Amino Acids in Higher Plants

633 Pages·2015·5.51 MB·English

by  J. P. F. D'Mello

Amino Acids in Higher Plants

Amino Acids in Higher Plants
Edited by
J.P.F. D’Mello
Formerly of SAC, University of Edinburgh King’s
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Library of Congress Cataloging-in-Publication Data
Amino acids in higher plants / edited by J.P.F. D’Mello.
pages cm
Includes bibliographical references and index.
ISBN 978-1-78064-263-5 (alk. paper)
1.  Amino acids. 2.  Plants--Metabolism.  I. D’Mello, J.P. Felix.
QK898.A5A56 2015
572′.65--dc23
2014033212
ISBN-13: 978 1 78064 263 5
Commissioning editor: Rachel Cutts
Assistant editor: Alexandra Lainsbury
Production editor: James Bishop
Typeset by SPi, Pondicherry, India
Printed and bound in the UK by CPI Group (UK) Ltd, Croydon, CR0 4YY
Contents
Contributors xix
Preface xxiii
Glossary xxvii
PART I ENZYMES AND METABOLISM
1 Glutamate Dehydrogenase 1
G.O. Osuji and W.C. Madu
1.1 Abstract 1
1.2 Introduction 2
1.3 Glutamate Dehydrogenase Structure and Localization 2
1.4 Control Plants and Control Glutamate Dehydrogenase 3
1.5 Availability of Ammonium Ions 4
1.5.1 Ammonium ion contents of experimental tissues and plants 4
1.5.2 Glutamate deamination in mitochondria 5
1.6 Glutamate Dehydrogenase-Linked Schiff Base Amination Complex 5
1.6.1 Pesticide treatment and ammonium ion fertilization 5
1.6.2 Pesticide treatment, ammonium ion fertilization and protein contents 6
1.7 Protect the Glutamine Synthetase-Glutamate Synthase Cycle in
Glutamate Dehydrogenase Research 7
1.8 Molecular Biology of Glutamate Dehydrogenase 8
1.8.1 The supply of a-ketoglutarate from the citric acid cycle
to glutamate dehydrogenase and glutamate synthase 8
1.8.2 Aminating and deaminating activities 16
1.8.3 Amination-based crop yield doubling biotechnology 19
1.8.4 The aminating cassette of glutamate dehydrogenase isoenzymes 19
1.9 Food Security 20
1.10 Conclusions 23
Acknowledgements 24
References 24
v
vi Contents
2 Alanine Aminotransferase: Amino Acid Metabolism in Higher Plants 30
A. Raychaudhuri
2.1 Abstract 30
2.2 Introduction 30
2.3 Structure and Functions of Alanine 31
2.3.1 Structure of alanine 31
2.3.2 Functions of alanine 31
2.4 Alanine Metabolism 32
2.4.1 Alanine metabolism by alanine aminotransferase 33
2.5 Specific Cellular and Sub-Cellular Functions of Alanine
Aminotransferase 33
2.5.1 Homologues and tissue localization 34
2.5.2 Sub-cellular localization 35
2.6 A Phylogenetic Analysis of Alanine Aminotransferase 35
2.7 Purification of Alanine Aminotransferase 36
2.8 Protein Characterization of Alanine Aminotransferase 36
2.8.1 Subunits and substrate specificities 36
2.8.2 Kinetics and reaction mechanism 38
2.8.3 Inhibitors of the enzyme 43
2.8.4 Crystal structure 44
2.9 Diverse Roles of Alanine Aminotransferase in Plants 45
2.9.1 Roles in metabolism 45
2.9.1.1 Roles in carbon metabolism 45
2.9.1.2 Roles in photorespiration 47
2.9.1.3 Role in nitrogen use efficiency 48
2.9.2 Role in stress biology 48
2.9.2.1 Roles in hypoxia 49
2.9.2.2 Other abiotic and biotic stresses 50
2.10 Conclusions 50
References 52
3 Aspartate Aminotransferase 57
C.D. Leasure and Z-H. He
3.1 Abstract 57
3.2 Introduction 57
3.3 The Vitamin B Cofactor 58
6
3.4 Enzyme Function 58
3.4.1 The reaction mechanism 60
3.4.2 Enzyme properties 61
3.5 Enzyme Structure 61
3.5.1 K258 61
3.5.2 R292* 61
3.5.3 R386 61
3.5.4 D222 62
3.5.5 Y225 62
3.6 Enzyme Genetics 62
3.7 The Enzyme during Plant Development 63
3.8 The Role of Aspartate in Plants 63
3.8.1 C metabolism 64
4
3.9 Other Roles of Aspartate Aminotransferase 64
3.9.1 Moonlighting 64
3.9.2 Genetic engineering with aspartate aminotransferases 64
Contents vii
3.10 Future Research 65
3.11 Conclusions 65
References 65
4 Tyrosine Aminotransferase 68
A.O. Hudson
4.1 Abstract 68
4.2 Introduction 68
4.2.1 Aminotransferases: a brief introduction 68
4.2.2 A brief history of aminotransferase activity in plants 69
4.2.3 Oligomeric state, cofactor requirement and mechanism
of action of action of aminotransferases 69
4.3 Aminotransferases from the Model Organism Arabidopsis thaliana 70
4.4 The Anabolism of Tyrosine and Phenylalanine in Plants and Bacteria 71
4.4.1 The anabolism of tyrosine and phenylalanine in bacteria 71
4.4.2 A second pathway for the synthesis of tyrosine and
phenylalanine in plants 73
4.5 Properties of Tyrosine Aminotransferase Annotated
by the Locus Tag At5g36160 from Arabidopsis thaliana 74
4.5.1 Kinetic and physical properties 74
4.5.2 Substrate specificity 76
4.5.3 In vivo analysis of tyrosine aminotransferase 76
4.6 The Role of Tyrosine Aminotransferase in Plants 77
4.7 Conclusions 79
Acknowledgement 79
References 79
5 An insight Into the Role and Regulation of Glutamine Synthetase in Plants 82
C. Sengupta-Gopalan and J.L. Ortega
5.1 Abstract 82
5.2 Introduction 82
5.3 Classification of Glutamine Synthetase 83
5.4 Glutamine Synthetase in Plants 83
5.4.1 Chloroplastic glutamine synthetase 84
5.4.2 Cytosolic glutamine synthetase 84
5.5 Modulation of Glutamine Synthetase Expression in Transgenic Plants 86
5.6 Regulation of Glutamine Synthetase Gene Expression in Plants 88
5.6.1 Transcriptional regulation 88
5.6.2 Post-transcriptional regulation 89
5.6.3 Translational regulation 91
5.6.4 Post-translational regulation 91
5.7 Concluding Remarks 93
Acknowledgements 94
References 94
6 Asparagine Synthetase 100
S.M.G. Duff
6.1 Abstract 100
6.2 Introduction: the Role of Asparagine and Asparagine
Synthetase in Nitrogen Metabolism 100
6.3 Asparagine: History, Chemical Properties and Role in Plants 101
viii Contents
6.4 Asparagine Synthetase: an Early History of Research in Humans,
Microbes and Plants 102
6.5 The Occurrence of Asparagine Synthetase in Nature 104
6.6 The Expression and Function of Asparagine Synthetase in Plants 105
6.6.1 Nutritional and mineral deficiency 105
6.6.2 Seed germination 105
6.6.3 Light signalling 106
6.6.4 Developmental stage and tissue specificity 106
6.6.5 Environmental stress and carbohydrate depletion 107
6.6.6 Senescence and nitrogen remobilization 108
6.6.7 Seed maturation 108
6.6.8 Photorespiration 109
6.6.9 Nitrogen signalling and glutamine:asparagine ratio 109
6.6.10 Asparagine: a nitrogen carrier, storage compound,
detoxification mechanism and signal 110
6.7 Phylogeny, Subunit Structure and Enzymatic Activity
of Asparagine Synthetase 110
6.7.1 Phylogeny 110
6.7.2 Subunit structure 112
6.7.3 The enzymatic activities of asparagine synthesis 112
6.8 Kinetics, Reaction Mechanism and Crystal Structure
of B-type Asparagine Synthetases 112
6.8.1 Kinetics of plant asparagine synthetase 112
6.8.2 The crystal structure and reaction mechanism
of asparagine synthetase 114
6.9 Other Routes of Asparagine Synthesis in Plants 116
6.10 Asparagine Catabolism 116
6.11 Asparagine Synthetase and Agriculture 117
6.11.1 Seed protein content and crop yield 117
6.11.2 The impact of plant nutrition 118
6.11.3 Metabolic engineering and transgenic studies 118
6.12 Conclusions 120
Acknowledgements 120
References 120
7 Glutamate Decarboxylase 129
J.J. Molina-Rueda, A. Garrido-Aranda and F. Gallardo
7.1 Abstract 129
7.2 Introduction 129
7.3 Characteristics of Glutamate Decarboxylase in Plants 130
7.4 Glutamate Decarboxylase Gene Family 131
7.5 Expression of Glutamate Decarboxylase Genes 131
7.6 g-Aminobutyric Acid Synthesis and its Metabolic Context 135
7.6.1 The g-aminobutyric acid shunt pathway and stress 135
7.6.2 Alternative sources of g-aminobutyric acid
in plant tissues and transport 137
7.7 Classical and Recent Evidence Supporting the Functions
of Glutamate Decarboxylase and g-Aminobutyric Acid 137
7.8 Future Research 139
Acknowledgement 139
References 139
Contents ix
8 l-Arginine-Dependent Nitric Oxide Synthase Activity 142
F.J. Corpas, L.A. del Río, J.M. Palma and J.B. Barroso
8.1 Abstract 142
8.2 Introduction 142
8.3 Arginine Catabolism in Plants: Urea, Polyamines and Nitric Oxide 143
8.3.1 Urea metabolism 144
8.3.2 l-Arginine modulates polyamine and nitric oxide biosynthesis 144
8.3.3 Arginine and nitric oxide synthesis in higher plants 145
8.4 Modulation of l-Arginine-Dependent Nitric Oxide Synthase
Activity During Plant Development and Under Stress Conditions 147
8.4.1 Nitric oxide synthase activity during plant development 147
8.4.2 Nitric oxide synthase activity in plants under stress conditions 149
8.5 A Genetic Engineering Approach to Study of the Relevance
of Nitric Oxide Synthase Activity in Plants 150
8.6 Conclusions 150
Acknowledgements 151
References 151
9 Ornithine: At the Crossroads of Multiple Paths to
Amino Acids and Polyamines 156
R. Majumdar, R. Minocha and S.C. Minocha
9.1 Abstract 156
9.2 Introduction 156
9.3 Ornithine Biosynthesis and Utilization 158
9.4 Cellular Contents 159
9.5 Mutants of Ornithine Biosynthesis 160
9.6 Genetic Manipulation of Ornithine Metabolism and its
Impact on Amino Acids and Other Related Compounds 164
9.7 Ornithine Biosynthesis and Functions in Animals 168
9.8 Exogenous Supply of d- and l-Ornithine 169
9.9 Modelling of Ornithine Metabolism and Associated Flux:
Ornithine as a Regulatory Molecule 170
9.10 Conclusions 171
Acknowledgements 172
References 172
10 Polyamines in Plants: Biosynthesis From Arginine, and Metabolic,
Physiological and Stress-Response Roles 177
A.K. Mattoo, T. Fatima, R.K. Upadhyay and A.K. Handa
10.1 Abstract 177
10.2 Introduction 177
10.3 Substrates and Enzymes Catalysing Polyamine Biosynthesis 178
10.3.1 The route to the diamine putrescine 178
10.3.2 The route to higher polyamines, spermidine and
spermine/thermospermine 180
10.3.3 S-Adenosylmethionine decarboxylase 180
10.3.4 Spermidine synthase 181
10.3.5 Spermine/thermospermine synthases 181
10.4 Substrate Flux into the Polyamine Versus Ethylene Pathway 182
10.5 Back Conversion of Polyamines and Reactive Oxygen Species Signalling 183
10.6 Polyamines have an Impact on Metabolism 184