Plant Nucleotide Metabolism

Professor Hiroshi Ashihara is an Emeritus Professor at the Ochanomizu University, Tokyo, Japan. Dr Iziar A. Ludwig is a Postdoctoral Research Associate at the School of Medicine and Life Sciences, University Rovira I Virgili, Reus, Spain. Professor Alan Crozier is an Honorary Senior Research Fellow at the Department of Nutrition, University of California, Davis, CA, USA and the School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK.

• Preface xvPart I General Aspects of Nucleotide Metabolism 11 Structures of Nucleotide-Related Compounds 31.1 Introduction 31.2 Nomenclature and Abbreviations of Nucleotide-Related Compounds 31.3 Chemical Structures of Nucleotide-Related Compounds 51.3.1 Purines 51.3.1.1 Purine Bases 51.3.1.2 Purine Nucleosides 61.3.1.3 Purine Nucleotides 71.3.2 Pyrimidines 81.3.2.1 Pyrimidine Bases 91.3.2.2 Pyrimidine Nucleosides 91.3.2.3 Pyrimidine Nucleotides 101.3.3 Pyridines 111.4 Summary 11References 112 Occurrence of Nucleotides and Related Metabolites in Plants 132.1 Purines and Pyrimidines 132.1.1 Concentration of Purine and Pyrimidine Nucleotides 142.1.2 Concentration of Purine and Pyrimidine Bases and Nucleosides 162.2 Pyridine Nucleotides 172.2.1 Concentration of Pyridine Nucleotides 172.2.2 Concentration of Nicotinate and Nicotinamide 182.3 Concentration of Cytokinins 182.4 Alkaloids Derived from Nucleotides 182.5 Summary 19References 193 General Aspects of Nucleotide Biosynthesis and Interconversions 213.1 Introduction 213.2 De Novo Biosynthesis of Ribonucleoside Monophosphates 213.3 Interconversion of Nucleoside Monophosphates, Nucleoside Diphosphates, and Triphosphates 233.3.1 Nucleoside-Monophosphate Kinase 233.3.2 Specific Nucleoside-Monophosphate Kinases 243.4 Conversion of Nucleoside Diphosphates to Nucleoside Triphosphates 243.4.1 ATP Synthesis by Electron Transfer Systems 253.4.2 Substrate-Level ATP Synthesis 263.4.3 Nucleoside-Diphosphate Kinase 263.5 Biosynthesis of Deoxyribonucleotides 293.6 Nucleic Acid Biosynthesis 293.7 Supply of 5-Phosphoribosyl-1-Pyrophosphate 303.8 Supply of Amino Acids for Nucleotide Biosynthesis 333.9 Nitrogen Metabolism and Amino Acid Biosynthesis in Plants 333.10 Summary 34References 35Part II Purine Nucleotide Metabolism 394 Purine Nucleotide Biosynthesis De Novo 414.1 Introduction 414.2 Reactions and Enzymes 434.2.1 Synthesis of Phosphoribosylamine 444.2.2 Synthesis of Glycineamide Ribonucleotide 464.2.3 Synthesis of Formylglycineamide Ribonucleotide 464.2.4 Synthesis of Formylglycinamidine Ribonucleotide 474.2.5 Synthesis of Aminoimidazole Ribonucleotide 474.2.6 Synthesis of Aminoimidazole Carboxylate Ribonucleotide 484.2.7 Synthesis of Aminoimidazole Succinocarboxamide Ribonucleotide 484.2.8 Synthesis of Aminoimidazole Carboxamide Ribonucleotide 494.2.9 Synthesis of IMP via Formamidoimidazole Carboxamide Ribonucleotide 494.2.10 Synthesis of AMP 504.2.11 Synthesis of GMP 514.3 Summary 52References 525 Salvage Pathways of Purine Nucleotide Biosynthesis 555.1 Introduction 555.2 Characteristics of Purine Salvage in Plants 565.3 Properties of Purine Phosphoribosyltransferases 595.3.1 Adenine Phosphoribosyltransferase 595.3.2 Hypoxanthine/Guanine Phosphoribosyltransferase 595.3.3 Xanthine Phosphoribosyltransferase 625.4 Properties of Nucleoside Kinases 625.4.1 Adenosine Kinase 625.4.2 Inosine/Guanosine Kinase 645.4.3 Deoxyribonucleoside Kinases 645.5 Properties of Nucleoside Phosphotransferase 655.6 Role of Purine Salvage in Plants 665.7 Summary 66References 666 Interconversion of Purine Nucleotides 716.1 Introduction 716.2 Deamination Reactions 716.2.1 Routes of Deamination of Adenine Ring 736.2.2 AMP Deaminase 736.2.3 Routes of Deamination of Guanine Ring 746.2.4 Guanosine Deaminase 756.3 Dephosphorylation Reactions 756.4 Glycosidic Bond Cleavage Reactions 766.4.1 Adenosine Nucleosidase 766.4.2 Inosine/Guanosine Nucleosidase 786.4.3 Non-specific Purine Nucleosidases 786.4.4 Recombinant Non-Specific Nucleosidases 786.5 In Situ Metabolism of 14C-Labelled Purine Nucleotides 796.5.1 Metabolism of Adenine Nucleotides 796.5.2 Metabolism of Guanine Nucleotides 806.6 In Situ Metabolism of Purine Nucleosides and Bases 806.6.1 Metabolism of Adenine and Adenosine 826.6.2 Metabolism of Guanine and Guanosine 836.6.3 Metabolism of Hypoxanthine and Inosine 846.6.4 Metabolism of Xanthine and Xanthosine 846.6.5 Metabolism of Deoxyadenosine and Deoxyguanosine 856.7 Summary 88References 897 Degradation of Purine Nucleotides 957.1 Introduction 957.2 (S)-Allantoin Biosynthesis from Xanthine 977.2.1 Xanthine Dehydrogenase 997.2.2 Urate Oxidase 1007.2.3 Allantoin Synthase 1017.3 Catabolism of (S)-Allantoin 1017.3.1 Allantoinase 1037.3.2 Allantoate Amidohydrolase 1047.3.3 (S)-Ureidoglycine Aminohydrolase 1047.3.4 Allantoate Amidinohydrolase 1057.3.5 Ureidoglycolate Amidohydrolase 1057.3.6 (S)-Ureidoglycolate-urea Lyase 1057.3.7 Urease 1057.4 Purine Nucleotide Catabolism in Plants 1067.5 Accumulation and Utilization of Ureides in Plants 1077.5.1 Ureides in Plant Tissues and Xylem Sap 1077.5.2 Role of Ureides in Nitrogen Storage and Transport 1097.5.3 Role of Ureides in Germination and Development of Seeds 1097.5.4 Ureide Formation in Nodules of Tropical Legumes 1107.5.5 Other Role of Ureides in Plants 1107.6 Summary 111References 111Part III Pyrimidine Nucleotide Metabolism 1178 Pyrimidine Nucleotide Biosynthesis De Novo 1198.1 Introduction 1198.2 Reactions and Enzymes of the De Novo Biosynthesis 1218.2.1 Synthesis of Carbamoyl-phosphate 1218.2.2 Formation of Carbamoyl-aspartate 1238.2.3 Formation of Dihydroorotase from Carbamoyl-aspartate 1238.2.4 Formation of Orotate from Dihydroorotate 1248.2.5 Synthesis of UMP from Orotate 1258.2.6 Synthesis of CTP from UTP 1268.3 Control Mechanism of De Novo Pyrimidine Ribonucleotide Biosynthesis 1278.3.1 Fine Control of the De Novo Pathway 1278.3.2 Coarse Control of the De Novo Pathway 1298.4 Biosynthesis of Thymidine Nucleotide 1298.4.1 Formation of dUMP 1298.4.2 Conversion of UMP to dUMP via dUTP 1308.4.3 Conversion of dUMP to dTMP 1308.4.4 Thymidine Monophosphate Kinase 1318.5 Summary 131References 1319 Salvage Pathways of Pyrimidine Nucleotide Biosynthesis 1379.1 Introduction 1379.2 Characteristics of Pyrimidine Salvage in Plants 1379.3 Enzymes of Pyrimidine Salvage 1399.3.1 Uracil Phosphoribosyl Transferase 1409.3.2 Uridine/Cytidine Kinase 1429.3.3 Thymidine Kinase 1439.3.4 Deoxyribonucleoside Kinase 1449.3.5 Nucleoside Phosphotransferase 1449.4 Role of Pyrimidine Salvage in Plants 1459.5 Summary 146References 14610 Interconversion of Pyrimidine Nucleotides 14910.1 Introduction 14910.2 Deaminase Reactions 14910.2.1 Cytidine Deaminase 14910.2.2 Cytosine Deaminase 15210.2.3 Deoxycytidylate Deaminase 15210.3 Nucleosidase and Phosphorylase Reactions 15210.3.1 Uridine Nucleosidase 15210.3.2 Thymidine Phosphorylase 15310.4 In Situ Metabolism of 14C-Labelled Pyrimidines 15310.4.1 Metabolic Fate of Orotate 15410.4.2 Metabolic Fate of Uridine and Uracil 15410.4.3 Metabolic Fate of Cytidine and Cytosine 15610.4.4 Metabolic Fate of Deoxycytidine 15710.4.5 Metabolic Fate of Thymidine 15810.5 Summary 159References 16011 Degradation of Pyrimidine Nucleotides 16511.1 Introduction 16511.2 Enzymes Involved in the Degradation Routes of Pyrimidines 16611.2.1 Dihydropyrimidine Dehydrogenase 16711.2.2 Dihydropyrimidinase 16711.2.3 𝛽-Ureidopropionase 16811.3 The Metabolic Fate of Uracil and Thymine 16811.4 Summary 169References 170Part IV Physiological Aspects of Nucleotide Metabolism 17312 Growth and Development 17512.1 Introduction 17512.2 Embryo Maturation 17512.3 Germination 18012.3.1 Purine Metabolism in Germination 18012.3.2 Pyrimidine Metabolism in Germination 18312.4 Organogenesis 18512.5 Breaking Bud Dormancy 18612.6 Fruit Ripening 18612.7 Storage Organ Development and Sprouting 18612.8 Suspension-Cultured Cells 18712.8.1 Nucleotide Pools 18712.8.2 Nucleotide Biosynthesis 18812.8.3 Nucleotide Availability 18812.9 Molecular Studies 18912.10 Summary 189References 18913 Environmental Factors and Nucleotide Metabolism 19513.1 Introduction 19513.2 Effect of Phosphate on Nucleotide Metabolism 19513.3 Effect of Salts on Nucleotide Metabolism 19913.4 Effect of Water Stress 20213.5 Effect of Wound Stress 20213.6 Effect of Iron Deficiency 20513.7 Effect of Light 20613.8 Summary 206References 206Part V Purine Alkaloids 21114 Occurrence of Purine Alkaloids 21314.1 Introduction 21314.2 Chemical Structure of Purine Alkaloids 21314.3 Occurrence of Purine Alkaloids in Plants 21514.3.1 Purine Alkaloids in Tea and Related Species 21514.3.2 Purine Alkaloids in Coffee and Related Species 21814.3.3 Purine Alkaloids in Maté 22014.3.4 Purine Alkaloids in Cacao and Related Species 22114.3.5 Purine Alkaloids in Cola Species 22314.3.6 Purine Alkaloids in Guaraná and Related Species 22314.3.7 Purine Alkaloids in Citrus Species 22414.3.8 Purine Alkaloids in Other Plants 22514.4 Summary 226References 22615 Biosynthesis of Purine Alkaloids 23115.1 Introduction 23115.2 A Brief History of Caffeine Biosynthesis Research 23115.3 Caffeine Biosynthesis Pathway 23415.3.1 N-Methyltransferase Nomenclature 23615.3.2 Formation of 7-Methylxanthine from Xanthosine 23615.3.3 7-Methylxanthosine Synthase 23715.3.4 N-Methylnucleosidase 24015.3.5 Formation of Caffeine from 7-Methylxanthine 24115.3.6 Caffeine Synthase 24115.3.7 Theobromine Synthase 24415.4 Genes and Proteins of Caffeine Synthase Family 24515.5 Xanthosine Biosynthesis from Purine Nucleotides 24915.5.1 De Novo Purine Route 24915.5.2 Adenosine Monophosphate Route 25115.5.3 S-Adenosyl-L-methionine Cycle Route 25115.5.4 Nicotinamide Adenine Diphosphate Catabolism Route 25215.5.5 Guanosine Monophosphate Route 25315.6 Summary 253References 25316 Physiological and Ecological Aspects of Purine Alkaloid Biosynthesis 25916.1 Introduction 25916.2 Physiology of Caffeine Biosynthesis 25916.2.1 Purine Alkaloid Biosynthesis in Different Species 26116.2.2 Camellia 26116.2.3 Coffea 26416.2.4 Theobroma 26416.2.5 Maté 26616.2.6 Guaraná 26716.2.7 Citrus 26816.3 Subcellular Localization of Caffeine Biosynthesis 26816.3.1 Caffeine Synthase 26816.3.2 The De Novo Route Enzymes 26916.3.3 The AMP Route Enzymes 27016.3.4 The SAM Route Enzymes 27016.3.5 Subcellular Localization and Transport of Intermediates 27016.4 Regulation of Caffeine Biosynthesis 27016.5 Ecological Roles of Caffeine 27116.5.1 Allelopathic Function Theory 27116.5.2 Effect of Caffeine on Plant Growth 27216.5.3 Allelopathy in Natural Ecosystems 27316.5.4 Chemical DefenceTheory 27416.6 Summary 274References 27517 Metabolism of Purine Alkaloids and Biotechnology 28117.1 Introduction 28117.2 Metabolism of Purine Alkaloids 28117.2.1 Methylurate Biosynthesis 28117.2.2 The Major Pathway of Caffeine Degradation 28217.2.3 Purine Catabolic Pathways in Alkaloid Plants 28417.3 Diversity of Purine Alkaloid Metabolism in Plants 28517.3.1 Coffea Species 28517.3.2 Camellia Species 28617.3.3 Maté Species 29017.3.4 Cacao Species 29017.3.5 Other Plant Species 29017.3.6 Bacteria 29117.4 Biotechnology of Purine Alkaloids 29317.4.1 Decaffeinated Coffee Plants 29317.4.2 Decaffeinated Tea Plants 29417.5 Caffeine-Producing Transgenic Plants 29517.5.1 Antiherbivore Activity 29517.5.2 Antipathogen Activity 29617.6 Summary 298References 298Part VI Pyridine Nucleotide Metabolism 30118 Pyridine (Nicotinamide Adenine) Nucleotide Biosynthesis De Novo 30318.1 Introduction 30318.2 Two Distinct Pathways of De Novo Nicotinate Mononucleotide Biosynthesis 30318.3 The Outline of the De Novo Pathway of NAD Biosynthesis in Plants 30418.4 Enzymes Involved in De Novo NAD Synthesis in Plants 30718.4.1 l-Aspartate Oxidase and Quinolinate Synthase 30818.4.2 Quinolinate Phosphoribosyltransferase 30918.4.3 Nicotinate Mononucleotide Adenylyltransferase 30918.4.4 NAD Synthetase 31018.4.5 NAD Kinase 31018.5 Summary 310References 31019 Pyridine Nucleotide Cycle 31519.1 Introduction 31519.2 Pyridine Nucleotide Cycle 31519.2.1 Major Pyridine Nucleotide Cycles in Plants 31719.2.2 Alternative Pyridine Nucleotide Cycles in Plants 31819.2.3 Rate-Limiting Step of the Pyridine Cycle 31919.3 Catabolism of NAD 32019.3.1 Reactions from NAD to Nicotinate 32019.3.2 Degradation of Pyrimidine Ring 32019.3.3 Nicotinate Conversion to Nicotinate-N-Glucoside and N-Methylnicotinate 32119.4 Enzymes Involved in NAD Catabolism 32119.4.1 Direct NAD Cleavage Enzymes 32119.4.2 NAD Pyrophosphatase 32119.4.3 5′-Nucleotidase and Nicotinamide Riboside Nucleosidase 32219.4.4 Nicotinamidase and Nicotinamide Riboside Deaminase 32219.5 Salvage of Nicotinamide and Nicotinate 32319.5.1 Nicotinate Phosphoribosyltransferase 32319.5.2 Nicotinate Riboside Kinase 32419.6 Summary 325References 325Part VII Pyridine Alkaloids 32920 Occurrence and Biosynthesis of Pyridine Alkaloids 33120.1 Introduction 33120.2 Occurrence of Pyridine Alkaloids 33320.2.1 Trigonelline in Plants 33320.2.2 Other Pyridine Alkaloids in Plants 33420.3 Biosynthesis of Pyridine Alkaloids 33520.3.1 Trigonelline Biosynthesis 33520.3.2 Nicotinate N-Glucoside Biosynthesis 33620.3.3 The Diversity of Biosynthetic Reactions 33720.3.3.1 Ferns 33820.3.3.2 Gymnosperms 33820.3.3.3 Angiosperms 33920.3.3.4 Nicotinate Conjugate Formation 34020.3.4 Biosynthesis of Ricinine 34120.3.5 Biosynthesis of Nicotine (Pyridine Ring) 34320.4 Summary 345References 34521 Physiological Aspect and Biotechnology of Trigonelline 35121.1 Introduction 35121.2 Physiological Aspect of Trigonelline Biosynthesis 35121.2.1 Coffee 35121.2.2 Leguminous Plants 35421.3 Physiological Aspect of Nicotinate N-Glucoside Biosynthesis 35621.4 The Role of Trigonelline in Plants 35621.4.1 Role of Trigonelline as a Nutrient Source 35721.4.2 Role of Trigonelline as a Compatible Solute 35721.4.3 Trigonelline and Nyctinasty 35821.4.4 Cell Cycle Regulation 35821.4.5 Detoxification of Nicotinate 35921.4.6 Signal Transduction 36021.4.7 Role of Host Selection by Herbivores 36021.5 Biotechnology of Trigonelline 36021.6 Summary 362References 363Part VIII Other Nucleotide-Related Metabolites 36722 Sugar Nucleotides 36922.1 Introduction 36922.2 The Sugar Nucleotide Moiety 37022.3 Enzymes of Sugar Nucleotide Biosynthesis 37122.3.1 UDP-Glucose Pyrophosphorylase 37122.3.2 UDP-Sugar Pyrophosphorylase 37422.3.3 Sucrose Synthase 37622.4 Localization of UDP-Glucose-Producing Enzymes 37722.5 UDP-Glucose-Interconversion 37722.6 Other Metabolites 37922.6.1 Cyclic Nucleotides 37922.6.2 Diadenosine Tetraphosphate 38122.6.3 Purine Alkaloid Glucosides 38222.7 Summary 382References 38223 Cytokinins 38723.1 Introduction 38723.2 Adenosine Phosphate-Isopentenyl Formation 38823.3 trans-Zeatin Phosphate Synthesis 38923.4 Formation of Cytokinin Bases 38923.5 Effect of Nucleotide Enzymes in Cytokinins 39023.5.1 Cytokinin Inactivation by Adenine Phosphoribosyltransferase 39023.5.2 Homeostasis of Cytokinin by Adenosine Kinase 39223.5.3 Endodormancy of Potato and Purine Nucleoside Phosphorylase 39223.6 New Purine-Related Plant Growth Regulators 39223.7 Summary 393References 394Part IX Dietary Plant Alkaloids, Their Bioavailability, and Potential Impact on Human Health 39724 Bioavailability and Potential Impact on Human Health of Caffeine, Theobromine, and Trigonelline 39924.1 Caffeine 39924.1.1 Dietary Caffeine 39924.1.2 Bioavailability and Bioactivity of Caffeine 40024.2 Theobromine 40424.2.1 Interactions with Flavan-3-ols 40424.2.2 Toxicity ofTheobromine 40624.3 Trigonelline 40624.3.1 Dietary Trigonelline 40624.3.2 Bioavailability and Bioactivity of Trigonelline 40724.4 Summary 409References 409Index 415