Tai Lieu Chat Luong 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 Buildings Campus, Edinburgh, UK CABI is a trading name of CAB International CABI 38 Chauncy Street Suite 1002 Boston, MA 02111 USA CABI Nosworthy Way Wallingford Oxfordshire OX10 8DE UK Tel: +44 (0)1491 832111 Fax: +44 (0)1491 833508 E-mail: info@cabi.org Website: www.cabi.org Tel: +1 800 552 3083 (toll free) E-mail: cabi-nao@cabi.org © CAB International 2015 All rights reserved No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners A catalogue record for this book is available from the British Library, London, UK 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 78064 263 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 G.O Osuji and W.C Madu 1.1 Abstract 1.2 Introduction 1.3 Glutamate Dehydrogenase Structure and Localization 1.4 Control Plants and Control Glutamate Dehydrogenase 1.5 Availability of Ammonium Ions 1.5.1 Ammonium ion contents of experimental tissues and plants 1.5.2 Glutamate deamination in mitochondria 1.6 Glutamate Dehydrogenase-Linked Schiff Base Amination Complex 1.6.1 Pesticide treatment and ammonium ion fertilization 1.6.2 Pesticide treatment, ammonium ion fertilization and protein contents 1.7 Protect the Glutamine Synthetase-Glutamate Synthase Cycle in Glutamate Dehydrogenase Research 1.8 Molecular Biology of Glutamate Dehydrogenase 1.8.1 The supply of a-ketoglutarate from the citric acid cycle to glutamate dehydrogenase and glutamate synthase 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 Acknowledgements24 References24 v vi Contents 2 Alanine Aminotransferase: Amino Acid Metabolism in Higher Plants A Raychaudhuri 30 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 Aminotransferase33 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 References52 3 Aspartate Aminotransferase C.D Leasure and Z-H He 3.1 Abstract 3.2 Introduction 3.3 The Vitamin B6 Cofactor 3.4 Enzyme Function 3.4.1 The reaction mechanism 3.4.2 Enzyme properties 3.5 Enzyme Structure 3.5.1 K258 3.5.2 R292* 3.5.3 R386 3.5.4 D222 3.5.5 Y225 3.6 Enzyme Genetics 3.7 The Enzyme during Plant Development 3.8 The Role of Aspartate in Plants 3.8.1 C4 metabolism 3.9 Other Roles of Aspartate Aminotransferase 3.9.1 Moonlighting 3.9.2 Genetic engineering with aspartate aminotransferases 57 57 57 58 58 60 61 61 61 61 61 62 62 62 63 63 64 64 64 64 Contents vii 3.10 Future Research 65 3.11 Conclusions 65 References65 4 Tyrosine Aminotransferase A.O Hudson 68 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 thaliana70 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 thaliana74 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 Acknowledgement79 References79 5 An insight Into the Role and Regulation of Glutamine Synthetase in Plants C Sengupta-Gopalan and J.L Ortega 82 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 Acknowledgements94 References94 6 Asparagine Synthetase S.M.G Duff 6.1 Abstract 6.2 Introduction: the Role of Asparagine and Asparagine Synthetase in Nitrogen Metabolism 6.3 Asparagine: History, Chemical Properties and Role in Plants 100 100 100 101 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 Acknowledgements120 References120 7 Glutamate Decarboxylase J.J Molina-Rueda, A Garrido-Aranda and F Gallardo 129 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 Acknowledgement139 References139 Contents ix 8 l-Arginine-Dependent Nitric Oxide Synthase Activity142 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 Acknowledgements151 References151 9 Ornithine: At the Crossroads of Multiple Paths to Amino Acids and Polyamines R Majumdar, R Minocha and S.C Minocha 156 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-Ornithine169 9.9 Modelling of Ornithine Metabolism and Associated Flux: Ornithine as a Regulatory Molecule 170 9.10 Conclusions 171 Acknowledgements172 References172 10 Polyamines in Plants: Biosynthesis From Arginine, and Metabolic, Physiological and Stress-response Roles A.K Mattoo, T Fatima, R.K Upadhyay and A.K Handa 177 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/thermospermine180 10.3.3 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United States of America 97, 22920–22925 Zimmerli, L., Hou, B.H., Tsai, C.H., Jakab, G., Mauch-Mani, B and Somerville, S (2008) The xenobiotic b-aminobutyric acid enhances Arabidopsis thermotolerance The Plant Journal 54, 144–151 Index AAP (amino acid permease) transporters 320, 329 ABC (ATP-binding cassette) transporters 304–305 abiotic stress 262–263, 560, 562–563 abscisic acid (ABA) 186, 266–267, 526, 556, 558 ACC synthase 182, 545, 546, 570 acceptable daily intakes (ADIs) 475, 476 acetyl coenzyme A (acetyl-CoA) 197 N-acetyl-Glu kinase (NAGK) 158, 160 N(d)-acetylornithine 163, 510, 518, 543 N-acetylserine (NAS) 207 O-acetylserine (OAS) biosynthesis 195 cluster genes identification 207–209, 208, 209 molecular functions 210–211, 211 regulation 209–210 in sulfur status signalling 196, 207, 212 O-acetylserine(thiol)-lyase (OASTL) 195–196 in cysteine synthase complex 199–202, 200, 222–224, 223 family isoforms, functions 224–229 phylogeny 222, 223 acetyltransferases serine acetyltransferase 195–207 serotonin N-acetyltransferase (SNAT) 400, 402–403, 406 acid hydrolysis 482–483, 488 acivicin 450, 451 ackee fruit (Blighia sapida) 512, 520, 521–522 acrylamide 118, 487, 488 acute toxicity testing 471, 518 additive interactions 522, 557, 559 adenosine 5'-phosphosulfate reductase (APR) 206, 207–209, 221, 225 S-adenosylmethionine (SAM) homeostatic regulation in cells 183 inhibition of aspartate kinase 236 role in metabolic pathways 180, 182, 545 S-adenosylmethionine decarboxylase (SAMDC) 180–181 ADME studies (toxicology) 470 advanced glycation end-products (AGEs) 566 agmatine 144, 178–179 agmatine iminohydrolase (AIH) 179–180 alanine (Ala) accumulation in oxygen deficiency 268–270, 269 functions in plants 31–32 metabolism 32, 32–33 structure and natural occurrence 31, 31 alanine aminotransferase (AlaAT) enzyme characterization 30 inhibitors 43, 43 kinetics and reaction mechanism 38, 41–42, 42 molecular structure 44, 44–45 reaction catalysed 33, 33 subunit structures and substrates 36–38, 39–40 localization in cells and tissues diversity of specific activities 33–34 homologues in different tissues 34–35 sub-cellular locations and activities 35 phylogenetic analysis 35–36, 37 purification 36, 38 roles in plant biology 30–31, 45, 51 carbon and nitrogen metabolism 45–48, 46 stress responses 48–50, 268–269, 269 alanine:glyoxylate aminotransferase (AGT) 35 albizziin 450–451, 451 585 586 Index alcohol dehydrogenase (ADH) 267 algae, carbon/nitrogen metabolism 282–283, 286–287 alkali hydrolysis 483–485, 484, 486 alkaloids 167 allelopathy 442, 443, 454, 514 amine oxidases, copper-containing (CuAO) 145, 183 amino acid permease (AAP) transporters 320, 329 amino acid–polyamine–organocation superfamily see APC transporters amino acids analogues 448, 450, 454, 510, 510–511 analytical methods composition of plant products 488–492 data presentation 488 free amino acid content 487 sample preparation 482 techniques 481–482, 482–487 biosynthesis connection with glucosinolate metabolism 440–441 role of ornithine 157, 159 in stress 262–263, 264 d- and l- isomers 491–492, 552–553 export dynamics 298–307 metabolic availability (in foods) 499–503 summary of roles in plants 538–541 b-aminobutyric acid (BABA) 515, 518, 525–527, 563 g-aminobutyric acid see GABA S-aminoethyl-l-cysteine (AEC) 239, 454, 454 aminomethylphosphonic acid (AMPA) levels in plants 463–466, 467 microbiological product in soil 467–468, 469, 470 aminotransferases in Arabidopsis genome 51, 70–71, 71, 72 catalytic properties 32, 68–69, 69 inhibitors 43, 449, 449–450, 454 metabolic roles in plants and animals 69, 550, 552 specific enzymes alanine aminotransferase 33–51 aspartate aminotransferase 57–65 tyrosine aminotransferase 71–79 structures and action mechanisms 69–70, 70 ammonium ions (NH4+) assimilation green microalgae 282–283 vascular plants 84, 283, 284, 318 metabolic availability 4–5 produced and oxidised by soil microbes 317–318 released by photorespiration 109, 278 amplified fragment length polymorphisms (AFLPs) 210 antagonistic interactions 514, 518, 556, 558, 558 anthranilate synthase (AnS) 86, 362, 363–364 APC transporters 137, 303–304, 304 aphid feeding, plant responses 163, 565 Arabidopsis thaliana (model organism) aminotransferase genes 51, 70–71, 71, 72 glutamate decarboxylase gene family 132 SERAT and OASTL (cysteine synthase) enzymes 222, 222 arginase 144, 512–513, 523, 542, 560 in animals 168 arginine (Arg) analogues (non-protein AAs) 144, 510, 520–521 metabolic roles 542 in defence responses 560 l-arginine catabolism in plants 143, 143–147 synthesis in urea cycle 513, 513 residues R292* and R386 in AspAT apoprotein 61–62 arginine decarboxylase (ADC) 164, 165, 167, 178–179 aromatic amino acids analogues (non-protein AAs) 510–511 biosynthesis and roles 71–73, 72, 73, 547–549, 548 effects of deficiency 462 ascaulitoxin aglycone 454, 455 asparaginase (Asnase) 102–103, 116–117 asparagine (Asn) biosynthesis 102, 103, 116, 116, 319 catabolism 116–117, 117 quantitative analysis 483, 487 roles in plants 100, 102, 110, 120 accumulation in abiotic stress 271 agricultural implications 117–118 N status, importance relative to glutamine 109, 328 structure and properties 101, 101–102 asparagine synthetase (AsnS, AS) discovery and research 102–104, 120 enzyme characterization kinetics and reaction mechanism 112–114, 114, 115, 115–116 molecular structure 112, 114–115 reactions catalysed 104, 112, 113 inhibition by albizziin 450–451 metabolic engineering with transgenics 87–88, 118–120 occurrence of A and B forms 104–105 phylogeny 110, 111–112 roles in plant metabolism 101, 105–106, 107–109 expression in stress 271 tissue-specific expression 106–107 Index 587 aspartate (aspartic acid, Asp) in C4 metabolism 64 residue D222 in AspAT apoprotein 62 synthesis and roles in plants 57–58, 63–64 allosteric control of glycolysis 290 aspartate metabolic pathway 234–238, 235, 264, 270–272 aspartate aminotransferase (AspAT, AAT) enzyme structure and function reaction mechanism 60–61 structure 44, 58–59, 61–62 substrate affinities 61 transamination reaction 59, 59–60 genetic regulation expression and localization during development 63, 65 genes and gene products 62–63 genetic engineering opportunities 64 roles in plant metabolism 57–58, 65 long-chain fatty acid uptake 64 nitrogen and C4 pathways 63–64 vitamin B6 homeostatic sensing 63 aspartate kinase (AK) 236–237 aspartate semialdehyde dehydrogenase (ASADH) 237 aspergillomarasmine A 454, 456 ATP (adenosine triphosphate) enzyme binding sites 83, 115 production pathways 46, 50, 266, 288 requirement for asparagine synthesis 101, 102, 104, 104 used in sulphate assimilation 220, 221 ATP-binding cassette (ABC) transporters 304–305 autophagy 228–229 auxin biosynthesis endogenous auxin types 341, 348, 348–349 evolution in plants 352–354 history of research 341–342 pathways 342–348, 347, 354, 548 regulation environmental responses 350–351 genetic, mechanisms 349–350 homeostasis, role of conjugates 352, 353, 549, 554 hormonal 351–352 tissue and cellular sites 342 see also indole acetic acid availability amino acids bioavailability in foodstuffs 497–503, 566 non-protein amino acids 508 for plant stress tolerance 263 energy 93, 263, 271 metabolic availability (MA) assay 499–503 metabolic sources of NH4+ ions 4–5 nitrogen, in soils 315–318, 319 avenanthramides (Avs) 372–375, 373, 375 BABA (b-aminobutyric acid) 515, 518, 525–527, 563 barley (Hordeum spp.) 368 BCNA (b-cyanoalanine) 512, 518, 519, 524 benzoxazinones (Bxs) defence response mechanisms 371–372 glycosylation and toxicity 369–371 synthetic pathway 364–368, 365 bialaphos 449, 451, 452, 453 bioavailability of AAs in foods 497–503 biotic stress responses see allelopathy; defence responses bisavenanthramides (bisAvs), antifungal activity 374–375, 375 BMAA (b-N-methylamino-l-alanine) 510, 515, 521, 524 BOAA (b-N-oxalylamino-l-alanine) 510, 519, 521 branched-chain amino acids (BCAAs) 270, 545–547 aminotransferases (BCATs) 438, 546 Brassica forage toxicity 512, 519, 524, 528, 529 brassinosteroids 441, 546 C4 metabolism AlaAT as C/N metabolism shuttle 34, 45, 46 aspartate and AspAT involvement 64 Ca-binding protein kinases 267 cadaverine 167 callose deposition 372, 442, 526 calmodulin (CaM) binding domain in GAD 130, 131, 134, 134 complex, with nitric oxide synthase 145 camalexin 226, 346, 563, 564 cAMP (cyclic adenosine monophosphate) 403 canavanine metabolism 512–513, 513 detoxification 527 as potential anti-cancer drug 144 toxicity 515, 517–518, 520, 522–523 cancer therapy 394, 528–529, 569 carbamoyl phosphate synthatase (CPS) 164 carbon metabolism primary pathways in plants 278–282, 279, 284 responses to carbon depletion 107–108 responses to nitrogen supply 282–284 roles of AlaAT 45–47, 46 carcinogens 472–473 CAS (b-cyanoalanine synthase) 226–227 castor oil seed (Ricinus communis) metabolism 287 Cauliflower mosaic virus (CaMV) promoter 158, 165 cell walls phenolic polymers 377, 380 reinforced by avenanthramides 375, 376 chitin, elicitor of Avs in oat leaves 374, 376 chloroplastic glutamine synthetase (GS2) 84, 88 588 Index chorismate as aromatic AA precursor 71–73, 72, 73 secondary metabolite derivatives 374 chromatography (in AA analysis) 486, 487, 492 citrulline (Cit) 158, 164, 542–543 climate change impacts 22, 315–316, 330 cofactors, pyridoxal-5'-phosphate (active vitamin B6) as AlaAT cofactor 33, 44, 44–45 as AspAT cofactor 58, 59 competitive inhibition 452, 523 complementary DNA (cDNA), in enzyme characterization 74, 239, 241 cornexistin 449, 450 crop yield GDH amination-based doubling 19, 20–23, 22 genetic improvement and Asn metabolism 117–118 cross-talk, in signalling 351, 527, 554, 559, 563 CS26 (S-sulfocysteine synthase) 225–226 b-cyanoalanine (BCNA) 512, 518, 519, 524 b-cyanoalanine synthase (CAS, CYS-C1) 226–227 cyanogenic glucosides 369, 370, 436, 437 cycad flour toxicity 521 cycloserine 43, 44–45 CYS-C1 (b-cyanoalanine synthase) 226–227 b-cystathionase 450 cystathionine-g-synthase (CGS) 237 cysteine (Cys) biosynthesis 195–196, 199, 200, 222 cellular compartmentalization 224, 225 homeostatic regulation 222–224, 223 quantitative analysis 483, 490 roles in plants 220, 225–229, 545 l-cysteine desulfhydrase (DES) 227–229 cysteine synthase complex regulatory function 206, 222–224 structure and components 199–202, 200 see also O-acetylserine(thiol)-lyase cytosolic glutamine synthetase (GS1) 84–88 DABA (a,g-diaminobutyric acid) 519, 524 decarboxylases functions in plants and animals 550–551, 552 specific types S-adenosylmethionine decarboxylase 180–181 glutamate decarboxylase 129–139 glycine decarboxylase 543, 550–551 ornithine decarboxylase 522 tryptophan decarboxylase (TDC) 399, 401–402, 405–406 defence responses (biotic stress) categories of activity 442 hypersensitivity 150, 228 inducible responses 371–372, 374–375, 377–379 involvement of secondary compounds 549–550 modulation of nitrogen metabolism 119–120 physical responses 372, 377 and plant hormones 554, 567–568 resistance priming with BABA 526 signalling pathways 50 dehydrogenases aspartate semialdehyde dehydrogenase 237 glutamate dehydrogenase 2–20 homoserine dehydrogenase 236–237 deoxyxylulose phosphate (DXP) 58 derivatizing reagents 486, 492 DES (l-cysteine desulfhydrase) 227–229 developmental and reproductive toxicology (DART) 473–474 diamine oxidase (DAO) 171, 183 DIBOA/DIMBOA 364–366, 369 digestibility 498–499 dihydrodipicolinate synthase (DHDPS) 238–240, 453–454 dihydroxyacetone phosphate (DHAP) 286 Dof transcription factors 89 DOPA (3,4-dihydroxyphenylalanine) 401, 510–511, 517 drug/metabolite transporter family (DMT) 302–303 endocrine disruption 474 energy availability in stress 93, 263, 271 energy homeostasis 46–47, 50 environment abiotic stress factors 262–263, 560, 562–563 fate and behaviour of glyphosate 463, 466–469, 470 stress response enhancement 134, 526–527 enzymes in plants and animals, compared 550–553, 551 research on regulatory mechanisms 92, 572 salvage pathway in plants 58 substrate specificity in bacteria and plants 41 see also aminotransferases; decarboxylases; dehydrogenases; synthetases/synthases EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) 456, 462, 465 ethylene (ET), biosynthetic pathway 182–183, 544, 545 inhibition by rhizobitoxine 450 evolution see phylogenetic studies fertilizers, NH4Cl treatments in GDH activity research 6–7 flavin adenine dinucleotide (FAD) cofactor 145, 343, 344 flavin mononucleotide (FMN) 145 Index 589 flavin monoxygenase (FMO) 343 flavonoids 565 food security benefits of herbicide use 461 role of GDH amination in crop yield increase 2, 19, 20–23 GABA (g-aminobutyric acid) as non-protein amino acid 510 phytotoxicity 517 roles in plant biology 129, 137–139, 525 abiotic stress tolerance 267 GABA shunt pathway in stress 49, 135–136, 136, 171 in plant–pathogen interactions 307, 554 sources and transporters 137 synthesis control by GS 85, 292 gabaculine 449, 449–450 gene chip operating software 203 genotoxins 472 germination, seeds 105–106, 164, 329 gibberellin (GA) 89 b-glucosidases 369, 370–371 glucosinolates 369, 436–443, 439, 546, 565–566 glufosinate 451, 453 glutamate (glutamic acid, Glu) homeostasis 291–292, 541 metabolic roles and pathways 541 family stress response pathway 264, 264–267 linking carbon and nitrogen metabolism 14, 14–15, 135, 136, 138 biosynthesis 2, 3, deamination 5 feedback inhibition in glycolysis 290 receptor agonists 510, 521, 524, 541, 553 in transgenic tomatoes, effect on taste 134–135 glutamate decarboxylase (GAD) biological roles 129, 137–139 in GABA shunt pathway 135–136, 136, 267 regulation expression patterns 131–134, 135 GAD gene family, phylogeny 131, 132, 133 overexpression and silencing 134–135 role of ornithine 171 structures and properties 130, 130–131, 134 glutamate dehydrogenase (GDH) catalytic activities amination, with Schiff base complex 5–7 assay design considerations 4–5, 7–8 enzyme characteristics cellular localization isomerization response to stimuli 3–4, 6–7, molecular and active site structure 2–3 regulation in animals and plants 550, 560 roles in primary metabolism 8–16, 10, 11, 13 amination vs deamination, relative importance 16–19, 23–24 ammonia detoxification 105 research on activity in peanuts 19–20 RNA synthesis 2, 9–12 glutamate-like receptors (GLRs) 541, 553, 560 glutamate pyruvate aminotransferase (GPAT) see alanine aminotransferase glutamate semialdehyde (GSA) 266 glutamate synthase (GOGAT) 7–10, 63, 105 glutamate:glyoxylate aminotransferases (GGATs) activity regulation 34 kinetic properties 41–42, 42 in peroxisomes 35, 47 structure compared with AlaAT 30, 33, 36 glutamine (Gln) analogues, as enzyme inhibitors 450–451 quantitative analysis 483 ratio to asparagine, N status signalling 109 regulation by GDU1 (Glutamine Dumper1) 301, 305–306 synthesis and amino-N transfer 83, 319, 328 glutamine synthetase (GS) genetic regulation post-transcriptional 89–90 post-translational 91–93 transcriptional 88–89 translational 91 inhibitors 451–453, 452 involved in photorespiration 109 isoforms in plants chloroplastic GS2 84 cytosolic GS1 84–86 phylogeny 83–84 modulation in transgenic plants 86–88 reaction catalysed 63, 83, 144 structural types, in pro- and eukaryotes 83, 453 glutathione, reduced (GSH) 92, 143, 206, 207 glycine (Gly) metabolic roles 543–544 structural relationship to glyphosate 462, 470 glycine betaine (GB) 543–544, 545, 560, 562–563 glycine decarboxylase 48, 543, 550–551 glycine N-methyltransferase (GNMT) 183 glycolysis 46–47, 50, 280–282, 281 glycosylation 368–369 glycosyltransferases (GTs) 369–370 glyphosate effects and impacts 463 environmental fate 466–469, 470 herbicidal action 462 mammals/humans, health risk assessment 469–476, 476 plant uptake and metabolism 463–466, 467 590 Index glyphosate (continued) history of development and use 461–462 structure and properties 462, 462–463 good agricultural practices (GAP) 464–465, 475 gostatin 449, 450 gramine 365, 368 grasses (Poaceae) 364 genome components 366–368 groundwater contamination 469 GS-GOGAT cycle protection during GDH studies 7–8 reactions and enzymes 83, 102, 103, 319 role in N assimilation 108, 116, 277–278, 278 tissue localization 318 guanidination method 489–490 heat processing damage 498, 499, 501, 503 heavy metal tolerance 207, 228, 265, 560 hemiparasitic plants 324–325 herbicides 450–454, 456, 461–466, 528 herbivores induced plant responses 371–372, 374–375, 379 glucosinolate regulation 441 host–insect interactions 553, 565, 571–572 plant defences chemical (constitutive) 364, 376–377 ‘mustard oil bomb’ 439, 440, 442–443 physical 377 histidine (His) biosynthesis 251–252, 256 localization and evolution 256 pathway and enzymes (HISNs) 252–256, 253 regulation 252, 256–257 properties and occurrence 251, 252 role in nickel hyperaccumulation 258 histidinol phosphate 255 homoarginine 520–521, 523 homoserine dehydrogenase (HSDH) 236–237 homoserine kinase (HK) 237–238 housekeeping genes 107 human health dietary concerns 21–22, 234, 237, 474–475, 499 drinking water quality 469, 475 effects of melatonin 391–395, 393 non-protein amino acids potential therapeutic uses 528–529 risks, in diet 520–522 nutraceutical products 169, 565–566 risk assessments for glyphosate 471–474, 475–476, 476 hydrolysis methods 482–486, 484, 486, 490–491 hydroponic solutions 443, 464 hydroxyindole O-methyltransferase (HIOMT) 400, 403–404, 407 5-hydroxytryptamine see serotonin 5-hydroxytryptophan (5-HTP) 401–402 hypersensitive response 150, 228 hypoglycins 511, 520, 524 hypoxia roles of AlaAT 35, 46–47, 49–50, 268–269 stress response pathways 267–270, 269 IAAO (indicator amino acid oxidation) technique 499, 499–500, 502–503 IAM (indole-3-acetamide) pathway 346–347 IAOx (indole-3-acetaldoxime) pathway 346 ileal digestibility 490, 498–499, 501, 503 imidazole acetol-phosphate (IAP) 254–255 imidazole glycerol phosphate (ImGP) 254 indicator amino acid oxidation (IAAO) technique 499, 499–500, 502–503 indolamine 2,3-dioxygenase (IDO) 414 indole-3-butyric acid (IBA) 348, 349 indole acetic acid (IAA) compared with melatonin 413 discovery 341 role of glutamine in synthesis 86 structure 348 see also auxin biosynthesis indole glucosinolate 346, 364, 438 indolic pathway, melatonin catabolism 407, 408 indospicine 519, 521, 523 inositol monophosphatase enzymes (IMPs) 255 insecticidal activity 517–518, 528 interactions see molecular interactions; pathogens, interactions with plants internal standards 488 inulin 119 ionotropic glutamate receptors (iGluR) 541, 553 IPA (indole-3-pyruvate) pathway 343–345, 344, 345, 354 isoleucine (Ile) 272, 545–546 isothiocyanates 440, 442, 442–443, 566 jack bean (Canavalia ensiformis), toxicity 512, 518, 528 jasmonic acid (jasmonate, JA) inducing serotonin accumulation 379 isoleucine conjugate 547, 553 signal transduction in insect injury 565, 571 synergistic and antagonistic interactions 556, 558 a-ketoglutarate (a-KG) as amination substrate of GDH 2, 7, 12, 14 providing C backbone for N compounds 278 Index 591 regulation of GS activity 88 roles in AlaAT activity 32, 33, 42 kwashiorkor 21–22 kynuric pathway, melatonin catabolism 407–409, 408 lactate dehydrogenase (LDH) 267 LCMS (liquid chromatography–mass spectrometry) 487 least-squares non-linear regression 484, 484–486, 485, 486, 491 legumes methionine content 237 non-protein amino acids 508, 511–512, 515 symbiotic nitrogen-fixing bacteroids 306–307, 323–324, 546, 559 Leucaena leucocephala, toxicity 514, 515, 520, 521, 527–528 leucine (Leu) Leu-zipper proteins 546, 567 role in stress responses 270 leucine-rich repeat receptor kinase (LRR-RK) 546, 554 light regulation of gene expression 88 signalling responses 106, 568 livestock feedstuffs adverse effects of non-protein AAs 509, 512, 518–520, 527–528 digestibility 498–499 protein quallity 566 long-chain fatty acid uptake 64 low oxygen escape syndrome 49 lysine (Lys) analogues 239, 454, 454 dietary requirements and supply 234, 245, 566 metabolic availability assessment 501–502, 502 Maillard derivatives 488, 489 metabolism biosynthesis 234–235, 235, 238–240, 453–454 catabolism, degradation pathway 235, 240–243, 272 regulation and manipulation 235–236, 243–245, 244 quantitative determination methods 489–490 residue K258 in AspAT apoprotein 60, 61 lysine a-ketoglutarate reductase (LKR, LOR) 240–243, 272 Maillard reactions 488, 489, 498 major facilitator superfamily (MFS) transporters 305 mangotoxin 453 mass spectrometry 486–487 coupled with gas chromatography (GC-MS) 343, 396 inductively coupled plasma (ICP-) MS 210 maximum residue levels (MRLs) 475 melatonin biological functions roles and beneficial effects in animals 391–394, 392, 393 roles in higher plants 410–415, 411 biosynthetic pathway 396, 398, 404 enzymes and regulation 396, 399–400, 401–407 catabolism 407–409, 408 characteristics 390, 394–395 discovery and natural occurrence 391, 395–396, 397–398 detection and quantification in plants 409–410 metabolic availability (MA) assay 499–503 metabolic mimicry 524 metabolism amino acids of central importance 541, 569–570 comparative (animals and plants) 550–553, 551, 568 primary 278–282, 279, 284, 540 research engineering, with transgenics 118–120, 290–292, 364 methods and approaches 272–273 secondary 363–364, 508–509, 549–550 see also stress metabolism methionine (Met) content in legumes 237 quantitative analysis 483, 490, 490–491 role in ethylene biosynthesis 450, 544, 545 synthesis and degradation 544–545 methionine cycle 180, 182 methionine sulfoximine 107, 452, 452 S-methyl-5'-thioadenosine (MTA) 180 methyl jasmonate (MeJA) 163, 167, 556 b-N-methylamino-l-alanine (BMAA) 510, 515, 521, 524 S-methylcysteine sulfoxide (SMCO) 513, 519, 523–524, 527, 528 microorganisms degradation of glyphosate 467–468, 470 effects of non-protein AAs on ecology 508, 515 fungal spore germination 375, 375 phytotoxic secondary compounds 499, 449–450 responses to root exudates 306 in rumen of livestock 513, 514, 520, 527–528 in soil, competition with roots 318, 320–321 microwave hydrolysis 483 592 Index mimosine metabolism 513–514, 524 detoxification 527–528 potential uses 528, 529 toxicity 515, 517, 520, 521 mitochondria glycine metabolism 48, 543 used in GDH activity assays mitogen-activated protein kinases (MAPK) 267 molecular interactions electrostatic 185 integration in complex systems 545, 558–559 types of interaction 554, 556, 557–558, 558 molecular weights 488 Moore and Stein procedure 481–482 ‘mustard oil bomb’ 439, 440, 442–443 mycorrhizae 321–323 myrosinase 439, 440, 442 neurotoxins 474, 487, 512, 524 nickel, hyperaccumulation in plants 258 nitrate (NO3-) in post-transcriptional regulation 90 resupply to N-starved plants 283–284 transported in xylem sap 326 uptake by roots 87, 138, 318 nitric oxide (NO) effects of non-protein AAs on production 523, 525 metabolic roles 143, 147, 149–150, 159 signalling in N-fixation 92 physiological sources 142, 145–147, 542, 543 nitric oxide synthase (NOS) activity regulation during development 147–149 in stress conditions 149–150 enzyme structure and activity 145–147, 146, 148 genetic engineering for stress resistance 150 nitrogen cycle (in ecosystems) 315–316, 330 nitrogen-fixing bacteria 306–307, 323–324 nitrogen metabolism assimilation 82–83, 277–282, 317–319 role of GS 93 remobilization in senescence 108, 144 resupply after starvation 90, 282–284 storage and transport within plants 31, 263, 298–302 role of l-arginine 143, 328 transpiration stream loading 325–328, 327 use of asparagine 100, 102, 110 xylem–phloem exchange 328–329 supply signalling, Asn:Gln ratio 109 uptake of organic (amino-) nitrogen 316–317, 319–325 see also urea cycle nitrogen use efficiency 48, 86, 117–118 S-nitrosoglutathione (GSNO) 143 NLP1 enzyme (putrescine synthesis) 178, 180 NMDA-like receptors 543, 556 nodulin-26 93 non-protein amino acids classification criteria 509–511, 510 distribution and concentrations 511, 511–512 metabolic roles 156, 509, 525–527 metabolism of specific types 512–514 potential applications 528–529, 530–531 toxicity 508–509, 514, 522–525 adverse effects on higher animals 518–520 anti-microbial activity 515 detoxification 527–528 human health risks 520–522 insecticidal activity 517–518 phytotoxicity 448, 451, 515–517, 516 nuclear magnetic resonance (NMR) analysis 184, 487 nucleotide metabolism 256, 257 nutraceutical supplements 169, 565–566 nutrition (human/animal diet) arginine supply and demand 168 bioavailability of amino acids 497–503, 566 dietary fibre importance 499, 503 effects of food processing on amino acids 488–489, 490, 491–492 lysine deficiency, cereals 234 methionine deficiency, legumes 237 protein–energy inadequacy (kwashirokor) 21–22 toxicology related to exposure 474–475, 514 nutrition (plant minerals) deficiencies and asparagine levels 105, 118 imbalances, Orn role in stress tolerance 167–168 nitrogen import/export physiology 298–300, 315–325 sulfate assimilation 195–196, 196, 220–222, 221 OAS (/OASTL) see O-acetylserine (/OAS(thiol)-lyase) oats (Avena sativa) 372–375 ornithine (Orn) biosynthesis and metabolism 156–158 in animals 168–169 flux modelling 170–172 in plants 157, 158–159 content, in cells 159–160, 160, 161–162 effects of exogenous supply 169–170 genetic regulation of pathways mutant studies 160, 163–164 transgenic modulation impacts 164–168, 166, 542 Index 593 ornithine aminotransferase (OAT) 164–165, 168, 266, 542 ornithine cyclodeaminase (OCD) 167 ornithine decarboxylase (ODC) 164, 165–167, 168, 178, 522 ornithine transcarbamoylase (OTC, OCTase) 164, 453 osmotic stress protection 168, 265–267, 272 oxaloacetate (OAA) 278–280 b-N-oxalylamino-l-alanine (BOAA) 510, 519, 521 oxetin 451, 452 2-oxoglutarate (2-OG) see a-ketoglutarate oxygen deficiency see hypoxia ozone chemiluminescence method 146–147, 149 P5C (Δ1-pyrroline-5-carboxylate) enzymes 266 Parkinson’s disease complex (ALS/PDC) 474, 521 pathogens, interactions with plants amino acid signalling 307 induced plant responses 371–372, 374–375, 377–379 glucosinolate metabolism 441, 442–443 plant chemical defence 364 resistance priming 526, 571 performic acid oxidation 482, 483 peribacteroid membrane (PBM) 323–324 pesticides degradation pathways 467 soil organic matter adsorption 468, 469 toxicology 472, 474 treatments in GDH activity research 6–7, usage regulation and approval 473, 475 phaseolotoxin 453, 453 phenylacetic acid (PAA) 348 phenylalanine (Phe) biosynthesis in bacteria 71–73, 72 in plants 73, 73, 547 interaction with phytotoxins 454 photodegradation 454 phenylalanine ammonia lyase (PAL) 524, 547, 569 phenylpropanoid pathway 77–78, 78, 79, 374, 524 release and re-assimilation of ammonia 85 3-phenylpropionic acid (PPA) 348 phloem exchange of amino-N with xylem 328–329 S-cells and glucosinolates 439, 440 phosphinothricin 451, 452, 453 3'-phosphoadenosine 5'-phosphosulfate (PAPS) 196, 221 phosphoenolpyruvate (PEP) 280–282, 281, 292 phosphoenolpyruvate carboxykinase (PEPCK) 64 phosphoenolpyruvate carboxylase (PEPC) metabolic engineering 290–291 structures and activity 279, 284–288, 285, 289–290 O-phosphohomoserine (OPH) 237–238 5-phosphoribosyl-3-pyrophosphate (PRPP) 252, 256, 257 photodegradation glyphosate 466–467 phenylalanine 454 protective mechanisms in high light S-sulfocysteine synthase 226 vitamin B6 58 photorespiration ammonium recycling 86, 109, 278, 451 role of AlaAT 35, 47–48 phylogenetic studies alanine aminotransferase 35–36, 37 asparagine synthetase 110, 111–112 components of cysteine synthase complex 222, 223 glutamate decarboxylase 131, 133 glutamine synthetase isoforms 83–84 Trp pathway defensive metabolism 381 gene cluster evolution, Bx pathway 366–368 glucosinolate biosynthesis 436, 437 serotonin induced by infection 378–379, 379 phytoalexins 150, 372–375, 570 phytochrome B 350 phytotoxins investigation strategies 449 types and actions 448–456 glucosinolate derivatives 442–443 glyphosate 462–466 non-protein amino acids 515–517, 516 PII proteins 158, 160 ping-pong reaction mechanisms of aminotransferases 42, 59, 59, 70 histidinol oxidation 256 plant products (used by humans) 565–566, 568–569 AA composition determination 488–492 uses of melatonin 415–416 polyamine oxidases (PAO) 183–184 polyamines biosynthesis from arginine 143, 144–145, 164 pathways and enzymes 178–182, 179, 182 deamination, and ROS signalling 145, 183–184 homeostatic regulation Orn pathway 159, 165–168 SAM substrate flux 180, 182–183 research questions 188 roles in plants growth and development processes 185–186 metabolic regulation 184, 184–185 responses to abiotic stress 186, 187, 263 types and occurrence in plants 177–178 see also APC transporters 594 Index post-transcriptional regulation 87, 89–90 post-translational regulation 91–93, 185, 242 potentiation mechanisms 526–527 PRFAR 254 programmed cell death 138–139, 150, 228 proline (Pro) accumulation in stress 168, 264–265, 560 regulation 266–267 primary and secondary metabolic roles 541–542 proline dehydrogenase (ProDH) 266 proline-rich proteins 560 protoxins 449, 451–453 PSorn (OCTase inhibitor) 453, 453 putrescine (Put) biosynthesis 178–180, 179 and ornithine metabolism 158, 165, 166 pyridoxal-5'-phosphate (PLP, active vitamin B6) active site reaction mechanism 60, 70 as cofactor alanine aminotransferase 33, 44, 44–45 aspartate aminotransferase 58, 59 glutamate decarboxylase 130 complexes with non-protein AAs 525 in cysteine synthase complex 222 pyridoxal kinase (PK) 58, 60 pyruvate decarboxylase (PDC) 267 pyruvate dehydrogenase complex 280, 282 pyruvate family stress response pathway 264, 267–270 pyruvate kinases (PK) activity engineering with knockout mutants 291 influence of Asp and Glu 288, 289–290, 290 function in plastids 280 structures and properties 288, 289 quality protein maize 243 quantitative real-time PCR analysis 202, 209 racemization 169, 491–492, 552–553 radioimmunoassays 396, 409 radiolabelling 299–300, 322 reactive oxygen species (ROS) accumulation in stress conditions 204, 226 detoxification by free AAs 263 H2O2 and polyamine-mediated signalling 145, 183–184 photocatalysed production 467 scavenging ability of GABA 135, 137 of melatonin 395, 407–409, 412 synergism with NO 556 repeat dose toxicity 471–472 research currect focus and recent advances 539–541, 566–569, 567 epidemiological, and public health concerns 472–473 future objectives and needs 329–330, 572–573 innovative directions and technologies 509, 570–572 residues, agrochemical 465–466, 475 respiration, supplying energy for N assimilation 278–279, 280–282 rhizobitoxine 450, 450 rhizosphere amino acid exchange processes 301–302, 306, 330 root–soil microbe interactions 318, 320–321, 443 roots development, effect of NOS activity 147–148, 164 exudates (amino acid secretion) 306, 317, 454 hemiparasitic associations 324–325 mycorrhizal associations 321–323 nitrogen uptake by root hairs 317 nodules and rhizobia 306–307, 323–324, 515 role of glutamine synthetase 84, 85, 92–93 uptake of glyphosate 464, 468 Roundup® 461–462 see also glyphosate saccharopine dehydrogenase (SDH) 240–243, 272 salicylic acid (SA) biosynthesis 526, 547, 548, 569 signalling, in stress and defence 547–549, 554, 563, 568 synergistic and antagonistic interactions 556 salt tolerance 186, 265, 543 SAM (/SAMDC) see S-adenosylmethionine (/decarboxylase) sample preparation (for AA analysis) 482 SAT see serine acetyltransferase secondary compounds 363, 363, 508–509, 540, 549–550 seeds export of amino acids from coat 300 germination 105–106, 164, 329 maturation 108–109 non-protein amino acid content 508 protein content 117–118 selenoamino acids human therapeutic potential 529 metabolism and toxicity 515, 519, 521, 523 structures and occurrence 510, 512 selenomethionine 513, 519 senescence 108, 149, 185–186, 228–229, 379–380 Index 595 serine (Ser) phosphorylation 491 recovery in acid hydrolysis 483, 486 serine acetyltransferase (SERAT, SAT) genetic regulation gene expression patterns 202–204, 203 SERAT gene family structures 196, 197, 198–199 transgenic overexpression 206–207 metabolic functions 195–196, 211–212 analysis using knockout mutants 204, 204–206, 205 phylogeny 222, 223 properties and localization 197, 199, 199, 200 as part of cysteine synthase complex 199–202, 200, 222–224, 223 serine hydroxylmethyltransferase (SHM) genes 210–211 serine:glyoxylate aminotransferase (SGAT) 47 serotonin (5-hydroxytryptamine) occurrence in plants, and effects on animals 375–377 role in defence against grass crop pathogens 377–379, 380 role in senescence 379–380 serotonin N-acetyltransferase (SNAT) 391, 400, 402–403, 406 shade avoidance (SAV 3) 343, 351 shikimate pathway in aromatic compound biosynthesis 71 blockage by glyphosate 462, 569 signal transduction 553–554, 555 abscisic acid 556, 558 direct and indirect roles of AAs 299, 540, 551–552, 553–554, 555 ethylene 545, 556 hydrogen peroxide 183–184 integration of signal cascades 558–559, 563, 567, 570–571 jasmonate 556, 558, 565 nitric oxide 142 roles of non-protein amino acids 510, 526–527 salicylic acid 547–549 slope-ratio assays 500, 500–501, 502 SMCO (S-methylcysteine sulfoxide) 513, 519, 523–524, 527, 528 spermidine (Spd) 166, 526 biosynthesis 179, 180 spermidine synthase (SPDS) 181, 185 spermine (Spm) 166 biosynthesis 179, 180, 181–182 spermine synthase (SPMS) 181–182 stress biology 48–50 stress metabolism general model 563–564, 564, 572 response metabolic pathways 540, 567 asparagine synthesis in C depletion 107–108, 271 GABA shunt 135–136, 136, 267 mitigation by non-protein AAs 509, 525–527 oxygen deficiency responses 267–270, 269 polyamines, protective roles 186 proline accumulation 264–267 specific responses 525, 561–562 biotic stresses 442, 559–560, 563, 564–565 environmental stresses 562–563 environmental (abiotic) stresses 262–263, 560, 562–563 see also defence responses succinic semialdehyde dehydrogenase (SSADH) 135, 136, 267 sulfate reduction 206, 221 uptake and transport 208, 220–221 S-sulfocysteine synthase (CS26) 225–226 sulfur amino acids analogues 510, 513, 519, 545 availability in foods 501 metabolic roles in plants 544–545 sulfur metabolism 105, 195–196, 196, 219–220 surfactants, toxicity 471 synergistic interactions 556, 557 synthetases/synthases inhibitors 450–453 specific types asparagine synthetase 102–116 glutamine synthetase 83–93 nitric oxide synthase 145–150 systemic acquired resistance (SAR) 228, 547, 559 systemin 540, 559 tabtoxin 451, 452 TCA (tricarboxylic acid) cycle activity in seeds 109 bypassed by GABA shunt 135 contribution of (nutritionally) essential AAs 272 effect of exogenous l- and d-Orn 169–170 modulation in hypoxia 46, 50 regulation and flux control 280, 283 teratogenicity, risk assessment 473–474 tetrahydrobiopterin (BH4) 145 thermospermine (T-Spm) 179, 180, 182 threonine (Thr) 234, 235, 236, 237 endogenous dietary losses 498 in foods, effects of processing 491 metabolic availability assessment 501, 502 recovery in acid hydrolysis 483, 486 threonine dehydratase (TD) 565, 571 Tobacco mosaic virus (TMV) 149 TOR regulation 91, 184–185 596 Index toxicology biochemical toxicity mechanisms 522–525 classification of adverse effects 514 dose dependence 474–475 testing and standards 469–472 types of toxicity carcinogens and cancer risks 472–473 developmental/reproductive toxicity 473–474 endocrine disruption testing 474 genotoxicity 472 goitrogenic toxins 443, 520 neurotoxins 474, 519 see also phytotoxins transaminases see aminotransferases transcription factors 89, 441, 570 transcriptional gene regulation 88–89, 257 translational regulation 91 transpiration stream 325–326 transport inhibitor response 343, 352 transporter proteins families, in amino acid transport 137, 302–305, 304, 320 glucosinolate symporters (GTR) 440 regulation 305–306, 307, 318 sulfate transporters 220–221 tryptamine (TAM) pathway 347–348 tryptophan (Trp) biosynthetic pathway branch points 365, 366, 438 reactions and enzymes 362–363 regulation 363–364 secondary products 363, 363, 549, 563 as precursor of melatonin 390, 396 quantitative determination 483–485, 484, 485, 486 tryptophan 5-hydroxylase (T5H) 396, 399, 401, 404–405 tryptophan decarboxylase (TDC) 347, 378, 399, 401–402, 405–406 tyrosine (Tyr) biosynthesis in bacteria 71–73, 72 in plants 73, 73, 548, 549 phosphorylation and nitration 92, 554, 567 recovery in acid hydrolysis 483 residue Y225 in AspAT apoprotein 60, 62 in stress/defence responses 563 m-tyrosine phytotoxicity 454, 455 tyrosine aminotransferase anabolic roles 71–73 aromatic amino acid biosynthesis 71–73, 72, 77 synthesis of secondary metabolites 77–78 enzyme characterization purification 74, 74 reaction kinetics 74–76, 75, 76 reactions catalysed 74, 75 structure 79 substrate specificity 76, 76 in vivo activity assays 76–77, 77 UDP-glycosyltransferases (UGT) 369 urea cycle analogues and congeners 510, 518, 524–525 in animals 169 in nitrogen metabolism, pathways 143, 144, 522 arginine/canavanine synthesis 512–513, 513, 542 urease 144 3'-UTR-mediated transcript destabilization 90 vacuolar membrane transport 302 valine (Val) 270, 546 victorin 543, 550 viniferins 375 vitamin B6 photolysis by UV-B, homeostatic response 63 vitamers and roles in plants 58 weed control see herbicides wheat (Triticum aestivum) 367–367 World Health Organization (WHO) chemical safety assessments 469, 475, 476 dietary guidelines 234 wound response 167, 559–560, 564–565 xylem amino acid import/export 299–301, 305, 326, 328–329 N transport compounds in tree sap 326–328, 327 Yang cycle 344, 544, 545 yield (crops) see crop yield zeolin 245