Nucleic Acids and Proteins in Plants I

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.

Contenu

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 Phosphory…