubers of Leguminosae.- 7.2 Solanum tuberosum Tubers.- 7.3 Ipomoea batatas Tubers.- 7.4 Dioscorea spp. Tubers.- 7.5 Manihot esculenta Tubers.- 7.6 Colocasia esculenta, Xanthosoma sagittifolium, Canna edulis, Maranta arundinacea Tubers.- 8 Proteins in Specialized Structures.- 8.1 Cell Wall Proteins.- 8.1.1 Extensin.- 8.1.2 Enzymes.- 8.2 Pollen Proteins.- 8.2.1 Intine Proteins.- 8.2.2 Exine Proteins.- 8.2.3 Nutritional Value of Pollen.- References.- 9 Cereal Storage Proteins: Structure and Role in Agriculture and Food Technology.- 1 Introduction.- 2 Anatomical Structure of the Cereal Grain; Protein Content and Protein Distribution.- 3 Classification of the Cereal Proteins.- 4 The Protein Constituents.- 4.1 Albumin and Globulin.- 4.2 Prolamin.- 4.3 Glutelin.- 5 Agricultural Aspects.- 5.1 Breeding High-Protein Wheats.- 5.2 High-Lysine Barley.- 5.3 High-Lysine Maize.- 5.4 Protein Improvement in Rice.- 5.5 High-Lysine Sorghum.- 5.6 Triticale.- 6 Technological Aspects.- 6.1 Milling Quality of Wheats.- 6.2 Bread.- 6.3 Biscuits (Cookies).- 6.4 Pasta Products (Macaroni, Spaghetti, Vermicelli and Noodles).- 6.5 Breakfast Cereals from Wheat.- 6.6 Chapatis.- 6.7 Use of Zein Films.- 6.8 Identification of Cereal Varieties.- References.- 10 Biochemistry and Physiology of Leaf Proteins.- 1 Introduction.- 2 Ribulose Bisphosphate Carboxylase (RuBPCase).- 3 Proteinase Inhibitors.- 4 Nitrate Reductase (NR).- 5 Nitrite Reductase (NiR).- 6 Phenylalanine Ammonia-Lyase (PAL).- References.- 11 Microtubule Proteins and P-Proteins.- 1 General Introduction.- 2 Tubulin and Associated Proteins.- 2.1 Introduction.- 2.2 Tubulin.- 2.2.1 Methodology.- 2.2.2 Distribution.- 2.2.3 Physical and Chemical Properties.- 2.3 Proteins Associated with Tubulin.- 2.3.1 Introduction.- 2.3.2 Proteins Involved in Assembly.- 2.3.3 Enzymes Associated with Tubulin.- 2.4 Tubulin Assembly.- 2.4.1 Introduction.- 2.4.2 In Vitro Studies.- 2.4.3 In Vivo Assembly.- 2.5 Plant Tubulin: Special Considerations.- 2.6 Conclusions.- 3 P-Proteins.- 3.1 Introduction.- 3.2 Distribution.- 3.3 Ultrastructural Studies.- 3.3.1 Morphology.- 3.3.2 Ontogeny.- 3.3.3 Histochemistry.- 3.4 Biochemical Studies.- 3.4.1 Methodology.- 3.4.2 Physical and Chemical Properties.- 3.4.3 Lectin Activity.- 3.5 Role of P-Proteins: Hypotheses.- 4 General Conclusions.- References.- 12 Plant Peptides.- 1 Introduction.- 2 Peptides with a Specific Structure or Function.- 2.1 Glutathione.- 2.2 ?-Glutamyl Peptides.- 2.3 Algal Peptides.- 2.4 Peptides in the Phloem and Xylem.- 2.5 Symbiosis.- 2.6 Peptide Hormones.- 2.7 Peptides and Plant Pathology.- 2.8 Miscellaneous Peptides.- 3 Peptides as Metabolic Intermediates: The Peptide Pool.- 3.1 Introduction.- 3.2 Tissues of Rapid Protein Synthesis.- 3.3 Mature Tissues.- 3.4 Tissues Showing Rapid Protein Hydrolysis.- 4 Peptide Transport.- 4.1 Algae.- 4.2 Higher Plants.- 5 Concluding Remarks.- References.- 13 Immunology.- 1 Introduction.- 2 Immunology of Soluble Enzymes.- 3 Immunology of Biologically Active Proteins Other than Enzymes.- 3.1 Lectins (Phytohaemagglutinins).- 3.2 Protease Inhibitors.- 3.3 Phytochrome.- 3.4 Leghaemoglobin.- 3.5 Proteins Related to Incompatibility Reactions.- 3.6 Proteins of Unknown Nature Associated with Development in Plant.- 4 Immunology of Storage Proteins.- 4.1 Storage Proteins of Legume Seeds.- 4.2 Storage Proteins of Cereal Grains.- 4.3 Storage Proteins of Other Crops.- 5 Immunological Properties of Integral Proteins of Sub-Cellular Structures.- 6 Concluding Remarks.- References.- II. Nucleic Acids and Proteins in Relation to Specific Plant Physiological Processes.- 14 Seed Development.- 1 Introduction.- 2 Changes in Structure and Composition of Seeds During Development.- 2.1 Embryogenesis and Seed Growth.- 2.2 General Compositional Changes During Seed Development.- 2.2.1 DNA.- 2.2.2 RNA.- 2.2.3 Total Nitrogen.- 2.2.4 Soluble Nitrogen.- 2.2.5 Protein Nitrogen.- 2.3 Changes in Cell Structure.- 2.3.1 Endoplasmic Reticulum and Dictyosomes.- 2.3.2 Vacuoles.- 2.3.3 Protein Bodies.- 2.3.4 Stereological Analysis of Cell Structures During Storage Tissue Development.- 3 Nucleic Acids.- 3.1 DNA Metabolism.- 3.2 Protein Genes and Their Inheritance in Seeds.- 3.3 RNA Metabolism.- 3.3.1 RNA Polymerase Activity.- 3.3.2 Metabolism of Different Types of RNA in Developing Seeds.- 3.3.3 Poly(A)+-RNA from Developing Seeds.- 3.3.4 cDNA Complementary to Poly (A)+-RNA from Seeds and the Molecular Cloning of DNA.- 3.3.5 tRNA and the Biosynthesis of Storage Proteins During Seed Development.- 4 Ribosomes and Polysomes.- 5 Protein Synthesis During Seed Development and Its Regulation.- 5.1 Pattern of in Vivo Protein Formation.- 5.1.1 Albumins and Globulins from Cereals and Legumes.- 5.1.2 Prolamins and Glutelins from Cereal Grains.- 5.2 In Vitro Biosynthesis of Seed Proteins — a Tool to Investigate Regulatory Processes of Storage Protein Formation.- 5.2.1 Cereal Prolamins.- 5.2.2 Intracellular Site of Storage Protein Formation.- 5.2.3 Legume Globulins.- 5.2.4 Changes in Storage Protein mRNA’s During Seed Development.- 5.3 Glycosylation of Storage Proteins During Seed Development.- 6 Protein Body Formation.- 7 The Influence of Environmental Factors on Protein Synthesis and Accumulation During Seed Development.- References.- 15 Protein and Nucleic Acid Synthesis During Seed Germination and Early Seedling Growth.- 1 Introduction.- 2 Protein Synthesis in Imbibing Embryos and Axes.- 2.1 Messenger RNA: Conserved, Synthesized, or Both?.- 3 RNA Synthesis in Imbibing Embryos and Axes.- 3.1 Ribosomal RNA.- 3.2 Transfer RNA Synthesis.- 3.3 The Sequence of RNA Synthesis During Germination.- 3.4 Enzymes and Precursors of RNA Synthesis.- 4 Protein and RNA Synthesis in Storage Organs.- 4.1 General RNA Metabolism.- 4.2 Synthesis of Enzymes Involved in Reserve Mobilization in Relation to Their mRNA’s.- 4.2.1 ?-Amylase Synthesis in the Barley Aleurone Layer.- 4.2.2 Castor Bean Endosperm and Cucumber Cotyledons.- 4.2.3 Cotton Seed Cotyledons: The Carboxypeptidase Message.- 5 Protein and RNA Synthesis in Relation to Dormancy Breaking.- 5.1 Dormancy Breaking by Hormones and Light.- References.- 16 Leaf Senescence.- 1 Introduction.- 2 Senescence as a Developmental Event.- 2.1 Changes in Photosynthetic Capacity.- 2.2 The Disassembly Processes.- 2.2.1 Changes in Stroma and Thylakoid Functions.- 2.2.2 Changes in the Chloroplast Envelope.- 2.2.3 Extraplastidic Changes.- 2.2.4 Changes in Respiration and Energy Supply.- 2.3 The Senescent Leaf as a Source of Mineral Elements.- 2.3.1 Mobilization of Nitrogen.- 2.3.2 Proteolysis.- 2.3.3 Metabolism and Loading.- 2.4 Characteristics of the Senescence Switch.- 2.4.1 Senescence is Genetically Programmed.- 2.4.2 Activity of the Chloroplast Genome.- 2.4.3 Requirement for Cytoplasmic Protein Synthesis.- 2.4.4 Transcription.- 2.4.5 Reversibility of Senescence.- 3 Senescence as a Growth Correlation.- 3.1 Correlative Regulation of Senescence.- 3.1.1 Competition Between Organs.- 3.1.2 Space.- 3.1.3 Light.- 3.1.4 Nutrients.- 3.2 The Role of Growth Regulators.- 3.2.1 Cytokinins.- 3.2.2 Gibberellins, Growth Retardants and Auxins.- 3.2.3 Abscisic Acid.- 3.2.4 Ethylene.- 3.2.5 Other Compounds.- 4 Senescence as an Adaptation.- 4.1 Senescence and the Plant Life Cycle.- 4.2 Survival of the Individual.- 4.2.1 Tactical Senescence.- 4.2.2 Strategic Senescence.- 4.3 Senescence and Survival of the Population.- 4.3.1 Monocarpic Senescence.- 4.3.2 Turnover.- 4.4 Senescence and Crop Yield.- 4.4.1 Objectives in Crop Improvement.- 4.4.2 Soyabeans.- 4.4.3 Wheat.- 4.4.4 Grasses.- References.- 17 Macromolecular Aspects of Cell Wall Differentiation.- 1 Introduction.- 1.1 Control of Enzyme Activity.- 1.2 The Cell Wall.- 2 The Enzyme Systems.- 2.1 Pectin Polysaccharides.- 2.2 Hemicellulose.- 2.3 Cellulose.- 2.4 Lignin.- 3 Site of Synthesis, Transport and Organization of Material During Differentiation.- 3.1 Polysaccharide Synthesis and Movement.- 3.1.1 Sites of Synthesis of Pectin and Hemicelluloses.- 3.1.2 Changes in the Products Synthesized by the Membrane System During Differentiation.- 3.1.3 Movement of Vesicles During Secondary Thickening.- 3.1.4 Formation of Cell Plate and Orientation of Cell Division.- 3.1.5 Microfibrillar Deposition.- 3.2 Lignification.- 4 Possible Control Signals for the Changes in Cell Wall Synthesis.- 4.1 Signals at the Cell Surface.- 4.2 Plant Growth Hormones as Signals.- References.- Author Index.- Plant Name Index.